2007 APS March Meeting Denver, Colorado

2007 APS March Meeting Denver, Colorado http://www.aps.org/meetings/march

i Monday, March 5, 2007 8:00AM - 11:00AM — Session A19 DCP: Focus Session: New Frontiers in Imaging I Colorado Convention Center 104

8:00AM A19.00001 Mobile NMR: Measuring Pixels, Images, and Spectra1 BERNHARD BLUEMICH, RWTH Aachen University — The vision of bringing nuclear magnetic resonance out of the lab to the doctor’s office, the chemical reactor, or the manufacturing site is becoming reality with the development of mobile NMR. Pioneered for well logging in the oil industry, the concept has been explored for materials testing in a more systematic way since the introduction of the NMR-MOUSE. This is a small, one-sided access NMR sensor which acquires the information of one pixel from a particular spot of a large object. As the sensor explores the stray-fields of a permanent magnet and an rf coil, the magnetic fields are inhomogeneous and the sensitive volume is limited to the region, where both fields are orthogonal and the Larmor frequency lies within the excitation bandwidth. By shaping the magnet and the coil geometries, the shape of the sensitive volume can be tailored to a thin slice or a larger volume a certain distance away from the sensor surface. In the first case, there is a strong field gradient in the depth direction, and in the second case, a homogeneous sweet spot of the field profile is desired. The first case is suitable for measuring high-resolution depth profiles, while the second case is suitable for chemical shift resolved spectroscopy and volume imaging. The basic concepts of open and closed mobile NMR sensors will be discussed along with applications from testing polymer products, cultural heritage, medical tissue, and rock cores.

1This work has been supported in part by the Miller Institute of Basic Research in Science, UC Berkeley.

8:36AM A19.00002 Ex-Situ Spectroscopic MRI , JEFFREY REIMER, UC Berkeley — Spectroscopic magnetic resonance imaging of a sample placed outside of both the radio frequency and the imaging gradient coils is presented. The sample is placed in a field with a permanent one-dimensional inhomogeneity. The imaging gradients used for phase encoding are designed to produce a static field that depends only on the transverse direction, uncoupling the effects associated with the single-sided nature of these coils. Two-dimensional imaging coupled with chemical shift information is obtained via the ex situ matching technique. Open-saddle geometry is used to match the static field profile for chemical shift information recovery.

8:48AM A19.00003 Nuclear magnetic resonance imaging with 90-nm resolution1 , M. POGGIO, C. L. DEGEN, H. J. MAMIN, D. RUGAR, IBM Research Division, Almaden Research Center, 650 Harry Rd., San Jose, CA 95120 — Using magnetic resonance force microscopy (MRFM), we demonstrate two-dimensional nuclear magnetic resonance imaging (MRI) with 90-nm lateral resolution for 19F nuclei in calcium fluoride. In terms of detectable volume, this represents a 60,000 fold improvement over the highest resolution conventional MRI. The high sensitivity of our measurement is achieved using a custom-made silicon cantilever with a 60-µN/m spring constant and a nanometer-scale FeCo magnetic tip that produces magnetic field gradients up to 14 G/nm. The spin manipulation protocol, called cyclic CERMIT, uses low duty cycle cantilever-driven adiabatic reversals to manipulate statistical spin polarization and generate a detectable cantilever frequency modulation. Work is underway to further improve measurement sensitivity, including the development of an efficient RF source aimed at reducing cantilever temperatures during imaging into the low millikelvin range. This and other improvements may allow MRFM to push deeper into the nanometer range.

1Work supported by DARPA QuIST and by the NSF through the Center for Probing the Nanoscale at Stanford University

9:00AM A19.00004 Imaging Contrast Effects in Alginate Microbeads , NINA SHAPLEY1, HOLLY HESTER- REILLY, Columbia University — We have investigated the use of alginate gel microbeads as contrast agents for the study of suspension flows in complex geometries using nuclear magnetic resonance (NMR) imaging. These deformable particles can provide imaging contrast to rigid polymer particles in a bimodal suspension (two particle sizes). Microbeads were formed of crosslinked alginate gel, with or without trapped oil droplets. Crosslinking of the aqueous sodium alginate solution or the continuous phase of an oil-in-water emulsion occurred rapidly at gentle processing conditions. The alginate microbeads exhibit both spin-spin relaxation time (T2) contrast and diffusion contrast relative to both the suspending fluid and rigid polystyrene particles. Large alginate emulsion microbeads flowing in the abrupt, axisymmetric expansion geometry can be clearly distinguished from the suspending fluid and from rigid polymer particles in both spin-echo and diffusion weighted imaging. The alginate microbeads, particularly those containing trapped emulsion droplets, offer potential as a positive contrast agent in multiple NMR imaging applications.

1Membership Pending

9:12AM A19.00005 , EIICHI FUKUSHIMA, New Mexico Resonance — No abstract available.

9:48AM A19.00006 Spin Sorting: Apparent Longitudinal Relaxation without Spin Transitions , MARK CONRADI, YULIN CHANG, JASON WOODS, SUSAN CONRADI, Washington University, DEPARTMENT OF PHYSICS TEAM — Nuclear spins experience forces in the presence of a magnetic field gradient. The forces cause the spin-up and spin-down nuclei to move in opposite directions, resulting in a flow of longitudinal magnetization. The effect can generate local longitudinal spin magnetization, though it does not involve transitions (flipping) of spins. This phenomenon, spin sorting, competes with true spin-lattice relaxation and is generally not observable when T1 is short. We present our calculations of 3 the longitudinal magnetization of diffusing spins with long T1 ( He) in magnetic field gradients and compare the calculations with experimental results. We show that the longitudinal spin magnetization due to spin sorting can be dominant at short times in such a system. We also show how this phenomenon can potentially be used to generate nuclear magnetizations larger than thermal equilibrium.

10:00AM A19.00007 Spin-Exchange Optical Pumping of Solid Alkali Compounds1 , BRIAN PATTON, Princeton University Physics Department, KIYOSHI ISHIKAWA, Graduate School of Material Science, University of Hyogo, Japan, YUAN-YU JAU, WILLIAM HAPPER, Princeton University Physics Department — Spin-exchange optical pumping of noble gases has been used for many years to create highly non- equilibrium spin populations, with applications ranging from fundamental physics[1] to medical imaging[2]. In this procedure, angular momentum is transferred from circularly-polarized laser light to the electron spins of an alkali vapor and ultimately to the nuclei of a gas such as 3He or 129Xe. Here we show experimentally that a similar process can be used to polarize the nuclei of a solid ﬁlm of cesium hydride which coats the walls of an optical pumping cell. We present nuclear magnetic resonance (NMR) data which demonstrate that the nuclear polarization of 133Cs in CsH can be enhanced above the Boltzmann limit in a 9.4-Tesla magnetic ﬁeld. Possible spin-exchange mechanisms will be discussed, as well as the extension of this technique to other compounds. [1] T. W. Kornack, R. K. Ghosh, and M. V. Romalis, Phys. Rev. Lett. 95, 23080 (2005). [2] M. S. Conradi, D. A. Yablonskiy, et al., Acad. Radiol. 12, 1406 (2005).

1This work was supported by AFOSR. 10:12AM A19.00008 Hyperpolarized water as an authentic magnetic resonance imaging contrast agent.1 , SONGI HAN, EVAN MCCARNEY, BRANDON ARMSTRONG, University of California Santa Barbara — Water itself in a highly 1H spin-polarized state is proposed as a contrast agent free contrast agent to visualize its macroscopic evolution in aqueous media by magnetic resonance imaging (MRI). Hyper-polarization suggests an ideal contrast mechanism to highlight the ubiquitous and speciﬁc function of water in physiology, biology and materials because the physiological, chemical and macroscopic function of water is not altered by the degree of magnetization. We present an approach that is capable of enhancing the 1H MRI signal by up to two orders of magnitude, instantaneously, under ambient conditions, at 0.35 Tesla, by utilizing highly electron spin-polarized nitroxide radicals that are covalently immobilized onto a porous, water-saturated, gel matrix. The continuous polarization of radical-free ﬂowing water allowed us to distinctively visualize vortices in model reactors and dispersion patterns through porous media utilizing the remotely enhanced liquids to obtain unusually high image contrast (RELIC).

1The work was supported by the Dreyfus New Faculty Award and through the MRL program of the National Science Foundation under Grant No. DMR00-80034.

10:24AM A19.00009 Latest Developments in Dynamic MRI of Multi-Phase Systems , LYNN GLADDEN, University of Cambridge — In recent years there has been increasing interest in applying magnetic resonance techniques in areas of engineering and chemical technology. Central to many engineering applications is the need to characterise both hydrodynamics and chemical reaction in optically opaque three-dimensional environments; thus MRI is uniquely well-suited to such studies. This presentation addresses the application of MRI techniques which have suﬃciently fast data acquisition times that unsteady state processes can be imaged. The presentation will take as a theme the imaging of physical and chemical phenomena occurring within heterogeneous catalytic reactors - these systems are, typically, packings of catalytically active particles through which gas and liquid ﬂow causing chemical conversion as the reactants interact with the surface of the catalyst. The overall aim of our work is to use MRI to provide information such that we can understand the coupling of hydrodynamics and chemical kinetics in complex porous structures. Two particular areas will be addressed: ultra-fast MRI for studying hydrodynamics, with typical data acquisition times of 10-20 ms for a 2D velocity image, and polarisation enhancement techniques for chemical mapping.

Monday, March 5, 2007 8:00AM - 11:00AM — Session A26 DCP DBP: Focus Session: Protein Folding: Theory and Simulations I Colorado Convention Center 205

8:00AM A26.00001 Exploring The Folding Energy Landscape–Triumphs and Tribulations , PETER G. WOLYNES, University of California, San Diego — The folding process has become one of the best understood transformations of condensed matter,owing to the minimal frustration principle and the collective nature of the key bottlenecks in the folding process. I will discuss the limits of models based on topology alone and also highlight the eﬀects of residual frustration and co-factors in some puzzling examples that challenge the funnel paradigm.

8:36AM A26.00002 Simulating protein folding and aggregation on the 10 second timescale , VIJAY PANDE, Stanford University — Understanding how proteins self-assemble or “fold” is a fundamental problem in biophysics. Moreover, the ability to understand and quantitatively predict folding kinetics would have many implications, especially in the area of diseases related to protein misfolding, such as Alzheimer’s Disease. However, there are many challenges to simulating folding, most notably the great computational challenges of simulating protein folding with models with suﬃcient accuracy to make quantitative predictions of experiments. In my talk, I will discuss our recent work to combine distributed computing with a new theoretical technique (Markov State Models) in order to simulate folding on long timescales as well as the direct and quantitative experimental tests of these methods. I will conclude with the application of these methods to the study of the Abeta peptide, whose aggregation has been directly implicated as the toxic element in Alzheimer’s Disease.

9:12AM A26.00003 Understanding ensemble protein folding at atomic detail.1 , EUGENE SHAKHNOVICH, Harvard University — Here we present a new all-atom model and development of simple potential functions (inspired by discoveries of general principles of protein folding) that allow to fold small proteins from sequence to near native structure at an atomic level of detail. Availability of numerous successful all-atom folding trajectories and their novel graph theoretical analysis, makes it possible to gain a detailed atomic level understanding of folding pathways/intermediates/transition states for engrailed homeodomain - a small alpha-helical protein that has been recently studied experimentally.

1In collaboration with Isaac Hubner, Eric Deeds, and Jae Shick Yang, Harvard University.

9:48AM A26.00004 Investigating the Disordered States of Two Proteins Using Intramolecular Contact Formation , VIJAY SINGH, MICHAELA KOPKA, YUJIE CHEN, WILLIAM WEDEMEYER, LISA LAPIDUS, Michigan State University — Using the quenching of the triplet state of tryptophan by cysteine, we investigate the unfolded states of two structurally similar but sequentially non-homologous proteins, the IgG binding domain of proteins L and G, under a range of denaturing conditions. These proteins show remarkably similar dynamics of intramolecular diffusion marked by a decrease in contact formation at denaturant conditions that favor folding. A reaction limited rate and the diffusion limited rate are obtained by measuring the viscosity dependence of the intramolecular contact rate. To further investigate the polymer dynamics of the unfolded state under folding conditions, we modeled the proteins as a worm-like chain with excluded volume using Szabo, Schulten and Schulten (SSS) theory to estimate the effective persistence length and intramolecular diffusion constant at various concentrations of GdnHCl. The results reveal an unfolded state under folding conditions that is significantly more compact and less diffusive than the fully denatured state.

10:00AM A26.00005 Thermodynamics of the Beta-hairpin to Coil Transition using a Distance Constraint Model1 , OLEG VOROV, DONALD JACOBS, DENNIS LIVESAY, University of North Caroline, Charlotte — The configuration partition function is calculated exactly [1] for a distance constraint protein model that describes the beta-hairpin to coil transition. The model employs a Gaussian backbone chain of N atoms in which bonds may form to crosslink pairs of atoms in close proximity along the chain, represented by fluctuating distance constraints. Each distinct pattern of cross-linking bonds defines a constant energy over all atomic geometries that are consistent with the constraint topology. This geometrical degeneracy factor is directly calculated from configuration space integrals for each accessible constraint topology. All constraint topologies consistent with no pair of bonds that link two backbone atoms are themselves crossed are enumerated, leading to an analytical closed form expression for the configuration partition function. The phase diagram for the beta-hairpin to coil transition as a function of chain length has been studied. [1] O.K.Vorov, D.J.Jacobs, D.R.Livesay, subm. to Phys.Rev.Lett., 2006, in preparation.

1NIH Grant N R01 GM073082-01A1 10:12AM A26.00006 Computational studies of the structural properties of the monomer and dimer of Aβ(1-28)1 , XIAO DONG, WEI CHEN, NORMAND MOUSSEAU, Departement de physique and RQMP, Universite de Montreal, Montreal (QC), Cananda, PHILIPPE DERREUMAUX, Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7-Denis Diderot, Paris, France — Neurodegenerative diseases are linked with the self-assembly of normally soluble proteins into amyloid fibrils. In this work, in silico characterization of the structures of the monomer and dimer of Aβ(1-28) are studied with the coarse-grained OPEP model using the activation-relaxation technique (ART nouveau). We find a dominant anti-parallel β-sheet structure present for both the monomer and dimer. While the monomer does not adopt a stable conformation, it fluctuates around a well-defined structure: starting from the end point, the monomer wraps a first time around, producing a β-hairpin and returns on the other side of the N-terminal, forming a three-strand β-sheet. The dimer assembles in a similar fashion, but with the two strands interlocking. The thermodynamics of the molecular assemblies and various folding path-ways are further studied using molecular dynamics.

1This work is supported in part by the Alzheimer Society of Canada, NSERC and the Canada Research Chair Foundation. We thank the RQCHP for a generous allocation of computer ressources.

10:24AM A26.00007 Lattice Model Investigations of Protein Aggregation , YANXIN LIU, PREM CHAPA- GAIN, JOSE PARRA, BERNARD GERSTMAN, Department of Physics, Florida International University, Miami, FL 33199 — Protein aggregation is known to be important in a variety of diseases. We have expanded a well-known 3-dimensional protein folding computer lattice model with explicit side-chains in order to investigate the thermodynamics and statistical mechanics of protein aggregation between two chains. The modeling of a two-chain system presents technical and physics issues in addition to those found when modeling only a single chain. We report on preliminary results of the simulations.

10:36AM A26.00008 Effective potentials for Folding Proteins , CHUNG-YU MOU, National Tsing Hua University, Taiwan, NAN-YOW CHEN, Academic Sinica, Taiwan, ZHENG-YAO SU, National Center for High-Performance Computing, Taiwan — A coarse-grained off- lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.

10:48AM A26.00009 Forced Unfolding of the Coiled-Coils of Fibrinogen by Single-Molecule AFM , ANDRE BROWN, RUSTEM LITVINOV, DENNIS DISCHER, JOHN WEISEL, University of Pennsylvania — A blood clot needs to have the right degree of stiffness and plasticity for hemostasis, but the origin of these mechanical properties is unknown. Here we report the first measurements using single molecule atomic force microscopy (AFM) to study the forced unfolding of fibrinogen to begin addressing this problem. To generate longer reproducible curves than are possible using monomer, factor XIIIa cross-linked, single chain fibrinogen oligomers were used. When extended under force, these oligomers showed sawtooth shaped force-extension patterns characteristic of unfolding proteins with a peak-to-peak separation of approximately 26 nm, consistent with the independent unfolding of the coiled-coils. These results were then reproduced using a Monte Carlo simulation with parameters in the same range as those previously used for unfolding globular domains. In particular, we found that the refolding time was negligible on experimental time and force scales in contrast to previous work on simpler coiled-coils. We suggest that this difference may be due to fibrinogen’s structurally and topologically more complex coiled-coils and that an interaction between the alpha C and central domains may be involved. These results suggest a new functional property of fibrinogen and that the coiled-coil is more than a passive structural element of this molecule.

Monday, March 5, 2007 11:15AM - 1:39PM — Session B19 DCP: Focus Session: New Frontiers in Imaging II Colorado Convention Center 104

11:15AM B19.00001 NMR mapping of ionic currents and electro-osmotic flow in microsystem channel networks , RAINER KIMMICH, University of Ulm — Magnetic resonance tomography is known to provide images the contrasts of which are determined by a combination of several parameters. On the one hand these can be system parameters like spin density, relaxation times and diffusion coefficients. On the other hand, the contrasts will be affected by experimental parameters like echo time, repetition time, and by the type of the radio frequency pulse sequence used to generate the signals. In contrast to this, we are interested in “maps” where a well defined system parameter is quantitatively encoded in gray shades or colors. A frequently employed technique of this sort is mapping of pressure induced flow. Apart from this, the objective of the present study is to examine and compare maps of the ionic current density and electro-osmotic flow in channel networks on a microscopic length scale. As a paradigm for complex pore spaces, model objects of random and correlated site percolation clusters were fabricated and filled with electrolyte solutions. The experimental maps were compared with computational fluid dynamics simulations based on finite element techniques. The patterns observed in maps of the current density, pressure induced and electro-osmotic flow velocity strongly deviate from each other. This is due to the different transport resistance characteristics and the different nature of the driving forces. The patterns of the spatial distribution of the electric current density measured in the pore space of plastic objects (no electro-osmotic flow superimposed), for example, is totally different from those found in ceramic objects (electro-osmotic flow superimposed). Vortices and recirculation patterns have been observed for all transport quantities, but at different sites. The findings can be explained and elucidated on the basis of the computational fluid dynamics simulations and experiments with test objects especially designed for this purpose. (1) B. Buhai and R. Kimmich, Phys. Rev. Letters 96, 174501 (2006). (2) B. Buhai, T. Binser, and R. Kimmich, Appl. Magn. Reson., in press.

11:51AM B19.00002 Insights into the Distribution of Water in Operating Proton-Exchange Membrane Fuel Cells Using H-1 NMR Imaging. , RODERICK WASYLISHEN, KIRK FEINDEL, STEVEN BERGENS, Department of Chemistry, University of Alberta, Edmonton, AB Canada — The operation of proton-exchange membrane fuel cells (PEMFCs) depends critically on the amount and distribution of water throughout the FC (K.W. Feindel, S.H. Bergens, and R.E. Wasylishen ChemPhysChem, 2006, 7, 67-75). To study in-situ the distribution of water in an operating PEMFC using H-1 NMR imaging we constructed PEMFCs to operate within a 10 or 30 mm coil. Recent results provide the first images of the in-plane distribution of water within the PEM. The influence of gas flow configuration in a self-humidifying PEMFC was investigated, and the results are qualitatively in agreement with predictions from several theoretical models. The maximum power output occurs when water begins to accumulate in the cathode flow field, and the integral of the image intensity from the PEM correlates with the power output. The use of H-D exchange has been found effective to introduce contrast in H-1 NMR images. Our results demonstrate that H-1 NMR imaging is capable of providing information on the in-situ operation of PEMFCs that is difficult or impossible to obtain with other PEMFC diagnostic techniques. 12:03PM B19.00003 Concentration and Velocity Measurements of Both Phases in Liquid-Solid Slurries , STEPHEN ALTOBELLI, New Mexico Resonance, KIMBERLY HILL, University of Minnesota, ARVIND CAPRIHAN, New Mexico Resonance — Natural and industrial slurry flows abound. They are difficult to calculate and to measure. We demonstrate a simple technique for studying steady slurries. We previously used time-of-flight techniques to study pressure driven slurry flow in pipes. Only the continuous phase velocity and concentration fields were measured. The discrete phase concentration was inferred. In slurries composed of spherical, oil-filled pills and poly-methyl-siloxane oils, we were able to use inversion nulling to measure the concentration and velocity fields of both phases. Pills are available in 1-5mm diameter and silicone oils are available in a wide range of viscosities, so a range of flows can be studied. We demonstrated the technique in horizontal, rotating cylinder flows. We combined two tried and true methods to do these experiments. The first used the difference in T1 to select between phases. The second used gradient waveforms with controlled first moments to produce velocity dependent phase shifts. One novel processing method was developed that allows us to use static continuous phase measurements to reference both the continuous and discrete phase velocity images. ?

12:15PM B19.00004 NMR velocity imaging of single liquid drops , A. AMAR, S. STAPF, B. BLUEMICH, ITMC-RWTH Aachen, Germany — Liquid-liquid extraction processes are often found in industrial applications when a bulk phase needs to be purified from dissolved components. The extraction strategy consists of dissolving the impurities into a second, carrier phase, with optimal performance being guaranteed by maximizing both contact interface area and mass transfer rate, in the shape of a swarm of dispersed droplets. Their buoyancy-driven flow within the continuous medium induces internal fluid motion driven by momentum transfer at the drop surface. This convective transport enhances mass transfer and the efficiency of an extraction column. However, understanding mass transfer depends on a proper description of the flow field inside and outside the drops. For that purpose, a cell was built that enables the levitation of a single drop within a counterstream of water. NMR velocity imaging was then applied to drops of different fluids to monitor the internal dynamics as a function of drop size, age, and interface tension. Vortex-type patterns in at least part of the drop were observed where their size and velocity magnitude depended on the system impurity concentration.

12:27PM B19.00005 Velocity, correlation time and diffusivity measurements in highly turbulent gas flow by an MRI method , ZHI YANG, BEN NEWLING, UNB MRI Centre, University of New Brunswick — We present non-invasive, quantitative MRI wind-tunnel measurements in flowing gas (velocity > 10 m/s) at high Reynolds numbers (Re > 105). Our measurement method is three-dimensional and has the potential for saving time over traditional pointwise techniques. The method is suitable for liquids and for gases. We demonstrate the use of the technique on different test sections (bluff obstruction, clark Y-wing and cylinder). The mean velocity of gas flowing past those sections has been measured. We also investigate methods to measure flow correlation times by changing the acquisition interval between excitation of the sample and detection of the signal. This may be accomplished by making separate measurements or by using a multiple-point acquisition method. A measurement of correlation time allows us to map turbulent diffusivity. The MRI data are compared with computational fluid dynamics.

12:39PM B19.00006 Recent progress in NMR/MRI in petroleum applications1 , YI-QIAO SONG, Schlumberger-Doll Research — NMR has become an important technique for characterization of porous materials. In particular, its importance in petroleum exploration has been enhanced by the recent progress in NMR well-logging techniques and instruments. Such advanced techniques are increasing being accepted as a valuable service especially in deep-sea exploration. This paper will outline the recent progress of MR techniques at Schlumberger-Doll Research. Well- logging - The second generation NMR well-logging tool and the 2D NMR methods (D-T2, etc) enable measurements at several depths from the well bore allowing a one-dimensional profiling of the fluid. Such data have allowed quantification of fluid invasion during drilling, obtaining the properties of native fluids and identifying oil/gas zones. MRI- Rocks from oil reservoirs are heterogeneous (e.g. large range of pore sizes and porosity variation) due to the complex geological and geochemical histories. The spatial pattern of the heterogeneity has not been well studied. We have developed several NMR techniques to quantify pore length scale previously. In order to predict flow over a large length scale, it is necessary to determine spatial heterogeneity and pore connectivity over the relevant size. We have performed MRI on a series of carbonate rocks and found interesting patterns of the heterogeneity characteristics. Mathematics - It is well known that the Laplace inversion is non-unique and the resulting spectrum can be strongly dependent on the prior constraints, specific algorithm and noise. However, the different spectra can all be solutions consistent with data. It would be useful to have a robust criterion – independent of algorithms – to determine the properties of the resulting spectrum. Several methods will be described to examine the statistics of the solutions, uncertainty of the spectrum and its integrals and resolution.

1This work is partially supported by NIH EB003869-01.

1:15PM B19.00007 MRI measurements of heterogeneity in carbonate rock cores , ANDREW POMER- ANTZ, ERIC SIGMUND, YI-QIAO SONG, Schlumberger-Doll Research, SCHLUMBERGER-DOLL RESEARCH TEAM — Magnetic resonance imaging (MRI) provides spatially resolved measurements of the spin-spin relaxation time (T2) of brine that saturates the pores of carbonate rocks. Images with millimeter resolution reveal relaxation that can be well described by a double exponential in each voxel. From these images, it is possible to describe the length scales and extent of spatial heterogeneity both qualitatively and quantitatively. Qualitatively, the fitted values from each voxel can be combined into a histogram to make a T2 distribution, and histograms produced at different resolutions can be compared to each other and to the Laplace inversion of CPMG data for the whole core. Quantitatively, experimental semi-variograms can be constructed and analyzed using geostatistical techniques. In general, heterogeneity both above and below the 1 mm imaging resolution is observed, although the extent of heterogeneity is found to vary greatly between rock cores. In many cases, the qualitative features of the T2 distribution for the entire core are manifest in almost every individual voxel of microliter volume, indicating significant heterogeneity at short length scales.

1:27PM B19.00008 Visualization of the secondary flow formation during contraction flow of a viscoelastic fluid by NMR methods , GALINA PAVLOVSKAYA, Colorado State University — Viscoelastic fluids are known to exhibit a variety of flow transitions at low Re numbers. These fluids are also known to form secondary flows in the corners of abrupt contractions during the entry flow. We have applied NMR methods to determine the areas where the vortices are formed during the entry flow of a viscoelastic fluid in a tubular abrupt contraction. We have measured volume-averaged dispersion coefficients at different axial locations above the contraction entry plane. We also have measured velocity fields in the same spatial locations. In both types of experiments the flow encoding time was varied. We found no time dependence in the velocity fields while dispersion coefficient profiles were strongly dependent on the flow encoding time in the areas where vortices were formed. Based upon these results some information about the dynamics of the vortex formation in this type of flow could be deduced.

Monday, March 5, 2007 11:15AM - 2:15PM — Session B26 DCP DBP: Focus Session: Protein Folding: Theory and Simulations II Colorado Convention Center 205

11:15AM B26.00001 , DEVARAJAN THIRUMALAI, University of Maryland — No abstract available. 11:51AM B26.00002 Protein folding and dynamics from simulations of coarse protein models.1 , GERHARD HUMMER, Laboratory of Chemical Physics, NIDDK, National Institutes of Health — The dynamics and folding transitions of proteins are studied by computer simulations of coarse-grained models. The simulations are related to experimental studies of the unfolding of proteins under mechanical force, and the eﬀects of mutations on the folding rates using phi-value analysis. Coarse protein models have also been useful in studies of slow conformational transitions. Applications to the helix-to-sheet transition of an arc repressor mutant, and the open-to-closed transition of the calmodulin C-terminal domain indicate that local unfolding events can contribute signiﬁcantly to the slow dynamics of these proteins.

1co-authors: Robert B. Best and Yng-Gwei Chen.

12:27PM B26.00003 , HENRI ORLAND, Service de Physique Theorique — No abstract available.

1:03PM B26.00004 The folding of an “average” beta trefoil protein. , SHACHI GOSAVI, PAT JENNINGS, JOSE ONUCHIC, UCSD — The beta-trefoil fold is characterized by twelve beta strands folded into three similar beta-beta-beta-loop-beta (trefoil) units. The overall fold has pseudo-threefold symmetry and consists of a six stranded-barrel, capped by a triangular hairpin triplet. The loops connecting the beta-strands vary in length and structure. It is these loops that give the fold its varied binding capability and the binding sites lie in different parts of the fold. The beta-trefoil proteins have little sequence similarity (sometimes less than 17%) and bind a range of molecules, including other proteins, DNA, membranes and carbohydrates. Protein folding experiments have been performed on four of the beta trefoils, namely, interleukin-1 (IL1B), acidic and basic fibroblast growth factors (FGF-1 and FGF-2) and hisactophilin (HIS). These experiments indicate that the proteins fold by different routes. Folding simulations of the proteins identify the possible folding routes and also show that the shapes of the barriers are different for the different proteins. In this work, we design a model protein which contains only the core fold elements of the beta-trefoil fold. We compare the folding of this “average” protein to the folding of His, FGF and IL1B and make some connections with function.

1:15PM B26.00005 Life in a Crowd: Macromolecular Crowding and Confinement Effects on Protein Interactions in Living Systems , MARGARET CHEUNG, Department of Physics, University of Houston — Biological polymers carry out their functions in living systems where the environment is very concentrated or crowded by macromolecules. Physically, the composition of a cell is more than “a sack of water”; its consistency is closer to Jell-O. Experiments suggests that, because of this macromolecular crowding effect that confines polymeric dynamics, the kinetics and thermodynamics of protein folding and the association rate constants of protein-protein interactions in a cell (in vivo) are very different from that ina diluted test tube (in vitro). In order to quantitatively understand macromolecular crowding and confinement effects on protein dynamics, we used coarse-grained models that physically captured interactions between crowders and a protein. The folding rates of a model protein nonmonotonically increased with the volume fraction of the crowders. At lower volume fractions, depletion-induced attractions from crowders could be mapped according to the spherical confinement model. A result of spherical confinement was the destabilization of denatured states by disallowing extended configurations that were longer than the pore size. However, at higher volume fractions, conformational fluctuations of a protein were susceptible to the shape of the confining condition. Thus, an approximation of the spherical confinement to mimic crowding effects was no longer effective.

1:27PM B26.00006 2D IR Spectroscopy of Ubiquitin Unfolding Dynamics , ZIAD GANIM, HOI SUNG CHUNG, ANDREI TOKMAKOFF, Department of Chemistry, Massachusetts Institute of Technology — The unfolding dynamics of ubiquitin have been studied using a combination of amide I 2D IR spectroscopy and spectral calculations drawing on structures from molecular dynamics simulations. Equilibrium temperature- dependent 2D IR spectra and transient 2D IR spectra following a nanosecond temperature jump are used to follow the unfolding of ubiquitin’s β-sheet. The equilibrium 2D IR spectra show two features that arise from delocalized β-sheet vibrations of which differ by whether C=O oscillators vibrate parallel or perpendicular to its strands. Spectral changes in the transient difference spectrum start with an abrupt blue shift of the perpendicular diagonal region, which corresponds to the disruption of hydrogen bonds between water and solvent-exposed peptide groups. This change is followed over µs to ms time scales by a blue shift of the perpendicular region and disappearance of a cross peak, which reflect the gradual unfolding of the β-sheet of the protein. The experiments are compared with 2D IR spectra calculated from molecular dynamics trajectories of ubiquitin unfolding using a structure-based model for protein amide I spectroscopy.

1:39PM B26.00007 Generalization of distance to higher dimensional objects, and applications to biopolymer folding1 , STEVEN PLOTKIN, Department of Physics, University of British Columbia, Vancouver — The measurement of distance between two objects is generalized to the case where the objects are no longer points but are one-dimensional (strings) or many-dimensional (diﬀerential manifolds). Applications to biopolymer folding will be discussed.

1Support from the NSERC and the A.P. Sloan Foundation is gratefully acknowledged

1:51PM B26.00008 Collapse transition for self-avoiding random walks with hydrophobic interaction on a 2 dimensional lattice , MATHIEU GAUDREAULT, JORGE VINALS, Department of Physics, McGill University, Canada — We study the collapse transition of a protein model with an explicit coarse-grained model of solvent hydrophobicity using Monte Carlo simulation. The protein is modelled as self- avoiding random walk with nearest neighbour interaction on a two dimensional lattice by using the pivot algorithm. Without the solvent, universal quantities of the chain around the transition temperature are well known. Hydrophobicity is modelled through a lattice of solvent molecules in which each molecule can have q states, depending of an orientation variable. Only one state is energetically favoured, when two neighbouring solvent molecules are both in the same state of orientation. The monomers are placed in interstitial position of the solvent lattice, and are only allowed to occupy sites surrounded by solvent cells of the same orientation. The potential of mean force between two interstitial solute molecules is calculated, showing that the strength of attraction increases by increasing the free energy of H-bond formation while its range decreases. We also show that the temperature of the collapse transition is shifted in the presence of solvent, while the universal quantities of the protein transition are conserved.

2:03PM B26.00009 ABSTRACT WITHDRAWN —

Monday, March 5, 2007 2:30PM - 4:54PM — Session D19 DCP: Focus Session: New Frontiers in Imaging III Colorado Convention Center 104 2:30PM D19.00001 Tissue Imaging and Multidimensional Spectroscopy Using Shaped Fem- tosecond Laser Pulses , WARREN WARREN, Duke University — We use rapidly updatable, femtosecond pulse shaping and multidimensional spectroscopy to make new targets accessible by nonlinear optical imaging. For example, we observe two-photon absorption (TPA), sum frequency absorption (SFA) and self phase modulation (SPM)). Detection of TPA and related effects, such as the local quantum yield (fluorescence/absorption) permits direct observation of important endogenous molecular markers which are invisible in multiphoton fluorescence microscopy; it also permits excitation in the long-wavelength water windows which have significantly reduced scattering, but little endogenous two-photon fluorescence. The fundamental problem is that at the powers one might reasonably apply to tissue (e.g. 5 mW from a modelocked laser) typically 10−6of the light is removed by TPA, with the rest lost to scattering and linear absorption; and SPM does not broaden the spectrum in the dramatic way associated with (for example) continuum generation. A variety of solutions to these problems using femtosecond pulse shaping will be presented. The simplest solution, which uses amplitude modulation of a fs pulse train, has led to high quality microscopic images of the melanin distribution in melanotic lesions, and has led to discrimination between the different types of melanin in melanosomes. Shaping individual pulses instead of the envelope permits high sensitivity detection of both SPM and TPA via spectral hole refilling combined with heterodyne detection. We manufacture laser pulses with a narrow (ca. 3 nm) spectral hole, which can only be refilled by nonlinear processes; TPA causes refilling 180 degrees out of phase with the wings of the pulse, SPM is 90 degrees out of phase. By inserting a phase-coherent pedestal in the hole, then repeating the experiment with a different phase on a timescale rapid compared to any physiological processes, we can extract the phase of the refilling, hence the relative contributions of SPM and TPA. This method can extract excellent signatures from hemoglobin as well as melanin. We have also used it to image neurons firing in tissue, and to characterize off-diagonal peaks of contrast agents in two-dimensional spectra.

3:06PM D19.00002 Laser-detected Magnetic Resonance Imaging1 , SHOUJUN XU, Lawrence Berkeley National Laboratory, MARCUS DONALDSON, CHARLES CRAWFORD, SIMON ROCHESTER, University of California Berkeley, VALERIY YASHCHUK, Lawrence Berkeley National Laboratory, DMITRY BUDKER, ALEXANDER PINES, University of California Berkeley and Lawrence Berkeley National Laboratory — Magnetic resonance imaging is often performed in the presence of a superconducting magnet for high polarization and sensitive detection. However the cost and immobility of the system impose some restrictions on its applications. To overcome these limiting factors, we present an alternative detection technique: laser- based atomic magnetometry. This technique detects nuclear magnetization at virtually room temperature with an excellent sensitivity at low fields, eliminating the necessity of cryogenics and a homogenous high magnetic field. We show the characteristics of a gradiometer based on two atomic magnetometers and its coupling to a low-field encoding setup. Various flow images are obtained, with spatial resolution reaching sub-millimeter regime. Additional applications and future developments are discussed.

1This work was supported by the Director, Oﬃce of Science, Oﬃce of Basic Sciences, Materials Sciences Division of the U.S. Department of Energy.

3:18PM D19.00003 New Techniques for Signal Optimization in Harmonic and Multiphoton Absorption Fluorescence Microscopy , JEFF SQUIER, Colorado School of Mines — Nonlinear imaging with ultrafast lasers continues to broaden its application base as a significant tool for exploring and understanding biological structure and function at the microscopic level. The challenge is significant - the biological community needs to be able to quantitatively visualize 100 cubic micrometer volumes with a resolution of 50 nm, and do so in a dynamic fashion – millisecond time scales are desirable. In order to achieve these demanding imaging requirements we need to strive to achieve new levels of efficiency – improved resolution is a function of how many photons can be extracted from ever smaller volumes. Towards this end, in this talk we discuss new methods for fiber delivery of femtosecond pulses, spatio-temporal characterization of femtosecond pulses through high-numerical aperture optics, and adaptive spatio-temporal control of these pulses.

3:54PM D19.00004 Research Applications of Photoelectron Emission Microscopy , WAYNE HESS, GANG XIONG, ALAN JOLY, KENNETH BECK, Pacific Northwest National Laboratory, WEI WEI, J. MIKE WHITE, Department of Cheistry, University of Texas, MINGDONG CAI, J. THOMAS DICKINSON, Department of Physics, Washington State University — Photoelectron emission microscopy (PEEM) is a developing technique that images electrons emitted from conductor and semiconductor surfaces under UV, X-ray, or laser irradiation. Low energy PEEM can reveal surface morphology on a 10 nm scale and is sensitive material properties such as phase, adsorbed molecules, surface electronic structure, and other physical properties that affect work function and hence the photoelectron yield. We have used PEEM to study phase transformation in shape memory alloys diffusion of Cu in Cu/Ru bilayers and laser-induced oxygen vacancy creation on TiO2. Femtosecond laser irradiation from a frequency-doubled Ti:sapphire oscillator was used to remove bridge-bonded oxygen atoms. To further illustrate the utility of PEEM, we will discuss applications in different fields such as thermal-induced structural phase transformation of shape memory alloys and diffusion of Cu through an Ru barrier layer.

4:06PM D19.00005 Medical Applications of X-Ray Phase Contrast Imaging , CHRISTOPH ROSE- PETRUCK, CHRISTOPHER LAPERLE, THERON HAMILTON, GUOHUA CAO, PHILIP WINTERMEYER, GERALD DIEBOLD, JACK WANDS, Brown University — We report the use of an inline holographic x-ray imaging technique for medical purposes. In contrast to conventional x-ray radiography a phase- sensitive x-ray imaging method is employed. This phase-contrast x-ray imaging is fundamentally different from conventional x-ray shadowgraphy because the mechanism of image formation does not rely on differential absorption by tissues. Instead, x-ray beams undergo differential phase shifts in passing through an organ and subsequently interfere constructively or destructively at the x-ray camera. Hence, tissues are distinguished by their different indices of refraction rather than their absorptive properties. This imaging method is more than a thousand times more sensitive to density variations of tissues than conventional absorption methods and enables imaging of soft tissues with high contrast without the use of contrast agents. For example, we will present images of mouse livers yielding resolution of arterial capillaries as small as tens of micrometers. We also show the imaging technique operates in combination with ultrasound-induced, tissue-selective, differential movement of cancer tumors which highlights the tumor of interest and in some cases obviates the need for chemical contrasting agents.

4:18PM D19.00006 Optical/MRI Multimodality Molecular Imaging1 , LIXIN MA, Department of Radiology and International Institute for Nano and Molecular Medicine, University of Missouri-Columbia, CHARLES SMITH, Department of Radiology and Radiopharmaceutical Sciences Institute, University of Missouri-Columbia, PING YU, Department of Physics and Astronomy, University of Missouri-Columbia — Multimodality molecular imaging that combines anatomical and functional information has shown promise in development of tumor-targeted pharmaceuticals for cancer detection or therapy. We present a new multimodality imaging technique that combines fluorescence molecular tomography (FMT) and magnetic resonance imaging (MRI) for in vivo molecular imaging of preclinical tumor models. Unlike other optical/MRI systems, the new molecular imaging system uses parallel phase acquisition based on heterodyne principle. The system has a higher accuracy of phase measurements, reduced noise bandwidth, and an efficient modulation of the fluorescence diffuse density waves. Fluorescent Bombesin probes were developed for targeting breast cancer cells and prostate cancer cells. Tissue phantom and small animal experiments were performed for calibration of the imaging system and validation of the targeting probes.

1This work was supported by NIH P50-CA-103130. 4:30PM D19.00007 Compressed Sensing for Multispectral and Confocal Microscopy , KEVIN KELLY, Rice University, DHARMPAL TAKHAR, TING SUN, JASON LASKA, MARCO DUARTE, RICHARD BARANIUK — Compressive sensing is an emerging ﬁeld based on the revelation that a small number of random linear projections of a signal or an image contain enough information for reconstruction of a high resolution one. This technique has been applied to magnetic resonance imaging and neutron scattering. We have previously developed an optical camera based on this concept which is capable of megapixel images while utilizing a single photodiode for acquisition and implemented through the use of a digital micromirror device to randomly modulate and acquire the necessary projections of the image. In addition, this scheme allows for the rapid acquisition of multispectral information. We are now extending this scheme to imaging beyond the visible spectrum into the infrared and terahertz where high resolution image sensors are much more costly. Lastly we will present a scheme for utilizing this method in confocal microscopy similar to the ﬂying pinhole concept except that the individual pinhole is replaced by a complex random projection and reconstructed via linear programming.

4:42PM D19.00008 Source localization of auditory evoked responses from a human brain with an atomic magnetometer , K. KIM, H. XIA, A. BEN-AMAR BARANGA, D. HOFFMAN, M. V. ROMALIS, Department of Physics, Princeton University, Princeton, New Jersey 08544, USA — We report first measurements of auditory evoked fields (AEF) in a human brain with an atomic magnetometer system and discuss the techniques for magnetic source localization using this system. Until recent development of spin-exchange relaxation free (SERF) atomic magnetometers with a sensitivity of 0.5fT/Hz1/2, only SQUID magnetometers had sufficient sensitivity to measure a magnetoencephalograph (MEG). With simple multi-channel operation and no cryogenic maintenance, the atomic magnetometer provides a promising alternative for brain activity measurements. A clear N100m feature in AEF was observed after averaging over 600 stimuli. Currently the intrinsic magnetic noise level is 3.5 fT/Hz1/2 at 10 Hz. Optical detection of magnetic fields allows flexibility in magnetic mapping while in the same time imposing certain geometrical constraints. To investigate the magnetic source localization capabilities of the atomic MEG system we performed extensive numerical simulations and measurements with a brain phantom consisting of an artificial current source in a saline-filled sphere. We will discuss the results of numerical analysis and experimental implementation of magnetic source localization with atomic magnetometer.

Monday, March 5, 2007 2:30PM - 5:30PM — Session D26 DCP DBP: Focus Session: Protein Folding: Theory and Simulations III Colorado Convention Center 205 2:30PM D26.00001 Mechanisms of Protein Assembly and Folding: Lessons from Minimalist Models1 , JOSE ONUCHIC, CTBP - UCSD — Globally the energy landscape of a folding protein resembles a partially rough funnel. The local roughness of the funnel reflects transient trapping of the protein configurations in local free energy minima. The overall funnel shape of the landscape, superimposed on this roughness, arises because the interactions present in the native structure of natural proteins conflict with each other much less than expected if there were no constraints of evolutionary design to achieve reliable and relatively fast folding (minimal energetic frustration). A consequence of minimizing energetic frustration is that the topology of the native fold also plays a major role in the folding mechanism. Topological effects go beyond the structure of the TSE. The overall structure of the on-route and off-route (traps) intermediates for the folding of more complex proteins is also strongly influenced by topology. Going beyond folding, the power of reduced models to study the physics of protein assembly will be discussed. Since energetic frustration is sufficiently small, native topology-based models have shown that binding mechanisms are robust and governed primarily by the protein’s native topology. These models impressively capture many of the binding characteristics found in experiments and highlight the fundamental role of flexibility in binding.

1Supported by the NSF

3:06PM D26.00002 Direct application of a simple model to the quantitative analysis of experiments on an ultrafast folding protein , ERIC HENRY, National Institutes of Health — A simple Ising-like statistical-mechanical model for protein folding (Henry and Eaton, Chem. Phys. 307, 163-185, 2004) is used to analyze a broad set of experimental data on the ultrafast folding villin subdomain. In this model each residue in the protein sequence can adopt one of two possible microscopic states corresponding to native and non-native conformations; model protein states are identified with distinct sequences of native/non-native residues. The folding properties of the protein are determined entirely by the map of inter-residue contacts in the native structure. To compute partition functions by complete enumeration of all protein states, only those states are included that contain at most two contiguous sequences of native residues. Native contacts are only permitted between residues lying in such contiguous sequences. The stability of any state of the chain is determined by the offsetting effects of the stabilizing native contacts and the destabilizing entropy losses associated with fixing residues in the native conformation and with closing loops of nonnative residues created by contacts between distinct native sequences. In a least-squares fitting analysis, the temperature-dependent populations predicted by the model for all the protein states, combined with a simple description of the spectroscopic properties of individual states, are used to model the results of spectroscopic and thermodynamic experiments. The model reproduces the temperature dependence of the excess heat capacity, tryptophan fluorescence quantum yield, circular dichroism, and relaxation rates and amplitudes, as well as the effects of site-directed mutants on the folding rates and equilibrium constants.

3:42PM D26.00003 Desolvation effects and topology-dependent protein folding , ALLISON FERGUSON, ZHIRONG LIU, HUE SUN CHAN, Dept. of Biochemistry, Faculty of Medicine, University of Toronto — As a protein folds, water molecules must be excluded from the hydrophobic core, and thus desolvation barriers between the protein’s constituents must be crossed in order to reach the final folded state. Previous research on continuum Go¯-like protein models has demonstrated that pairwise-additive desolvation potentials lead to more thermodynamically and kinetically cooperative folding/unfolding transitions (Z. Liu and H. S. Chan, Phys. Biol. 2, S75-S85, 2005). The present work focuses on the role of this elementary desolvation potential in improving predictions of the well-known topology-folding rate relationship (K. W. Plaxco et al, J. Mol. Biol. 277, 985-994, 1998) of small single-domain proteins. Recent computational studies without desolvation barriers have shown (S. Wallin and H. S. Chan, J. Phys.: Condens. Matt. 18, S307-S328, 2006) that the observed correlation between topological parameters and folding rates is because these parameters may be proxies for rate-determining properties of the transition state, such as the activation free energy ∆G‡ and activation conformational entropy ∆S‡. Including the desolvation barrier in the model results in stronger correlations between measures of topology and simulated folding rates / transition state properties, reinforcing the theory that even simple representations of the desolvation effect are important for understanding crucial features of protein folding.

3:54PM D26.00004 Networks in Protein Folding , ERZSEBET´ RAVASZ REGAN, Beth Israel Deaconess Medical Center, Harvard Medical School, ZOLTAN´ TOROCZKAI, University of Notre Dame, Physics Department, G. GNANAKARAN, Los Alamos National Laboratory, T-10 — We take a networks approach to protein folding by identifying different protein conformations with nodes, while an elementary step of the system (rotation around a bond) that takes one configuration to another is defined as a link. The energies of configurations are scalar quantities associated with each node. Using this approach we can show that the scale-free nature of the observed protein conformation networks can be explained by simple results obtained on gradient networks. 4:06PM D26.00005 Intramolecular Vibrational Preparation of the Unfolding Transition State of ZnII-substituted Cytochrome c: Picosecond Time-Resolved Fluorescence and Dynamic Stokes Shift Studies1 , WARREN F. BECK, SANELA LAMPA-PASTIRK, Department of Chemistry, Michigan State University — We show that an intramolecular vibrational excitation provided by the radiationless decay of a covalently bound electronic chromophore can be exploited to drive a protein from its native folded state to the transition state for unfolding. Using this approach, we examine the effect of the polarity and viscosity of the solvent medium on the II II unfolding and refolding reactions of Zn -substituted cytochrome c at room temperature. The dynamic Stokes shift of the S1-state Zn –porphyrin is monitored using picosecond time-resolved fluorescence spectroscopy as a probe of the protein and solvent dynamics that are associated with the crossing of the unfolding transition state and with the subsequent unfolding and refolding trajectories. The results show that the solvent polarity controls the activation energy for the unfolding and refolding reactions; the solvent viscosity further controls the rate by frictionally hindering the moving polypeptide. These findings suggest an important role for the solvent in the kinetic control of protein-folding trajectories on the energy landscape.

1Supported by grants MCB-0091210 and MCB-0520002 from the NSF Molecular Biophysics program

4:18PM D26.00006 Single Mutation Effect on Lysozyme Stability and Misfolding , RUHONG ZHOU, IBM Thomas J. Watson Research Center — We propose a mechanism, based on an unprecedended 10+ microsecond molecular dynamics simulation, for the surprising misfolding of hen lysozyme caused by a single mutation (W62G). Our simulations of the wild-type and the mutant lysozyme in 8M urea solution at biological temperature (with both pH = 2 and pH = 7) reveal that the mutant structure is much less stable than the wild-type, with the mutant showing larger fluctuations and less native-like contacts. Analysis of local contacts reveals that the Trp62 residue is the key to a cooperative long-range interaction within the wild-type where it acts like a bridge between two neighboring basic residues. A native-like cluster or nucleation site can thus form near these residues in the wild-type, but not in the mutant. These findings, while supporting the general conclusions of a recent experimental study by Dobson and coworkers, provide a detailed but different molecular picture of the misfolding mechanism.

4:30PM D26.00007 On the Mechanism of Protein Unfolding by Pressure A Molecular Dynam- ics Simulation Study , J. RAUL GRIGERA1, ANDRES MCCARTHY , CARLOS FERRARA, IFLYSIB — Proteins are denaturized at high pressure and the mechanism of such a denaturation is still on debate. We have studied lyzozyme and apomyoglobin, under pressure up to 0.3GPa using molecular dynamics simulation. Lysozyme shows more stability, although it cannot retain the native structure. On the other hand apomyoglobin shows a continuing unfolding process during the 180 ns simulation time. The analysis of the hydrophilic and hydrophobic proteins Solvent Accessed Surface clearly shows the increment of the hydrophobic exposed area in the formation of crevices and in the appearing of hydrophobic ‘spikes’ around the overall surface. The observation of the final state, within the simulation time, shows a clear effect on the conformational state of the proteins. Comparing the behavior of the proteins with de aggregation state of simple non-polar solutes at different pressures we have been able to conclude that the driving force of the denaturation is the change in the hydrophobic contribution to the native folding due to the changes of water structure under pressure, which have been shown both experimental and by computer simulation.

1CONICET-UNLP-CIC

4:42PM D26.00008 Free Energy Landscape - Settlements of Key Residues. , SVETLANA AROUTIOUNIAN, Dillard University — FEL perspective in studies of protein folding transitions reflects notion that since there are ∼10N conformations to scan in search of lowest free energy state, random search is beyond biological timescale. Protein folding must follow certain fel pathways and folding kinetics of evolutionary selected proteins dominates kinetic traps. Good model for functional robustness of natural proteins - coarse-grained model protein is not very accurate but affords bringing simulations closer to biological realm; Go-like potential secures the fel funnel shape; biochemical contacts signify the funnel bottleneck. Boltzmann-weighted ensemble of protein conformations and histogram method are used to obtain from MC sampling of protein conformational space the approximate probability distribution. The fel is F(rmsd) = -1/β•Ln[Hist(rmsd)], β=kB T and rmsd is root-mean-square-deviation from native conformation. The sperm whale myoglobin has rich dynamic behavior, is small and large - on computational scale, has a symmetry in architecture and unusual sextet of residue pairs. Main idea: there is a mathematical relation between protein fel and a key residues set providing stability to folding transition. Is the set evolutionary conserved also for functional reasons? Hypothesis: primary sequence determines the key residues positions conserved as stabilizers and the fel is the battlefield for the folding stability. Preliminary results: primary sequence - not the architecture, is the rule settler, indeed.

4:54PM D26.00009 Interplay between secondary and tertiary structure formation in a lattice model alpha helical hairpin peptide , PREM CHAPAGAIN, Department of Physicss, Florida International University, BERNARD GERSTMAN, Department of Physics, Florida International University, THEORETICAL BIOPHYSICS GROUP TEAM — We present results from Monte Carlo simulations of folding dynamics of a model alpha helical hairpin peptide. The dynamics shows that the peptide chain folds in a two step fashion that involves the formation of partial helical segments followed by the formation of a stable tertiary structure by joining these semi-stable helical segments. The interplay between the formation of secondary and tertiary structures during the folding process was investigated by calculating the heat capacity and other thermodynamic quantities at various simulation temperatures. In addition to a sharp peak in the heat capacity curve for the transition between unfolded state and folded native state, the helix-random coil transition in the unfolded state is also cooperative.

5:06PM D26.00010 Impact of solvent pH on buried charge formation and protein quake of photoactive yellow protein , AIHUA XIE, SANDIP KALEDHONKAR, LORAND KELEMEN, WOUTER D. HOFF, ANUPAMA THUBAGERE, Oklahoma State University — Embedding a charge group inside a protein in a low dielectric environment is energetically unfavorable. Therefore, most charged groups are solvent exposed. We have developed a hypothesis that a new buried charge transiently formed in a non-polar environment serves as an electrostatic epicenter that drives protein quake (protein conformational changes). Here we report an experimental study on the eﬀects of solvent pH on the protonation states of buried ionizable groups, and their correlation with protein quakes. Time-resolved Fourier transfer infrared (FTIR) diﬀerence absorbance spectroscopy is the major experimental technique for simultaneous detection of the proton transfer event (to generate a new buried charge) and the protein quake event. The results are expected to provide insight into the impact of solvent pH on protein structural dynamics in general.

5:18PM D26.00011 First Principles Study of the Reaction Mechanism for Intein C-terminal Cleavage , PHILIP SHEMELLA, SAROJ NAYAK, Department of Physics, Applied Physics & Astronomy, BRIAN PEREIRA, SHEKHAR GARDE, GEORGES BELFORT, Department of Chemical & Biological Engineering. Rensselaer Polytechnic Institute. Troy, NY — Protein splicing, consisting of the excision and ligation of two flanking sequences (the exteins), is auto-catalyzed by the internal sequence (the intein). It has been shown experimentally that by mutating the critical first residue of the intein, the first step of splicing is inhibited, although intein C-terminal cleavage can still occur independently. Using a tripeptide model system with QM methods, we have investigated the effect of different mutants in order to provide an atomic level understanding of this mechanism. We find that the reaction energy barrier for asparagine cyclization can be controlled by mutation of non-essential residues: specifically we found that the barrier with a methionine mutant is larger than to the barrier for cysteine, resulting in slower C-terminal cleavage in agreement with experiment. The accuracy of our model system is further confirmed by comparing results with that of a combined quantum mechanics and molecular mechanics (QM/MM) approach. These results suggest that certain mutations in inteins could be used to control the reaction rate without affecting the overall reaction mechanism and could exploited for many applications including molecular switches, sensors and controlled drug delivery. Tuesday, March 6, 2007 8:00AM - 10:48AM — Session H19 DCP: Focus Session: New Frontiers in Imaging IV Colorado Convention Center 104

8:00AM H19.00001 Molecular Dynamics Underlie the Nature of MRI Signals: The NMR Shutter-Speed , CHARLES S. SPRINGER, JR., Oregon Health & Science University — Motions of the spin-bearing molecules can have profound effects on the very nature (the exponentiality) of the macroscopic NMR signal. Quantitative mechanistic protocols often involve varying the equilibrium molecular kinetics (usually by temperature change) relative to the “NMR time-scale” (SS−1), usually ill-defined as the absolute difference of resonance frequencies [|∆ω|] in sites between which spins are exchanged. This holds true for the equilibrium water molecule exchange between tissue compartments and distinct populations. 1 However, in vivo studies must [by regulation] be isothermal, and the tissue H2O MRI signals remain essentially isochronous [∆ω = 0]. In NMR, an equilibrium process is manifest in the context of its “exchange condition.” It only “appears” to be fast or slow by comparison of its actual rate constant with its system “shutterspeed” (SS). [A nonzero ∆ω is the first, but not only, SS: its dimension is reciprocal time.] The process kinetics can be measured only if its NMR condition is varied at least partway between the fast- and slow exchange limits. In an isothermal study with no catalyst, this can be accomplished only by varying 1 −1 the pertinent SS. An MRI contrast reagent (CR) increases the laboratory frame H2O relaxation rate constant, Ri [≡ (Ti) ; i = 1,2]. For an isochronous exchange process, the SS is the intrinsic |∆Ri| for the sites. In quantitative dynamic-contrast-enhanced (DCE) studies, analytical pharmacokinetic modeling is 1 accomplished on region-of-interest (ROI) or pixel by pixel H2O signal time-courses following bolus CR injections. Accounting for the equilibrium transendothelial and transcytolemmal water interchange processes (a three-site exchange situation) is crucial for modeling accuracy: the relevant SS values vary during the CR bolus passage. This is so for DCE studies of cancer, multiple sclerosis, and myocardial blood flow variation. It is necessary for the successful discrimination of malignant and benign breast and prostate lesions. One can expect a SS for almost any NMR experiment. This includes diffusion weighted and rotating-frame 1 longitudinal relaxation of in vivo H2O signals. In these latter cases, the pertinent SS can be manipulated solely by adjustment of pulse sequence parameters, leading to completely non-invasive protocols.

8:36AM H19.00002 Human Regional Pulmonary Gas Exchange with Xenon Polarization Transfer (XTC) , IGA MURADIAN, JAMES BUTLER, MIRKO HROVAT, GEORGE TOPULOS, ELIZABETH HERSMAN, IULIAN RUSET, SILVIU COVRIG, ERIC FREDERICK, STEPHEN KETEL, F.W. HERSMAN, SAMUEL PATZ — Xenon Transfer Contrast (XTC) is an existing imaging method (Ruppert et al, Magn Reson Med, 51:676-687, 2004) that measures the fraction F of 129Xe magnetization that diﬀuses from alveolar gas spaces to septal parenchymal tissue in lungs in a speciﬁed exchange time. As previously implemented, XTC is a 2-breath method and has been demonstrated in anesthetized animals. To use XTC in humans and to avoid issues associated with obtaining identical gas volumes on subsequent breath-hold experiments as well as precise image registration in post-processing, a single breath XTC method was developed that acquires three consecutive gradient echo images in an 8s acquisition. We report here initial measurements of the mean and variance of F for 5 normal healthy subjects as well as 7 asymptomatic smokers. The experiments were performed at two lung volumes (∼45 and 65% of TLC). We found that both the mean and variance of F increased with smoking history. In comparison, standard pulmonary function tests such as DLCO FEV1 showed no correlation with smoking history.

8:48AM H19.00003 Quantitative Magnetic Resonance Imaging of 3-He Gas Transport , RICHARD E. JACOB, KEVIN R. MINARD, Pacific Northwest National Laboratory, Richland, WA — In magnetic resonance (MR) imaging the use of laser-polarized 3-He dramatically increases detection sensitivity and facilitates gas visualization. Here, the potential use of 3-He MR imaging for quantifying gas transport in the respiratory tract of laboratory rodents is examined by studying laminar flow in a straight pipe with a diameter comparable to the rat trachea (∼ 3.2 mm). At physiological flow rates (∼ 4 ml/s), laminar-like features are observed in 2D images of axial diffusion, and the structure of observed flow lamina differs significantly from predictions based on the Navier-Stokes equations. To reconcile these results, we formulate a statistical model of gas transport that accounts for Brownian motion on the imaging time scale. The model uses the 2D solution to the diffusion equation to describe how diffusing gas molecules sample the stationary flow field. The effects on MR measurements are then formulated in terms of the mean flow velocity, higher order correlation functions, and the details of data acquisition. Comparison between modeling and experiment shows that MR imaging results are accurately predicted for different gas mixtures and acquisition conditions. The model is generally applicable to any flow conduit, resulting in a quantitative basis for noninvasive gas transport studies.

9:00AM H19.00004 Human Pulmonary Diffusion Weighted Imaging at 0.2T with Hyperpolar- ized 129Xe1 , ADRIAN SINDILE, UNH, IGA MURADIAN, MIRKO HROVAT, CHRISTINA JOHNSON, WILLIAM HERSMAN, SAM PATZ — Unlike hyperpolarized 3He inhalations, which achieve a high degree of gas mixture homogeneity due to the higher diffusion constant, hyperpolarized 129Xe requires additional precautions to assure gas mixture homogeneity. A homogeneous concentration of Xe inside the human lungs is necessary to allow the use of ADC values as a reproducible measure of lung physiology and structure. To determine whether observed ADC differences are due to regional variations in Xe dilution, which would affect diffusitivity, we measured ADC as a function of a number of exhaling/rebreathing cycles (breaths). The results of our investigations into these differences will be presented.

1This work was supported by NIH RO1 HL073632.

9:12AM H19.00005 Large Production of Hyperpolarized 129-Xe for MRI Applications , IULIAN RUSET, F.W. HERSMAN, JAN DISTELBRINK, STEPHEN KETEL, SILVIU COVRIG, IGA MURADIAN, ADRIAN SINDILE — Although 129-Xe was the first hyperpolarized gas to be used in MRI studies, the research community has focused on 3-He, mainly because of the larger quantities of hyperpolarized gas available. Xenon has advantages over helium, such as natural abundance, lower diffusion, and high solubility in blood. It presents a large frequency chemical shift when dissolved in blood, tissue, brain, or trapped in molecular cages. A new design of a high-flow low-pressure spin-exchange optical pumping Rb-Xe polarizer was recently demonstrated by our group. The concept of counterflowing the gas mixture against laser light and dividing the polarizing cell in three operational zones has resulted in an increase with over an order of magnitude in the output magnetization compared with previously reported polarizers. We were able to produce hyperpolarized xenon at 64% polarization for 0.3 liters/hour flow rate and 22% polarization at 6 liters/hour. We also demonstrated a new design of freezing and thawing hyperpolarized xenon with minimum losses. We will present the concept of the high-flow low-pressure counterflowing xenon polarizer, its performance, as well as new optical pumping laser technologies. We will discuss optimization plans for xenon polarizing systems based on experimental observed limitations and theoretical modeling. 3 9:24AM H19.00006 Rapid Production of Hyperpolarized He Gas for MRI1 , BENJAMIN C. ANGER, University of Utah, RICHARD E. JACOB, KEVIN R. MINARD, Pacific Northwest National Laboratory, BRIAN T. SAAM, University of Utah — Hyperpolarized (HP) 3He gas created via spin-exchange optical pumping (SEOP) is widely used as a signal source in MRI applications. One drawback to conventional SEOP is the time required for polarization. The process normally requires 10 - 20 hours to achieve 40-50% polarization in enough gas (∼1 L) for a single imaging experiment. Two recent advances in the physics of SEOP have led to dramatic enhancements in polarization efficiency: the use of spectrally narrowed diode-laser arrays and hybrid SEOP, which employs both potassium and rubidium as alkali-metal intermediaries. We have combined these techniques in constructing two polarizers, a prototype system at Utah and a more fully engineered system at PNNL. We report >60% 3He polarization in 0.5 bar·L of gas in valved and refillable glass cells, achieved in under 4 h. With the apparatus described we are able to produce several liters of polarized 3He per day.

1Supported by NIH NHLBI RO1 HL073598.

9:36AM H19.00007 Double Quantum Filtered NMR Spectroscopy and Imaging , GIL NAVON, Tel Aviv University — As a result of the anisotropic motion of water molecules interacting with ordered biological tissues the proton-proton dipolar interaction and the deuteron quadrupolar interaction do not average to zero leaving some residual splittings. The technique of double quantum ﬁltered (DQF) NMR capitalizes on this phenomenon, opening new possibilities to probe biological processes and to obtain a new kind of contrast in MRI. In the talk new applications of the DQF pulse sequences to the study of nerves, enabling the measurement of intercompartmental water exchange in sciatic and optic nerves, the study of the ﬁber architecture in cartilage under normal, compressed and diseased conditions and the imaging of tendons, enabling the monitoring their healing process following injury.

10:12AM H19.00008 Hyperpolarized Krypton-83 as a MRI Contrast Agent , ZACKARY CLEVELAND, GALINA PAVLOVSKAYA, KARL STUPIC, Colorado State University, JOHN REPINE, Webb-Waring Institute, THOMAS MEERSMANN, Colorado State Univeristy — Hyperpolarized krypton-83 (I = 9/2) yields NMR signal enhancements [1] of 1200 to 4500 times that of thermal equilibrium value depending on the composition of the optical pumping gas mixture. The quadrupolar relaxation of krypton-83 provides surface sensitive contrast in MRI [2] and yields information about surface hydrophobicity [3], surface-to-volume ratio, surface temperature, and surface hydration. These characteristics make hp krypton-83 MRI a promising technique for materials science applications and medical diagnosis. Experimental hp krypton-83 results in model systems with biomedically relevant coatings (e.g. lung surfactant and cigarette tar) are presented. Additionally, preliminary results from hp krypton-83 in excised rodent lungs are discussed. (1) ZI Cleveland, et al., Chem. Phys., 2006. 124(4) 044311. (2) GE Pavlovskaya, et al., Proc. Natl. Acad. Sci. U.S.A.,2005. 102: 18275-18279. (3) KF Stupic, et al., Solid State Nucl. Magn. Reson., 2006. 29: 79-84.

10:24AM H19.00009 Introducing Hyperpolarized Xenon-131 Directly Detected by NMR Spec- troscopy , KARL STUPIC, ZACKARY CLEVELAND, GALINA PAVLOVSKAYA, THOMAS MEERSMANN, Colorado State Univeristy — Previously, high-field NMR and MRI applications of hyperpolarized (hp) noble gasses focused on the isotopes helium-3 (spin I = 1/2), xenon-129 (spin I = 1/2) [1], and more recently krypton-83 (spin I = 9/2) [2]. In this contribution, hp xenon-131 (spin I = 3/2) was generated by spin-exchange optical pumping and separated from the rubidium vapor for high field NMR detection at 14.1 T field strength. Xenon-131 is of particular interest because of its quadrupolar nature that can be utilized for the study of surfaces [3] and for the investigation of high magnetic field effects on the electronic structure of the noble gas atom [4]. In addition, this isotope is a useful probe for quadrupolar processes during gas transfer and during NMR/MRI detection. Experiments with xenon-131, including multiple quantum filtered NMR spectroscopy [3], provides insights into similar processes present in krypton-83 and its more complicated spin system [5]. [1] D. Raftery Ann. Rep. NMR Spec., 57, 208 (2006). [2] G. Pavlovskaya, et al., Pro. Natl. Acad. Sci. U.S.A. 102, 18275 (2005). [3] T. Meersmann et al., Phys. Rev. Lett. 80, 1398 (1998). [4] T. Meersmann and M. Haake, Phys. Rev. Lett. 81, 1211 (1998). [5] Z. Cleveland, et al., J. Chem. Phys.124, 044312 (2006).

10:36AM H19.00010 Spin relaxation in hyperpolarized krypton-83 and xenon-129 , THOMAS MEERS- MANN, ZACKARY CLEVELAND, KARL STUPIC, GALINA PAVLOVSKAYA, Colorado State University — The potential medical application of hyperpolarized (hp) krypton-83 (spin S = 9/2) [1] make a better insight into the NMR relaxation behavior of this isotope desirable, in particular since the relaxation limits the observed signal intensity but also provides a source for MRI contrast. The quadrupolar relaxation of krypton-83 is shown to be highly dependent on temperature, optical pumping gas mixture, the nature of surrounding surfaces and the applied magnetic ﬁeld strength [2, 3]. The relaxation is mainly caused by quadrupolar interactions during brief surface adsorption periods of the krypton atoms onto the surrounding container walls. In contrast to xenon-129, interactions with paramagnetic impurities in the surface or with gas phase oxygen are not signiﬁcant. 1) Pavlovskaya, et al. Proc. Natl. Acad. Sci. U.S.A.,2005. 102: 18275-18279; 2) Cleveland, Z.I., et al. J. Chem. Phys., 2006. 124(4) 044311; 3) Stupic, K.F et al. Solid State Nucl. Magn. Reson., 2006. 29: 79-84.

Tuesday, March 6, 2007 8:00AM - 10:48AM — Session H26 DCP: Focus Session: Non-adiabatic Molecular Dynamics and Control at Conical Intersections I Colorado Convention Center 205 8:00AM H26.00001 Electronically Excited States and Conical Intersections in Cytosine and its Analogs , SPIRIDOULA MATSIKA, Temple University — Conical intersections between two and three electronic states of the same symmetry have been found to play a key role in nonadiabatic processes. In recent years many studies have shown that conical intersections are important in the photophysics of nucleobases and facilitate radiationless decay to the ground state. Interestingly, there are molecules very similar in structure to the nucleobases which show very different photophysical behavior, i.e., longer excited state lifetimes and high quantum yields of fluorescence. An important question that arises is what causes the different behavior between nucleobases and their fluorescent analogs. In this work we present studies of cytosine and several of its analogs in an effort to correlate the molecular structure to the photophysical behavior. Large scale ab initio multireference configuration interaction methods (MRCI) are being used. Our results show the presence of many seams of two- or three-state conical intersections in both types of systems and energetic differences seem to be the cause of the different photophysical behavior. A mixed quantum mechanical/ classical mechanical (QM/MM) approach where the solute is described with the MRCI method will also be presented as a means to study the effect of the solvent on excited states. 8:36AM H26.00002 Coherent Control of the Photo-isomerization of Retinal in Bacteri- orhodopsin , R. J. DWAYNE MILLER1, University of Toronto — Proteins are highly evolved structures in which their central role is to direct chemical or solar energy into functions. A central tenet in biology is that proteins have evolved to stabilize the transition states processes directing energy transduction into functions. In the transition state region, the motions are fairly localized such the wave properties of matter can lead to destructive and constructive interferences that have a pronounced effect on transmission probabilities along reaction coordinates. Further, the time scale for motion through a transition state, often involving a conical intersection, is comparable to the currently believed decoherence times for electronic and vibrational degrees of freedom governing this motion. The question arises whether the phases of the underlying matter waves could play a role in directing biological processes. In order to address this question, we exploited coherent control protocols using shaped laser fields to determine whether or not the absolute quantum yield of the photo-isomerization of retinal in bacteriorhodopsin (bR) could be achieved using weak field conditions to probe the natural function. Through feedback-controlled amplitude and phase variation of the spectral components comprising the excitation pulse, we could selectively enhance or suppress the isomerization quantum yield by 20% in either direction. Our experimental observation illustrates that the wave properties of matter, as manifest on vibrational quantum coherences, can play a role in biological processes to the point that they can even be manipulated.

1Institute for Optical Sciences, Departments of Chemistry and Physics, 80 St. George Street, Toronto, ON, M5S 3H6, Canada

9:12AM H26.00003 Anion Photoelectron Spectroscopy of Deprotonated Cytosine and Thymine at 5.826 eV , TERRY YEN, BRADLEY F. PARSONS, SEAN M. SHEEHAN, DANIEL M. NEUMARK, University of California, Berkeley — UV radiation from sunlight is one of the most ubiquitous and lethal forms of environmental carcinogens. Luckily, perhaps as a result of selective pressure by molecular evolution, DNA is remarkably stable to photochemical decay. The solar UV photons are absorbed primarily by the building blocks of DNA, the nucleobases, which undergo ultrafast nonradiative relaxation processes back to the ground state by internal conversion. It has been suggested that the nucleobases’ excited singlet states of pi-sigma-star character, which are dissociative along the NH stretch coordinate, play a key role in the relaxation pathways. Studying the dynamics of the excited states of deprotonated nucleobases is therefore of great importance in understanding the photostability of DNA. Excited state dynamics of the deprotonated nucleobases cytosine and thymine has been investigated using anion photoelectron spectroscopy at 5.826 eV. In the experiments, a laser is used to detach an electron from a mass selected deprotonated nucleobase anion and the electron kinetic energy (eKE) is measured using velocity-map imaging (VMI). Through VMI, information is obtained on the nature of the excited states involved in the non-radiative processes of DNA.

9:24AM H26.00004 Comparing the electronic relaxation of pyrimidine bases and nucleosides in aqueous solution , STEPHEN BRADFORTH, ASKAT JAILAUBEKOV, University of Southern California, DELMAR LARSEN, University of California, Davis, CHRISTI CHESTER, University of Southern California — The ultrafast deactivation of DNA bases excited in the ultraviolet is known to occur by rapid nuclear motion through conical intersections between different electronic potential energy surfaces. How the intersections between these surfaces and the dynamics over these surfaces are modified by surrounding the base with water is a significant open question in DNA photophysics. Using a broadband transient absorption apparatus with 30 fs time resolution, we observe dispersed spectra from 300 – 700 nm revealing excited-state dynamics originating for U and T both as nucleobases and nucleosides. New sub-100fs dynamics is observed, including stimulated emission. The deactivation pathways and spectral signatures of the various intermediates are compared to data from gas-phase time-resolved photoelectron spectroscopy and non-adiabatic quantum-classical simulations.

9:36AM H26.00005 ABSTRACT HAS BEEN MOVED TO L26.00002 — 9:48AM H26.00006 Photoisomerization selectivity in conjugated π-bond systems through local microenvironment , AARON VIRSHUP, Dept. of Physics, Univ. of Illinois at Urbana-Champaign, TODD MARTINEZ, Dept. of Chemistry, Univ. of Illinois at Urbana-Champaign — Photoisomerization represents one of the simplest means to convert light energy into mechanical motion on the molecular scale. Theoretical models of photobiology often require description of not only a small photochemically active chromophore, but also the eﬀects of the much larger solvent or protein environment containing the chromophore. We have recently developed a program for carrying out excited state QM/MM studies of photodynamics using ab initio quantum chemistry techniques for the QM region, and modeling the time evolution of the system with the Full Multiple Spawning method for molecular dynamics. With this method, we show how local charge environments can be used to manipulate and enhance the photoisomer selectivity of small conjugated molecules.

10:00AM H26.00007 Excited State Dynamics of DNA and RNA bases1 , HANNELI HUDOCK, University of Illinois at Urbana-Champaign, Dept of Chemistry, BENJAMIN LEVINE, University of Illinoisat Urbana-Champaign, Dept of Chemistry, TODD MARTINEZ, University of Illinois at Urbana-Champaign, Dept of Chemistry — Recent ultrafast spectroscopic experiments have reported excited state lifetimes for DNA and RNA bases and assigned these lifetimes to various electronic states. We have used theoretical and simulation methods to describe the excited state dynamics of these bases in an effort to provide a mechanistic explanation for the observed lifetimes. Our simulations are based on ab initio molecular dynamics, where the electronic and nuclear Schrodinger equations are solved simultaneously. The results are further verified by comparison to high-level ab initio electronic structure methods, including dynamic electron correlation effects through multireference perturbation theory, at important points along the dynamical pathways. Our results provide an explanation of the photochemical mechanism leading to nonradiative decay of the electronic excited states and some suggestions as to the origin of the different lifetimes. Comparisons between pyrimidines illustrate how chemical differences impact excited state dynamics and may play a role in explaining the propensity for dimer formation in thymine.

1HH gratefully acknowledges the NIH Molecular Biophysics Training Grant at UIUC

10:12AM H26.00008 Probing solvation effects at conical intersections by ultrafast photoelectron imaging , BENOIT SOEP, LIONEL POISSON, CNRS, KEVIN RAFFAEL, Washington University St Louis, JEAN MICHEL MESTDAGH, CNRS, LABORATOIRE FRANCIS PERRIN TEAM1 — The electronic excitation of polyatomic molecules is generally followed by relaxation of the electronic energy to the ground state or to metastable, low lying states such as triplet states in hydrocarbons. It can be extremely rapid whenever conical intersections between the surfaces are at play, owing to their structural changes. Since, in general, relaxation is observed in condensed phases, it is essential to conduct the relevant experiments in the presence of a perturbing medium, here the surface of an argon cluster. We address the coupling of two excited configurations in a molecule possessing charge transfer intermediates thus prone to medium effects. We shall compare here the observation of the free and deposited molecule at the surface of argon clusters. The effect of the cluster and the possibility to record significant photoelectron spectra is thus described that represents an innovation for large systems. We made use of the anisotropy of the photoelectron angular distribution of the electrons to unravel the dynamics of the several excited configurations that are traversed during the electronic relaxation.

1DRECAM/SPAM 10:24AM H26.00009 Azobenzene optical switch controlled by external force1 , MARTIN KONOPKA, Slovak University of Technology, NIKOS DOLTSINIS, DOMINIK MARX, Ruhr-Universitaet Bochum, IVAN STICH, Slovak University of Technology — External pulling force can be employed to manipulate optical switching properties of azobenzene molecule which is a promising system for molecular electronics devices. We perform density functional treatment of azobenzene terminated by S-H groups with pulling force applied via restraints on the sulfur atoms. We treat the system both at zero and room temperature and among other quantities focus on separation between ground (S0) and ﬁrst excited (S1) singlet states. The separation is crucial for cis ↔ trans reisomerization rate. For trans isomer we observe decrease of the S1-S0 separation with increased stretching force and the molecule length. For cis isomer we ﬁnd opposite: the separation increases thus lowering photoisomerization rate. Another interesting point is mechanically induced cis → trans inversion in the ground state which occurs for extensions above 5 A.˚

1Support by Folkswagenstiftung (STRESSMOL) and APVT (APVT-20-0192-02) are acknowledged.

10:36AM H26.00010 Control of molecular fragmentation using shaped femtosecond pulses , MARCOS DANTUS, VADIM LOZOVOY, Michigan State University — The ability to tailor the excitation laser pulse by pulse shaping has inspired a number of scientist to search for special pulses that would be capable of inducing selective bond fragmentation or specific molecular rearrangements. This presentation will summarize results from a comprehensive look at the interaction of shaped laser pulses with para-nitrotoluene molecules. We have performed exhaustive experimental evaluation over very different pulse shaping strategies such as chirp, sinusoidal modulation, sinusoidal phase, binary phase, binary amplitude, binary phase and amplitude. For all these methods we recorded hundreds of mass spectra together with the integrated second harmonic generation (SHG) as an independent parameter related to pulse complexity or pulse duration. As expected, the integrated SHG of a given laser pulse correlates linearly with the total amount of ions detected. We were surprised, however, that the fragmentation patterns observed varied simply and predictably with the integrated SHG regardless of pulse shaping strategy. This implies that the integrated SHG fraction compared to a transform limited pulse is an excellent predictor of the fragmentation pattern for a given molecule. The implications of our findings for this and other molecules will be discussed from the fundamental point of view of bond selective chemistry. The development of applications for molecular recognition will also be discussed.

Tuesday, March 6, 2007 8:00AM - 11:00AM — Session H35 DBP DCP: Emerging Spectroscopic Techniques Colorado Convention Center 405

8:00AM H35.00001 BREAK — 9:48AM H35.00002 Real-time detection of multiple biomolecular reactions on a functionalized glass surface using a scanning oblique-incidence optical reflectivity difference (an ellipsometric technique).1 , YUNG-SHIN SUN, JAMES P. LANDRY, XIANGDONG ZHU, Dept. of Physics, Univ. of California at Davis — One of the enabling platforms in proteomic research is parallel (high-throughput) detection of multiple biomolecular interactions on a microarray. To keep conformational and in turn functional integrity of protein molecules, label-free detection is desirable. We have developed an oblique-incidence optical reflectivity difference (OI-RD) technique for label-free measurements of protein reactions with molecular targets in microarray format immobilized on functionalized glass surface. As an ellipsometric technique, OI-RD measures changes in thickness and/or optical dielectric response instead of fluorescence. By incorporating total internal refection geometry and a multi-element photodiode array detector, we demonstrate how such the OI-RD technique can be efficiently used to measure multiple protein reactions in real time with surface-immobilized molecules or molecular groups on a glass substrate.

1This work is supported by NSF Center for Biophotonics Science and Technology, UC-GREAT, and NIH.

10:00AM H35.00003 In Situ X-ray Reflectivity Studies of Protein Adsorption onto Function- alized Surfaces1 , ANDREW RICHTER, Valparaiso University — The adsorption of protein films onto solid surfaces, both artificial and naturally occurring, have been widely studied using a variety of techniques due to their importance in medicine, biomedical applications, and the general understanding of protein structure and function. What have yet to be performed are in situ, time-resolved, high-resolution structural studies of these systems. We have begun a project that uses the technique of in situ x-ray reflectivity to obtain highly resolved structural information with time resolution on the order of minutes. This talk will present our first findings of serum albumin and immunoglobulin G films on hydrophobic self-assembled monolayers. The protein films are readily observable, showing extensive denaturing after adsorption with a slow decay of density into the aqueous solution. Additionally, a thin low-density region that occurs between the hydrophobic film and the solution persists after protein deposition. Comparisons to films that are removed from solution, the influence of solution concentration, the effects of x-ray damage, and the time scales for protein film formation and evolution will also be discussed.

1This work is supported by an award from Research Corporation, CC6924

10:12AM H35.00004 Mid-IR spectra of the bio-related molecules in the gas phase , YONGJUN HU, ELLIOT R. BENSTEIN, Department of Chemistry, Colorado State Univ. — Mid-IR spectra of gas phase bio-related molecules R-OH, R-COOH and simple non-aromatic amino acids, such as glycine and valine, detected by vacuum ultraviolet (VUV), 10.5 eV single photon ionization of supersonically expanded and cooled samples, are presented and discussed. Molecules and their fragment species, generated by a proton transfer reaction following ionization, are identified by time of flight mass spectroscopy. The fundamentals and overtones of the CH and OH stretches and some combination bands are identified in the spectra. Rotational resolution for the OH mode and its first overtone yield an estimate of ∼50 K for the methanol monomer in the supersonic beam. Two neutral C2H5OH conformers can be identified by high sensitivity IR plus VUV nonresonant ionization and fragmentation detected (NRIFD-IR) vibrational spectroscopy. Free OH and NH stretches are missing in the spectrum of glycine and valine, indicating that the strong intra-molecular hydrogen bonds are formed in these gas phase species.

10:24AM H35.00005 Single Quantum Dots Imaged with Resonance Rayleigh Scattering Do Not Blink , DAVID W. WARD, WEI MIN, ETHAN S. KARP, XIAOLIANG SUNNEY XIE, Harvard University, Department of Chemistry and Chemical Biology — Semiconductor quantum dots have become a robust fluorescent marker for the life sciences. Two key issues limit the broad use of quantum dots as fluorescent markers: heterogeneous emission and non-radiant dark populations. All bright quantum dots blink stochastically, have considerable heterogeneity in their emission, and have fluctuations in their fluorescence lifetimes, limiting their utility as single particle trackers by introducing potentially large interruptions in particle trajectories. Further, a significant fraction does not fluoresce at all, undermining biophysical studies such as immuno-fluorescence. We present an alternative or complement to fluorescent imaging of quantum dots. We have developed a new technique, resonant Rayleigh scattering (RRS) microscopy, for imaging single quantum dots which does not exhibit blinking. Detection of individual quantum dots, both surface immobilized and freely diffusing in aqueous solution, is demonstrated. Non-fluorescent populations of quantum dots are visible through RRS microscopy. Though other non-fluorescence detection techniques exist they are significantly more complicated than our technique, which requires minimal alteration of a conventional confocal fluorescence microscope. 10:36AM H35.00006 Development of 0.24 THz pulsed electron paramagnetic resonance to “film” proteins in action with the UCSB free electron laser , SUSUMU TAKAHASHI, DAN G. ALLEN, KIYOTAKA AKABORI, MELISSA ANHOLM, HIEU NGUYEN, SANGWOO KIM, MARK S. SHERWIN, University of California Santa Barbara, JOHAN VAN TOL, LOUIS- CLAUDE BRUNEL, National High Magnetic Field Laboratory — Pulsed electron paramagnetic resonance (EPR) is extremely useful to study the fast dynamics of molecules. Currently, most high-power pulsed EPR experiments are performed near 10 GHz, with a time resolution of 100 ns. The spin dephasing times of spin labels on proteins in aqueous solution are tens of ns. Thus, conventional pulsed EPR measurements of proteins are performed on frozen samples. There exist instruments which operate at 95 GHz with time resolution shorter than 100 ns. We present the development of a 0.24 THz pulsed EPR system which is expected to have sub-ns time resolution, enabling the EPR study of proteins in solution. The system uses the UCSB free electron laser (FEL) to produce kW-level pulses at 240 GHz. A “pulse-slicer” shortens the FEL’s microsecond pulses to the ns range. Sequences of two or three pulses separated by up to 25 ns will be made using a home-made delay line. A superheterodyne detection system is being fabricated to be sensitive enough to detect 1nW signals and also protected from kW FEL inputs.

10:48AM H35.00007 Three-Dimensional Imaging of Single Large Macromolecules Using Equally Sloped Tomography1 , E. LEE, B. FAHIMIAN, J. MA, University of California at Los Angeles, C. IANCU, C. SULOWAY, E. WRIGHT, G. JENSEN, California Institute of Technology, J. MIAO, University of California at Los Angeles, UNIVERSITY OF CALIFORNIA AT LOS ANGELES TEAM, CALIFORNIA INSTITUTE OF TECHNOLOGY COLLABORATION — We report the development of equally sloped tomography for the reconstruction of the 3D structure of single large macromolecules. In a combination of pseudo-polar fast Fourier transform and the oversampling method with an iterative algorithm, equally sloped tomography makes superior 3D reconstruction to conventional tomography which has an intrinsic drawback due to the use of equally angled 2D projections. By employing equally sloped tomography and cryo electron microscopy, we have obtained the 3D structure of single hemocyanin protein molecules and HIV viruses at ∼ 5 nanometer resolution. Preliminary analysis based on cross- correlation has indicated that the 3D images using equally sloped tomography are superior to those of the conventional method. We believe this general approach will ﬁnd broad applications in high-resolution 3D imaging of large macromolecules.

1NSF, DOE

Tuesday, March 6, 2007 11:15AM - 2:15PM — Session J2 DCP DCOMP GSNP: Prize Session (DCP, DCOMP, GSNP) Colorado Convention Center Four Seasons 4 11:15AM J2.00001 Frontiers of Surface Science. Structure, Bonding and Dynamics on the Nanoscale at High Pressures and at the Buried (solid-liquid and solid-solid) Interfaces , GABOR A. SOMORJAI, Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley — Model surfaces from single crystals to monodispersed nanoparticles are investigated at high pressures and at liquid interfaces by sum frequency generation (SFG) vibrational spectroscopy and high pressure scanning tunneling microscopy. The phenomena discovered by surface studies at low pressures in the past, adsorbate-induced restructuring, the chemical activity of surface defects, surface mobility of adsorbates and coadsorption-induced ordering are detected at high pressures as well. Newly discovered surface phenomena include the low melting point of nanoparticles, the coadsorption of water and hydrogen at polymer and metal surfaces, respectively, and hot electron ﬂow during exothermic processes across oxide-metal interfaces (nanodiodes). Applications of surface science expanded into nanosciences, catalysis, tribology, polymers, biointerfaces, microelectronics, energy conversion and environmental chemistry will be discussed.

11:51AM J2.00002 Aneesur Rahman Prize Talk , DAAN FRENKEL, FOM Institute for Atomic and Molecular Physics — During the past decade there has been a unique synergy between theory, experiment and simulation in Soft Matter Physics. In colloid science, computer simulations that started out as studies of highly simpliﬁed model systems, have acquired direct experimental relevance because experimental realizations of these simple models can now be synthesized. Whilst many numerical predictions concerning the phase behavior of colloidal systems have been vindicated by experiments, the jury is still out on others. In my talk I will discuss some of the recent technical developments, new ﬁndings and open questions in computational soft-matter science.

12:27PM J2.00003 Conformation-specific spectroscopy and dynamics in the complexity gap1 , TIMOTHY ZWIER, Purdue University — Studies of the spectroscopy and conformational isomerization dynamics of flexible molecules typically fall into one of two size regimes: (i) small-molecule studies in which the molecule possesses two minima and a single barrier (e.g., cis-trans isomerization about a double bond) or (ii) large macromolecules for which it is impossible to describe the potential energy surface in exhaustive detail (e.g., protein folding). Between them is a ‘complexity gap’ of considerable proportions. This talk will describe our group’s contributions to studies of molecules that are in that complexity gap in the sense that they have potential energy surfaces containing tens to hundreds of minima, and many times that number of transition states. By employing double resonance laser spectroscopy of isolated molecules cooled in a supersonic expansion, it is possible to obtain the ultraviolet and infrared spectral signatures of the individual conformational isomers of these molecules free from interference from others present in the sample. This foundation of spectroscopic data also serves as the basis for conformation-specific studies of the dynamics of conformational isomerization. In these studies, either infrared excitation or stimulated emission pumping (SEP) is used to excite a single conformation with a well-defined internal energy, thereby initiating conformational isomerization. By re-cooling the products prior to interrogation downstream, the energy thresholds for isomerization between individual X→Y reactant-product pairs can be determined. Several examples from our recent work will be given to illustrate the kinds of insight that can be drawn from these studies regarding the conformational preferences, spectral signatures, barrier heights and relative energies of minima, fractional abundances, isomerization pathways, and internal energy flow accompanying isomerization.

1Supported by the National Science Foundation and the Department of Energy Basic Energy Sciences.

1:03PM J2.00004 Nicholson Medal - Award Talk , SHLOMO HAVLIN, Bar Ilan University — No abstract available. 1:39PM J2.00005 Nicholas Metropolis Award Talk: Quasi-static Modeling of Plasma and Laser Wakefield Acceleration1 , CHENGKUN HUANG, UCLA — Plasma wakefields driven by intense ultrashort charged particle or laser beams can sustain acceleration gradients three orders of magnitude larger than conventional RF accelerators. These wakefields are promising for accelerating charged particles in short distances for applications such as an energy booster of a linear collider and as a ultra-compact accelerator. In the Plasma Wakefield Accelerator (PWFA) or Laser Wakefield Accelerator (LWFA), the space charge force of an electron beam or the ponderomotive force of a laser beam expels plasma electrons away from its path, forming a bubble-like structure where the longitudinal electric field inside of it provides accelerating and the transverse Lorentz force provides focusing forces on electrons. Recently, quasi-monoenergetic beams from self-trapped plasma electrons in wakefields driven by intense laser beamd have been observed in experiments in many laboratories around the world, and a PWFA experiment performed at Stanford Linear Accelerator Center (SLAC) successfully demonstrated that the energy of particles at the tail of the driving electron can be doubled from ∼40 GeV to ∼80 GeV in just 80 cms. However, to fully understand these experiments requires a particle-based computer model because the interaction between the plasma and the driver is highly nonlinear. We have developed a highly efficient, fully parallelized, fully relativistic, three dimensional particle-in-cell code, QuickPIC, for simulating plasma wakefield acceleration. The model is based on what is called the quasi-static or frozen field approximation, which assumes that the driver does not evolve during the time it takes for it to pass a plasma particle and reduces a fully three-dimensional electromagnetic field calculation and particle push into a two-dimensional electrostatic field solve and particle push. This algorithm reduces the computational time by at least 2 to 3 orders of magnitude. Comparison with a fully explicit PIC model (OSIRIS) shows excellent agreement for problems of interest. QuickPIC simulations of the SLAC PWFA experiment have revealed important physics and achieved good agreement with experiment measurement. Theoretical analysis of the stability of acceleration can now be guided and verified by QuickPIC simulations.

1Work supported by DOE

Tuesday, March 6, 2007 11:15AM - 2:15PM — Session J19 DCP DCOMP: Frontiers in Electronic Structure Theory I Colorado Convention Center 104

11:15AM J19.00001 Post-Hartree-Fock Correlation Models , AXEL BECKE, Dalhousie University — We have developed post-Hartree-Fock correlation models for all of dynamical, nondynamical, and dispersion correlations, based on real-space modelling of the correlation hole. Many of the outstanding problems in the density-functional theory of atomic, molecular, and condensed matter systems arise from local exchange approximations. Our post-Hartree-Fock approach circumvents these. The latest developments will be reported,

11:51AM J19.00002 Resolutions of the Coulomb Operator , PETER GILL, Research School of Chemistry, Australian National University — The “Resolution of the Identity Operator” Iˆ ≡ |χnihχn| (1) is a mathematical device that can be used to decouple the bra and ket in an overlap matrix element

hf|gi = hf|χnihχn|gi (2) through the introduction of an infinite complete expansion basis {χn}. In practical implementations, where the basis set is finite and incomplete, (2) yields systematic approximations to difficult overlap integrals and is widely used in quantum physics and chemistry. We will present an analogous “Resolution of the Coulomb Operator” −1 r12 ≡ |φnihφn| (3) which allows one to expand Coulomb matrix elements −1 hf|r12 |gi = hf|φnihφn|gi (4) and we will discuss the potential utility of (4) in the efficient treatment of the matrix elements that arise in quantum chemistry and elsewhere.

12:27PM J19.00003 Spin Polarization Resolved Energetics of a Quasi One Dimensional Elec- tron Gas , LUKE SHULENBURGER, MICHELE CASULA, RICHARD M. MARTIN, University of Illinois at Urbana-Champaign, GAETANO SENATORE, Dipartimento di Fisica Teorica dell Universita di Trieste, and INFM-CNR Democritos — This work extends that of Casula et. al.1 by using Quantum Monte Carlo to calculate the exact energy of a quasi one dimensional electron gas at nonzero polarizations. We present a parameterization of the correlation energy suitable for LSDA density functional calculations2. The energy of the momentum resolved spin and charge excitations is also calculated via the intermediate 3 scattering function . At low densities, correlation opens a gap for charge excitations near 2kf for each spin species. The modes with periodicity close to the mean interparticle spacing are softened due to the formation of a quasi Wigner crystal. These eﬀects disappear as the density increases and correlation becomes less important. The calculated excitation spectrum agrees with the long wavelength behavior predicted by Luttinger liquid theory.

[1] M. Casula, S. Sorella and G. Senatore, cond-mat/0607130 (2006)

[2] Abedinpour, Polini, Xianlong and Tosi, private communication.

[3] S. Yamamoto, Physical Review Letters, 75, 3349 (1995)

12:39PM J19.00004 Electronic Counting Rules for the Stability of Metal-Silicon Clusters1 , JOSE ULISES REVELES, SHIV N. KHANNA, Department of Physics, Virginia Commonwealth University, Richmond, VA. 23284-2000, USA — Theoretical investigations of the ground state geometries, electronic structure, spin magnetic moment and the stability of the metal encapsulated neutral, cationic, and − + anionic MSi16 ( M= Sc, Ti, V) clusters have been carried out within a gradient corrected density functional formalism. ScSi16, TiSi16, and VSi16 are found to be particularly stable in agreement with recent experiments. It is shown that the enhanced stability can be reconciled within a model where each Si atom coordinated to the metal contributes one electron to the valence pool. We propose the use of the bond critical points (BCP) from the topological analysis of the electronic density, in order to identify the Si sites that are bonded to the metal atom. Clusters where the total number of valence electrons obtained by summing one electron from each Si site coordinated to metal atom and the valence electrons of the metal attain 20 are found to be particularly stable. Combined with the earlier reported stability at 18 electrons, it is proposed that such valence pools might be looked upon as a nearly free electron gas inside a silicon cage.

1We gratefully acknowledge ﬁnancial support from Department of Energy (DE-FG02-02ER46009). 12:51PM J19.00005 Compact Representations of Kohn-Sham Invariant Subspaces , FRANCOIS GYGI, University of California Davis, Davis CA 95616 — We present an algorithm for the computation of reduced numerical representations of the solutions of the Kohn-Sham equations. The method allows for a priori control of the error caused by the reduction process. When applied to Kohn-Sham wavefunctions expanded on a plane-wave basis, this approach leads to a substantial reduction of the size of the datasets used to restart ﬁrst-principles simulations, with controlled loss of accuracy. Examples of applications to jellium, liquid water and carbon nanotubes will be presented. A comparison with representations in terms of maximally localized Wannier functions will also be discussed.

1:03PM J19.00006 Density Functional Theory in Transition Metal Chemistry: A Self- Consistent Hubbard U approach , HEATHER KULIK, Massachusetts Institute of Technology, MATTEO COCOCCIONI, University of Minnesota, NICOLA MARZARI, Massachusetts Institute of Technology — Transition metals ions are reactive centers for a broad variety of biological and inorganic chemical reactions. Despite this central importance, density functional theory calculations based on local density or generalized gradient approximations (GGA) often fail qualitatively and quantitatively to describe multiplet splittings, relaxed structures, and reaction barriers for these systems. We have recently proposed1 augmenting the GGA functional with a Hubbard U which is obtained from a self-consistent linear response procedure. This fully ab initio GGA+U approach provides excellent agreement with accurate, correlated-electron quantum chemistry calculations for paradigmatic cases that include the ground state of the iron dimer and addition-elimination reactions on bare FeO+. We also show how a GGA+U approach may be applied to large-scale biological systems by preserving the favorable scaling of traditional density functional approaches with improved accuracy. 1) H. J. Kulik, M. Cococcioni, D. Scherlis and N. Marzari, PRL (2006).

1:15PM J19.00007 Linear Scaling First-Principles DFT Calculations with Grid-based Adaptive Orbitals1 , JEAN-LUC FATTEBERT, Lawrence Livermore National Laboratory — As an alternative to the Plane Waves approach for accurate and unbiased Density Functional Theory (DFT) simulations, we have developed a real-space approach which completely avoids use of Fourier transforms. An effective O(N) complexity is achieved by representing the electronic structure as a set of localized nonorthogonal orbitals. The efficiency of the approach has been demonstrated recently for molecular dynamics simulations in the microcanonical ensemble [J.-L. Fattebert and F. Gygi, Phys. Rev. B 73, 115124 (2006)]. Adapting the position of the localization regions on the fly is a key feature to enable accurate MD simulations. In this talk, we will report recent developments in adapting the size of localization regions to improve efficiency and address very general electronic structure problems.

1 This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

1:27PM J19.00008 How localized is “local?” Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory , VILE HAVU, VOLKER BLUM, MATTHIAS SCHEFFLER, Fritz-Haber Institut der MPG — Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO’s can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ∼tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc ≤ 3A˚ have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. 1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

1:39PM J19.00009 Bonding in elemental boron: a view from electronic structure calculations using maximally localized Wannier functions , TADASHI OGITSU, Lawrence Livermore National Laboratory, FRANCOIS GYGI, University of California, Davis, JOHN REED, ERIC SCHWEGLER, Lawrence Livermore National Laboratory, GIULIA GALLI, University of California, Davis — Boron exhibits the most complex structure of all elemental solids, with more than 300 atoms per unit cell arranged in interconnecting icosahedra, and some crystallographic positions occupied with a probability of less than one. The precise determination of the ground state geometry of boron—the so-called β-boron structure–has been elusive and its electronic and bonding properties have been difficult to rationalize. Using lattice model Monte Carlo optimization techniques and ab-initio simulations, we have shown that a defective, quasi-ordered β solid is the most stable structure at zero as well as finite T. In the absence of partially occupied sites (POS), the perfect β-boron crystal is unstable; the presence of POS lower its internal energy below that of an ordered α-phase, not mere an entropic effect. We present a picture of the intricate and unique bonding in boron based on maximally localized Wannier (MLWF) functions, which indicates that the presence of POS provides a subtle, yet essential spatial balance between electron deficient and fully saturated bonds. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/ LLNL under contract no. W-7405-Eng-48.

1:51PM J19.00010 Structural distortions in AlF3 derived using density functional methods , L. L. BOYER, M. J. MEHL, DAN FINKENSTADT, Center for Computational Materials Science, Naval Research Laboratory — The crystal structure of AlF3 at high temperatures has a simple cubic lattice. Below ∼ 730K the structure transforms to a rhombohedral (α-phase) structure with R3c symmetry, due to − an unstable R5 phonon. Density-functional based methods, from the least accurate rigid-ion model to highly-accurate all-electron Kohn-Sham models, yield − the triply degenerate R5 phonon that becomes unstable with decreasing volume at some critical volume Vc. Signiﬁcant variations for Vc and the equilibrium volume V0 among the models lead to large uncertainties for the energy diﬀerences between the cubic and rhombohedral structures, indicating that present density functional models are not reliable for accurate quantitative results in this case.

2:03PM J19.00011 Quantum Monte Carlo studies of transition metal atoms and molecules , RYO MAEZONO, Computational Materials Science Center, National Institute for Materials Science, Japan, LUCAS K. WAGNER, MICHAL BAJDICH, JINDRICH KOLORENC, LUBOS MITAS, North Carolina State University — We study electron correlation in selected transition metal atoms and molecules from the 3d series by variational and fixed-node diffusion Monte Carlo methods. We test several types of orbitals such as RHF, UHF, B3LYP and atomic natural orbitals in building the Slater determinants. We explore also several types of wave functions based on single determinant, GVB, limited CI expansions with both unoptimized and reoptimized weights. The aim of this study is to estimate the accuracy of various wave functions with regard to fixed-node biases and to provide benchmarks for high accuracy calculations with these types of atoms.

Tuesday, March 6, 2007 11:15AM - 2:03PM — Session J26 DCP: Focus Session: Non-adiabatic Molecular Dynamics and Control at Conical Intersections II Colorado Convention Center 205 11:15AM J26.00001 Aspects of conical intersections: Dynamics, bound states embedded in the continuum and short-lived electronic states , LORENZ CEDERBAUM, University of Heidelberg, Theoretical Chemistry — Conical intersections are omnipresent in polyatomic molecules and their presence gives rise to the most severe breakdown of the Born-Oppenheimer approximation. Several general aspects of conical intersections and of the dynamics through them will be addressed. Particular attention will be paid to the question what happens to the potential energy surfaces if the electronic states are metastable. In addition, it is shown that nuclear dynamics on coupled potential surface can lead to bound states embedded in the continuum. Non-Born-Oppenheimer effects are responsible for the binding of these states. Once the Born-Oppenheimer approximation is introduced, these states at best become resonances which decay via potential tunnelling. The tunnelling is completely suppressed by the coupling between the electronic states. Another important issue which will be touched upon is dynamics in the presence of conical intersections in macrosystems. Here, the number of modes is extremely large and, nevertheless, their impact close to the intersections cannot be neglected. It is shown that effective modes can be derived which reproduce exactly the short-time dynamics of the whole macrosystem at low cost. Numerical examples are given. References: H. Köppel, W. Domcke and L.S. Cederbaum, Adv.Chem.Phys. 57, 59 (1984) G.A. Worth and L.S. Cederbaum, Annu-Rev.Phys.Chem. 55, 127 (2004) L.S. Cederbaum, R.S. Friedman, V.M Ryaboy and N. Moiseyev, Phys.Rev.Lett. 90, 013001 (2003) S. Feuerbacher, T. Sommerfeld and L.S. Cederbaum, J.Chem.Phys. 120, 3201 (2004) L.S. Cederbaum, E. Gindensperger and I. Burghardt, Phys.Rev.Lett. 94, 113003 (2005)

11:51AM J26.00002 , ANNA KRYLOV, University of Southern California — No abstract available.

12:27PM J26.00003 Semiclassical Description of Non-Adiabatic Dynamics - Part I , NANDINI ANANTH, CHARULATHA VENKATARAMAN, WILLIAM MILLER, University of California Berkeley — Molecular dynamics simulations of systems that involve non-adiabatic transitions has always been challenging as this involves following the coupling between quantum states of the system. The behavior of such systems can best be modeled by making sure that the method used can not only provide a way to incorporate quantum effects, but can also ensures the equivalent treatment of the electronic and nuclear degrees of freedom. We use the classical electron model (Meyer-Miller) to do the latter ; while time evolution using the semiclassical initial value representation (SC-IVR) ensures the inclusion of quantum effects. We are currently studying the viability of this approach with a few test systems. In order to further study the effectiveness of this approach, we are working on several variations of the SC-IVR. For instance, the Forward Backward IVR (FB-IVR) is a variation of the SC-IVR that presents a simplified formulation for correlation functions with a double propagator. The Linearized IVR (LSC-IVR) is yet another variation which results in a more ‘classical’ formulation of the problem. Our observation and results obtained will be presented.

12:39PM J26.00004 Semiclassical description of non-adiabatic dynamics - Part II , CHARULATHA VENKATARAMAN, NANDINI ANANTH, WILLIAM MILLER, Dept. of Chemistry, U. C. Berkeley — Semiclassical IVR is a classical trajectory based method that is used to incorporate quantum eﬀects into classical MD simulations. This, in combination with the classical electron analog model of Meyer and Miller allows us to describe the dynamics on coupled electronic states. The classical electron analog model treats the relevant electronic and nuclear degrees of freedom of a system on the same footing. This achieves dynamical consistency which mixed quantum-classical approaches tend to lack. In joint work with Ananth and Miller, we are studying diﬀerent IVR approaches to describe non-adiabatic dynamics. One such formulation is “The Exact Forward-Backward IVR”; this has no other approximation other than the semiclassical description of quantum dynamics. Applications of this approach to various model problems will be presented.

12:51PM J26.00005 Non-adiabatic effects in photoelectron spectroscopy , MICHAEL SCHUURMAN, DAVID YARKONY, Johns Hopkins University — Recent developments in the construction of approximately diabatic second-order Hamiltonians in the vicinity of conical intersections have been employed to study photoelectron spectra of molecules in which nonadiabatic effects are preeminent. Our current approach explicitly includes all non-adiabatic coupling terms through second order, while requiring ab initio data at only (N[int] + 3) or (N[int] + 15) points for two and three-state intersections, respectively, where N[int] is the number of internal coordinates. This scaling allows very accurate wave functions to be used. Since the Hamiltonian is determined at a point of conical intersection, the method is “self-policing” in that the ability of the resultant surfaces to reproduce the vicinity of seams of intersection, as well as energy minima and the Franck-Condon region, is easily verified. We will report photoelectron spectra determined from these diabatic representations employing a harmonic oscillator basis and a Lanczos solver algorithm to diagonalize the resultant vibronic Hamiltonian matrices. The results of some initial applications will be discussed, with emphasis on the previously studied five membered heterogeneous ring systems, pyrazolyl (C3H3N2) and pyrrolyl (C4H4N) doublet radicals. These systems are of particular interest since they display low-lying conical intersections adjacent to both the neutral ground state geometries and the Franck-Condon region.

1:03PM J26.00006 Fast and accurate self-interaction-free methods for calculating electronic excitations , MARTIN HEAD-GORDON, University of California, Berkeley — Time-dependent density functional theory methods achieve both success and disaster in describing electronic excitations in molecules. Most disasters, such as catastrophic failures for charge-transfer excitations, arise due to self-interaction errors. In this talk, I discuss recent progress on the development of self-interaction free methods for calculating electronic excitations. These methods are based on low-order many-body theory, using auxiliary basis expansions to obtain high computational efficiency. To obtain satisfactory accuracy from non-self-consistent treatment of electron correlations, the use of one or two empirical parameters is explored to scale same-spin and opposite-spin correlations. Using opposite-spin terms only yields a reliable and efficient method which is applicable to molecules in the 100 atom regime, with asymptotically fourth order scaling of computation with molecular size. While calibrated for good performance in the Franck-Condon region, the prospects for extension to conical intersections will be briefly mentioned.

1:15PM J26.00007 Using quantum dynamics simulations to understand motion around a conical intersection , GRAHAM WORTH, University of Birmingham, U.K. — Quantum dynamics simulations provide a key support in understanding laser spectroscopy measurements. To do this, a model must first be able to reproduce, or be associated with, an observation. The model can then be analysed to provide a picture at the molecular level. Unfortunately the wavepacket propagation methods used in many quantum dynamics calculations are unable to treat more than a few degrees of freedom: a major bottleneck in photochemical systems where the dynamics is dominated by internal conversion through a conical intersection. The multi-configuration time-dependent Hartree (MCTDH) method is one approach that has been very successful in accurately treating non-adiabatic polyatomic systems. Combined with the vibronic coupling model Hamiltonian we have been able to study in detail the dynamics of a number of molecules as they pass through a conical intersection. Recent work, to be covered in this talk, focuses on the complex photochemistry of benzene, showing how a time-resolved photo-electron spectrum can be calculated and interpreted in terms of the underlying molecular dynamics. 1:27PM J26.00008 Direct dynamics using variational Gaussian wavepackets. Application to the intelligent control of benzene photochemistry1 , BENJAMIN LASORNE, MICHAEL J. BEARPARK, MICHAEL A. ROBB, Imperial College London, GRAHAM A. WORTH, University of Birmingham — The direct dynamics variational multi-configuration Gaussian wavepacket (DD- vMCG) method is based on the multi-configuration time-dependent Hartree (MCTDH) algorithm. It uses a time-dependent basis set of parameterised Gaussian functions, which are coupled so as to variationally provide the best possible representation of the wavepacket. This approach is designed to treat quantum effects in large molecules with on-the-fly calculation of the potential energy surface performed by an interfaced quantum chemistry program. Here, we apply this method to the study of the non-adiabatic photochemistry of benzene. Our aim is to rationalise how the way the wavepacket crosses the S1/S0 seam may modify the branching ratio Dewar benzene : benzvalene and enhance their production rather than non-radiative decay back to benzene. This study is intended to identify realistic non-radiative decay pathways that lead to alternative photochemical reactivity and to find corresponding targets that can be reached by optimal control experiments.

1Financial support by EPSRC is gratefully acknowledged (Grant No: GR/T20311/01).

1:39PM J26.00009 ABSTRACT WITHDRAWN — 1:51PM J26.00010 Towards Modeling Coherent Control in Ab Initio Multiple Spawning Meth- ods , TODD MARTINEZ, University of Illinois — Ab initio multiple spawning (AIMS) dynamics has been developed as a method to solve the nuclear and electronic Schr¨odingerequations simultaneously. In this talk, we present new extensions to the AIMS method which allow modeling light absorption with shaped laser pulses for the purposes of achieving coherent control. The new methods are tested on a variety of low-dimensional problems by comparison to numerically exact wavepacket dynamics.

Tuesday, March 6, 2007 11:15AM - 2:03PM — Session J35 DBP DCP DCOMP: Protein Water Interactions Colorado Convention Center 405 11:15AM J35.00001 Oscillatory Growth of Ice Crystals Observed in a Solution of Antifreeze Glycoprotein , YOSHINORI FURUKAWA, YOSHIHIRO NISHIMURA, SALVADOR ZEPEDA, HIROYUKI NAKAYA, ILTS, Hokkaido University, ET- SURO YOKOYAMA, Gakushuin University — One-directional growth experiments of ice crystals in an aqueous solution of antifreeze glycoprotein (AFGP) were carried out using a growth cell made of thin glass capillaries. When the interface tips of ice crystals were constructed by prismatic planes, the interface position changed periodically with time. These phenomena were not observed for the growth of basal planes in the AFGP solution or for the growth of ice crystals in pure water. We ﬁrst observed the oscillatory growth of ice crystals in the AFGP solution. Fluorescent labeled AFGP molecules were also used to observe the diﬀusion, incorporation, and segregation of the solute at the interface, in the solid and in solution. The periodic incorporation of AFGP molecules were clearly observed in conjunction with the growth rate changes.

11:27AM J35.00002 A model of self-oscillatory growth of ice crystals in antifreeze glycoprotein solutions , ETSURO YOKOYAMA, Gakushuin University, YOSHINORI FURUKAWA, ILTS, Hokkaido University — We discuss that an oscillatory crystal growth is observed not only in the growth of an ice crystal from AFGP solution but also in the motion of steps on the surface of ice crystals in the presence of AFGP molecules. Our model of the oscillatory growth of crystals accounts for two elementary processes relevant to the growth: 1) an interface kinetic processes for transformation into a crystalline phase at the interface, and 2) a diﬀusion process for the transport of latent heat liberated at the growing interface. In this talk, we propose the hypothesis of a hysteresis behavior of growth rate to explain the formation of periodic structures of a growing crystal without a change of external conditions. The self-oscillatory growth in the presence of AFGP adsorbed molecules can occur because of the coupling of interface kinetics to the transport of latent heat under constant growth conditions.

11:39AM J35.00003 Antifreeze Protein (AFP) and Antifreeze Glycoprotein (AFGP) Kinetics at the Ice/Solution Interface , SALVADOR ZEPEDA, HIROYUKI NAKAYA, YUKIHIRO UDA, Hokkaido University, ETSURO YOKOYAMA, Gakushuin University, YOSHINORI FURUKAWA, Hokkaido University — AFPs and AFGPs found in some fish, plants and insects are a necessary tool for surviving sub-freezing environments. They occur in a wide range of compositions and structure, but to some extent they all accomplish the same functions: they suppress the freezing temperature, inhibit recrystallization, and modify ice crystal growth. Here, we observe the exact location of AFGPs, Type I and Type III AFPs by 1-directional growth experiments using fluorescence and phase contrast microscopy as well as free growth experiments using 3-d confocal microscopy. In all cases, the proteins clearly adsorb at the interface. By comparing the fluorescent image with the corresponding phase contrast image we find that AFGPs incorporate only into the solid in veins and not into the ice lattice structure. Type I AFPs show similar behavior as AFGPs, but type III AFPs adsorb to specific planes within the ice lattice. We have also calculated the diffusion constants and the surface adsorption concentration from both types of experiments. Our results indicated that the different types of AFPs or AFGPs accomplish essentially the same function in slightly different ways and that it is not necessary for the protein adsorption to the ice interface to be as rigid as once thought.

11:51AM J35.00004 Protein slaving to the solvent and the relation to hydrodynamics , P. W. FENIMORE, GUO CHEN, B. H. MCMAHON, Los Alamos National Lab — Protein motions can be categorized by the nature of their coupling to solvent dynamics. Some protein motions, including the final ligand binding process in myoglobin (Mb), are largely independent of solvent fluctuations. Others, such as entry and exit of ligands from Mb require Debye-like α fluctuations in the solvent to proceed. A third class of motions, including the r. m. s. displacments of atoms are controlled by solvent β fluctuations. We show that a slaving picture of protein dynamics, kprotein = kα/n, where n is a nearly T-independent factor, known to be as large as 105, is consistent with an essentially hydrodynamic picture of α-slaved protein motions. Consistency with hydrodynamics (i. e. the Stokes-Einstein equation) can be demonstrated by considering changes to protein stability caused by ordinary experimental protocols for measuring viscosity- and T-dependent protein dynamics data. The decomposition of protein dynamics into several discrete classes suggests modelling techniques to simplify the simulation of protein dynamics.

12:03PM J35.00005 Dynamics of Lysozyme in a Glycerol-Water system , PAVAN GHATTY, GUSTAVO CARRI, The University of Akron — Bio-preservation of proteins is of great commercial and academic interest. A variety of sugars have been found to be effective in preserving the structure of proteins. This has been attributed and in some cases proved to their ability to form strong hydrogen bonds with proteins thus restricting their motion. The work presented here explores the hypothesis that glycerol, a tri-alcohol curbs the motion of protein. We have carried out a 10ns Molecular Dynamics simulation to study the phenomenon. The structure of Lysozyme (PDB code 193L) has been studied in three solutions of 10, 20 and 30 % by weight of glycerol in water. Glycerol molecules in all three solutions have shown a tendency to agglomerate around the protein. Strong hydrogen bonding has also been observed between glycerol molecules and the protein. With increasing time, the g(r) of glycerol molecules around proteins shows two peaks with increasing prominence suggesting the movement of glycerol cluster to positions closer to the protein surface. 12:15PM J35.00006 An extended dynamical solvation shell around proteins.1 , SEUNG JOONG KIM, U. of Illinois (UIUC), SIMON EBBINGHAUS, MATTHIAS HEYDEN, Ruhr-Uni. Bochum, Germany, XIN YU, U. of Nevada, UDO HEUGEN, Ruhr-Uni. Bochum, Germany, MARTIN GRUEBELE, U. of Illinois (UIUC), DAVID LEITNER, U. of Nevada, MARTINA HAVENITH, Ruhr-Uni. Bochum, Germany — Water solvating biomolecules in organisms has different properties from the bulk. Such solvation shells can be characterized by a variety of structural and dynamical measures. The fundamental question of biomolecule hydration is: how far out into the solvent does the influence of the biomolecule reach? We use terahertz absorption spectroscopy of the five helix bundle protein Lambda Repressor 6-85, coupled with molecular dynamics simulations, to show that correlated water motion at a sub-psec time scale persists to distances of at least 20 angstrom. We show this by determining that bulk water, water molecules mainly interacting with a single protein molecule, and water molecules interacting with more than one protein molecule have different absorption signatures in the THz frequency range, leading to an experimentally detectable non-monotonic dependence of the absorption coefficient on protein concentration. This trend is supported in the calculations, which further show that long-distance hydration is a dynamical effect correlating many water molecules, not one that noticeably perturbs the structural distribution of one or a few water molecules from the bulk value.

1This work was supported by a grant from the Human Frontiers Science

12:27PM J35.00007 Structural and dynamical properties of water in hydrophobic confinement, as probed by ab-initio molecular dynamics. , GIANCARLO CICERO, Politecnico of Torino, Torino, Italy, JEFFREY C. GROSSMAN, Center of Integrated Nanomechanical Systems, University of California, Berkeley, ERIC SCHWEGLER, LLNL, Livermore, CA, GALLI GIULIA, University of California, Davis, CA — Unraveling the microscopic properties of water confined in small channels will help understand fluid flow and transport at the nanoscale, and will shed light on the solvation of biomolecules. To date most of the properties of confined water are poorly understood and, in many cases, controversial. We present a first principles computational study of prototype systems —water confined between graphene sheets and inside carbon nanotubes– which have received widespread experimental attention and for which, however, such basic questions as diffusion at the nanoscale, and characteristics of the hydrogen bonded network remain unanswered. Our simulations show that the liquid density substantially increases at the water/surface interface, and that water diffusion is faster in highly confined structures, due to a decrease of the dipole moment in interfacial water molecules and correspondingly a decrease in H-bond network strength. We propose that many effects attributed to confinement in the past are actually interfacial effects due to subtle electronic structure rearrangements, and that these are amenable to vibrational and x-ray absorption spectroscopy investigations.

12:39PM J35.00008 Basal Plane Affinity of an Insect Antifreeze Protein , N. PERTAYA, Ohio University, S.Y. GAUTHIER, P.L. DAVIES, Queen’s University, I. BRASLAVSKY, Ohio University — sbwAFP is a powerful antifreeze protein (AFP) with high thermal hysteresis activity that protects spruce budworm (sbw) from freezing during harsh winters in the spruce and fir forests of USA and Canada. Different types of antifreeze proteins have been found in many other species and have potential applications in cryomedicine and cryopreservation. When an ice crystal is cooled in the presence of AFP below the non-equilibrium freezing point the crystal will suddenly and rapidly grow in specific directions. Hyperactive antifreezes like sbwAFP expand perpendicular to the c-axis (in the plane of the a-axes), whereas moderately active AFPs, like type III from fish, grow in the direction parallel to the c-axis. It has been proposed that the basis for hyperactivity of certain AFPs is that they bind and accumulate on the basal plane to inhibit c-axial growth. By putting fluorescent tags on these two types of AFPs we have been able to directly visualize the binding of different types of AFPs to ice surfaces. We do indeed find that the insect AFP accumulates on the basal plane of an ice crystal while type III AFP does not. Supported by CIHR and BNTI.

12:51PM J35.00009 Study of Hydrogen Bond and Dipolar Interaction in Water-like Fluid with Toy Model , Y.S. JHO, KAIST/UCSB, C.S. CHANG, KAIST/NYU, P.A. PINCUS, UCSB/KAIST, M.W. KIM, KAIST/UCSB — Hydrogen bond and dipolar interaction, which originated from the high polarizability of asymmetric water-like molecules, give rise to anomalous properties. Anionic interface of − + water-like fluid is understandable as a result of hydrogen bond and excluded interactions of OH and H3O . Range of dipolar interaction reaches over several water-like molecule size. And, the interaction between dipole and ion affects on about 20 times longer than the size of water-like molecule. Therefore, the interaction between charged particles within this range shows different behavior compared to interaction in a uniform dielectric medium. Toy model gives physical insights and helps comprehensions to complex phenomena. In this study we give the numerical simulation to investigate these phenomena.

1:03PM J35.00010 Density and Structure of Water under Confinement as Determined using Monte Carlo Simulations , SUMIT SHARMA, SANAT K. KUMAR, Columbia University — The structure and local density of water is thought to play an important role in phenomena such as protein adsorption. These properties of water under confinement between surfaces can be significantly different from those of bulk water. A change in the water’s structure, which is coupled to a change in the local density of the confined water in equilibrium with the bulk water, can create an attractive or repulsive force between the planar surfaces. This force itself can dominate the mechanism of adsorption when adsorbing molecules are within close proximity from adsorbent. In order to probe the effects of confinement further, Grand Canonical ensemble Monte Carlo (GCMC) simulations of Single Point Charge Enhanced (SPC/E) water confined between two planar surfaces of differing hydrophobicity, ranging from hydrophobic to hydrophilic, have been performed. The dependence of the water’s structure and local density on the hydrophobicity and distance between the two planar surfaces has been determined. Further, the effect of surface curvature will also be examined.

1:15PM J35.00011 The protein hydration transition , YUNFEN HE, JOSEPH KNAB, JING-YIN CHEN, ANDREA MARKELZ, Physics Department, State University of New York at Buffalo — We previously reported the hydration transition in the THz dielectric response for native state hen egg white lysozyme (HEWL). As hydration increases the response slowly increases until at 0.25h (gm water/gm protein) the absorbance and index sharply increase. The hydration level coincides with the filling of the first solvation shell. The THz dielectric response arises from relaxational and resonant vibrational response, where the vibrational response corresponds to delocalized structural motions sensitive to the conformation and the environment. We examine the contribution of low frequency vibrational modes to the hydration transition by calculating the normal mode density as a function of solvent content using CHARMM. We find that the density of low frequency modes increases with the increasing solvent content, but this increase does not show the transition seen experimentally. We discuss that another source for the hydration transition in the THz response may be the hydration dependence of the activation energy for glass-like beta fluctuations that contribute to the relaxational response.

1:27PM J35.00012 Inverted Solubility of the Pro 23 to Val Mutant of Human γD Crystallin– Altered Phase Diagram from a Single Amino Acid Substitution and the Effect of PEG , J.J. MCMANUS, A. LOMAKIN, M. BASAN, O. OGUN, MIT, Department of Physics, CMSE and Materials Processing Centre, A. PANDE, J. PANDE, Dept. of Chemistry, SUNY, Albany., G.B. BENEDEK, MIT, Department of Physics, CMSE and Materials Processing Centre — Many genetic cataracts are the result of single point mutations in the amino acid sequence of lens crystallin proteins. The P23T mutation in human γD-crystallin (HGD) is associated with several different cataract phenotypes. The solubility of the protein shows an inverse temperature dependence. This is in contrast with the native protein. The replacement of Thr23 with a Ser or a Val residue shifts the location of the inverted solubility line to higher concentrations [1]. We describe the phase diagram of the P23V mutant of HGD, which exhibits aggregation, crystallization and liquid-liquid phase separation (LLPS). We have used QLS to probe the interactions of the protein in the soluble region of the phase diagram. We have developed a model to describe the observed retrograde solubility of the protein. Using PEG we introduce a so-called “depletion interaction” to further investigate the origin of the retrograde solubility. [1] A. Pande, O. Anunziata, N. Asherie, O. Ogun, G.B. Benedek, J. Pande, Biochemistry 44, 2491-2500 (2005). 1:39PM J35.00013 Free energy study of uranyl complexes across water-oil and water-oil+tri- butyl phosphate (TBP) interfaces1 , MANORI JAYASINGHE, THOMAS L. BECK, University of Cincinnati — Free energy profiles of heavy metal ion complexes, UO2 (NO3)2, UO2 (NO3)2TBP2, and TBP, across the water-hexane and water hexane+TBP (50%/50%) interfaces, were calculated from molecular dynamics simulations. These complexes and interfaces are relevant to recently developed heavy-ion separation techniques. The solute complex with TBP, UO2 (NO3)2TBP2, shows strong interfacial activity in contrast to the free energy barrier for UO2 (NO3)2 at the water-hexane interface. Increased TBP concentration in the oil phase reduces the interfacial activity and better solvates the ion complexes and their ligands. The solute complex with TBP oriented parallel to the water-hexane+TBP interface binds more strongly to the hexane+TBP phase than to the pure hexane phase. The (un-complexed) TBP orientational probability distribution shows the polar head buried in water, while the nonpolar tails are buried in the oil phase, and hence TBP exhibits interfacial activity. The calculated density profiles at the interface show that TBP acts not only as a carrier for uranyl transport across the interface, but also as an “interface modifier”. Our simulation results are in agreement with the recent study of uranyl transport across chemically modified membranes with TBP based metal ion carriers.

1National Science Foundation Membrane Applied Science & Technology (MAST) Center grant.

1:51PM J35.00014 Differential Dielectric Spectroscopy of Protein Solutions: Observation of Protein Interactions , BRIAN MAZZEO, ANDREW FLEWITT, Cambridge University — Observation of a protein-protein interaction is illustrated by dielectric measurements on rabbit IgG (190 µg/ml) and Protein A (19 µg/ml) by a homemade dielectric cell and HP 4194A impedance analyzer. Frequency shifts of ratios 2.0 and 1.6 with respect to the individual relaxation characteristics of IgG and Protein A were obtained by dielectric spectroscopy, which has historically been used to determine the properties of solvated biomolecules to measure the hydrodynamic and electrical properties of individual proteins and of solution. Dielectric relaxation theory predicts changes in the dielectric relaxation characteristics of proteins due to protein interactions resulting in larger hydrodynamic volumes. Experimentally, bovine serum albumin, protein A, and rabbit IgG were added sequentially to phosphate buffer and the incremental dielectric changes were measured. The differential dielectric response, as a biophysical technique, gives insight into the interaction of the added protein with biomolecules in solution and can indicate the presence of protein-protein interactions.

Tuesday, March 6, 2007 2:30PM - 5:30PM — Session L18 DCP: Metal Clusters Colorado Convention Center 103

2:30PM L18.00001 ABSTRACT WITHDRAWN —

2:42PM L18.00002 ABSTRACT WITHDRAWN — 2:54PM L18.00003 Size-Selected Cluster Based Catalysts: Physical and Chemical Properties Studied by GISAXS, .Mass Spectrometry and UV-VIS Spectroscopy , STEFAN VAJDA, GREGORY BALLENTINE, ALEXANDRE BOUHELIER, Argonne National Laboratory, JOSEPH CALO, Brown University, JEFFREY ELAM, BYEONGDU LEE, CHIEH-TSUNG LO, CHRISTOPHER MARSHALL, STEPHANIE MUCHERIE, MICHAEL PELLIN, SOENKE SEIFERT, GARY WIEDERRECHT, RANDALL WINANS, Argonne National Laboratory — Properties of highly stable cluster-based model nanocatalysts are studied. Examples on size-selected clusters Aun (n=7-10), Agn (n=15-19), Ptn (n=8-10) and 1-3 nm particles supported on thin oxide ﬁlm coated ﬂat and mesoporous supports address cluster stability under realistic reaction conditions, selective stabilization of particles and their reactivity. In situ GISAXS allows for correlation of catalyst performance with its size and shape of the catalyst. Pt-cluster based catalyst supported on mesoporous membranes were tested in a commercial tester in oxidative dehydrogenation of propane and exhibited excellent propane conversion and superb selectivity towards propene production at moderate temperatures, 400-550 oC with and without SnO promoter. Au and Ag catalysts were tested in ethylene and propylene oxidation, showing an onset of the reactivity between 160-200 oC.

3:06PM L18.00004 Computational studies of small neutral vanadium oxide clusters and their reactions with sulfur dioxide , ELENA JAKUBIKOVA, SHENG-GUI HE, YAN XIE, Colorado State University, Department of Chemistry, YOSHIYUKI MATSUDA, Tohoku University, Department of Chemistry, ELLIOT BERNSTEIN, Colorado Stete University, Department of Chemistry — Vanadium oxide is a catalytic system that plays an important role in the conversion of SO2 to SO3. Density functional theory at the BPW91/LANL2DZ level is employed to obtain structures of VOy (y=1,. . . ,5), V2Oy (y=2,. . . ,7), V3Oy (y=4,. . . ,9), V4Oy (y=7,. . . ,12) and their complexes with SO2. BPW91/LANL2DZ is insufficient to describe properly relative V-O and S-O bond strengths of vanadium and sulfur oxides. Calibration of theoretical results with experimental data is necessary to compute enthalpies of reactions between VxOy and SO2. Theoretical results indicate SO2 to SO conversion occurs for oxygen-deficient clusters and SO2 to SO3 conversion occurs for oxygen-rich clusters. Subsequent experimental studies confirm the presence of SO in the molecular beam as well as the presence of VxOy complexes with SO2. Some possible mechanisms for SO3 formation and catalyst regeneration for solids are also suggested.

3:18PM L18.00005 Unbiased studies on structural and electronic properties of gold clusters with up to 58 atoms , YI DONG, MICHAEL SPRINGBORG, INGOLF WARNKE, University of Saarland, Germany — Isolated neutral AuN clusters are studied using a parameterized density-functional tight-binding method combined with genetic algorithms for N from 2 up to 58. Various descriptors are used in analysing the results, including stability, shape, and similarity functions, as well as radial distances of the atoms and the orbital energies, all as functions of N. Based on a harmonic approximation, also the heat capacity of the Au clusters are studied as a function of temperature.

3:30PM L18.00006 Quantized Ferromagnetism in Free Cobalt and Iron Clusters , XIAOSHAN XU, SHUANGYE YIN, RAMIRO MORO, ANTHONY LIANG, JOHN BOWLAN, WALT A. DE HEER, Georgia Institute of Technology — The magnetic moments µN for cobalt clusters CoN (20≤ N ≤200) measured in a cryogenic molecular beam are found to be quantized both in the ground state: µN ∼2N B and in ∗ the metastable excited state: µN ∼ NµB in contrast with the bulk where it is fractional: µN=∞=1.7NµB . For N=30, the ionization potentials of the excited state is about 0.1 eV lower than of the ground state while this difference diminishes with increasing size, which implies that the two states become degenerate at large sizes. The evolution from localized moments in small clusters to itinerant moments in the bulk appears to be related to the closing of this energy gap which results in a fluctuating ground state. These effects can be understood in terms of the Falicov-Kimball model. Two states are also observed in iron ∗ ∗ clusters, with µN ∼3NµB for FeN , and µN ∼ NµB for FeN (20≤ N ≤150). 3:42PM L18.00007 On the Stability of Sodium-Tin Zintl Ions in Gas phase experiments , A. REBER, J.W. GARBUS, S.N. KHANNA, Virginia Commonwealth University, W.J. ZHENG, O.C. THOMAS, J.M. NILLES, K.H. BOWEN, Johns Hopkins − University — A synergistic effort combining negative ion photoelectron spectroscopy of NanSnm clusters along with the first principles electronic structure studies has been used to demonstrate that Zintl ions found in solutions also exist as stable species in free clusters. The theoretical investigations are carried out − − − within a gradient corrected density functional approach. Our studies on NanSn4 clusters where n=0-4 and NaSnm clusters where m=4-7 show that Na3Sn4 −4 is a very stable cluster marked by a distorted tetrahedral tin core and can be regarded as (Na+)4(Sn4) gas phase analogue of the Na:Sn tetrahedral Zintl − − phase. In addition, the NaSn5 cluster is shown to be the most abundant species in the mass spectrum in the NaSnm series and its stability can be reconciled 2− with Sn5 Zintl ions. The existence of stable Zintl ions in the gas phase can provide an alternate approach to look for possible Zintl phases.

3:54PM L18.00008 On the stability and vibrational properties of super-polyiodides , NAICHE JONES, J. ULISES REVELES, SHIV KHANNA, Virginia Commonwealth University — We had earlier shown that a new class of polyhalides can be formed by combining − the Al13 super-halogen with the conventional halogen, I. Experimental reactivity studies demonstrate that the new super-polyhalides, Al13Ix , exhibit pronounced stability for even numbers of I atoms. Theoretical investigations probing the geometry and the electronic structure reveal that the enhanced stability is associated − − with pairs of I atoms occupying the on-top sites around the Al13 core. We had also demonstrated another series, Al14Ix , that exhibits stability for odd numbers of I atoms. In this work we have examined the vibrational properties of the new super-polyiodides using gradient corrected density functionals. It is shown that the low frequency modes involve motion of the central Al and that the geometrical progressions with high iodine coverage can be understood in terms of these vibrations.

4:06PM L18.00009 New Assemblies Combining Super-halogens and Super-alkalis , SHIV KHANNA, ARTHUR REBER, Virginia Commonwealth University, A. WELFORD CASTLEMAN JR., Penn State University — An Al13 cluster has been shown to exhibit behaviors reminiscent of halogen atoms with an electron aﬃnity comparable to a Cl atom while molecular units like K3O, called superalkalis, are known to have low ionization potentials. We have carried out ﬁrst principles electronic structure calculations to examine the stability and the electronic properties of compound clusters formed by combining super halogens with superalkalis. An Al13K3O unit is shown to be a strongly bound ionic molecule that can be assembled into stable cluster superatom assemblies of composition (Al13K3O)n. It will be shown that the individual clusters maintain their identity during the growth. The nature of the super-assemblies and their electronic properties will be highlighted.

4:18PM L18.00010 Nano-Assemblies using Designer Clusters , A.C. REBER, M. QIAN, S.N. KHANNA, Virginia Commonwealth University, A.W. CASTLEMAN JR., A. SEN, K.M. DAVIS, S.J. PEPPERNICK, A. UGRINOV, M.D. MERRITT, Penn State University — It is shown that a new procedure that combines studies on clusters in gas phase, theoretical investigation of the stability patterns, and the directed assembly in solutions can enable synthesis of nano-assemblies where the building blocks are designer clusters identified in gas phase. As a demonstration of its viability, we first examine As7K3 as a potential building block through gas phase molecular beam experiments starting from a dispersed mixture of bulk arsenic and potassium. Combining the experimental results with first principles electronic structure calculations, we identify As7K3 species as a uniquely stable Zintl entity that could affect self-assembly. Through directed assembly, we report success in synthesizing and characterizing a lattice of analogous super-cluster assembled material crystallized from the liquid phase. Electronic structure calculations on the nanoassembled material indicate that it is a wide band gap semiconductor.

4:30PM L18.00011 Optical and magnetic excitations in small transition-metal clusters using TDDFT1 , MICAEL OLIVEIRA, FERNANDO NOGUEIRA, Center for Computational Physics, University of Coimbra, Portugal, ANGEL RUBIO, Facultad de Quimicas, Universidad del Pais Vasco, Spain — Magnetic properties of transition-metal clusters have been the subject of intensive study in the last decades both theoretical and experimentaly. In particular, the importance of noncollinear eﬀects and spin-orbit coupling in those systems has recently gained great interest. In this work we use time dependent density functional theory (TDDFT) to study optical and magnetic excitations of small transition-metal clusters. In particular, we investigate the role of non-collinear magnetism and spin-orbit coupling in such phenomena. We present some results concerning the linear response calculations and show how noncollinear eﬀects and spin-orbit coupling modify the optical and/or magnetic spectra (including the natural magnetic dichroism spectroscopy). We will discuss further line of research that we are conducting to understand the size dependence magnetic response of this clusters for potential technological applications. The calculations are done within a real-time real-space TDDFT framework using the Octopus code.

1Finantial support by the EC Network of Excellence NANOQUANTA (NMP4-CT-2004-500198) and by the portuguese FCT (contract #SFRH/BD/12712/2003) is gratefully acknowledged.

4:42PM L18.00012 Methanol Formation from Carbon Monoxide and Hydrogen on Neutral Nb8 Clusters in the Gas Phase , YAN XIE, SHENG-GUI HE, ELLIOT BERNSTEIN, Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872 — Reactions of neutral Vn, Nbn, and Tan metal clusters (n ≤ 11) with (CO + H2)/He mixed gases and CH3OH/He in a flow tube reactor (P ∼ 14 Torr) are studied by time of flight mass spectroscopy. Metal clusters are generated by 532 nm laser ablation and reactants and products 2 are ionized by low fluence (∼200 µJ/cm ) 193 nm excimer laser light. Nbn clusters exhibit strong size dependent reactivity in reactions both with CO + H2 and CH3OH compared with Vn and Tan clusters. A remarkably strong mass peak Nb8COH4 is observed in the reaction of Nbn clusters with the mixed gases CO + H2 at various concentration of H2. This suggests a stable, low energy CH3OH structure may form on an Nb8 cluster. Methanol formation is not found on other Nbn (n 6= 8), Vn, and Tan clusters. In reactions of CH3OH with metal clusters Mn(M= V, Nb, Ta, n = 3-11), molecularly adsorbed products (MnCH3OH) are only observed on Nb8 and Nb10, whereas dehydrogenated products (MnCO) are observed for all other clusters. This observation supports the suggestion that CH3OH can be formed on Nb8 in the reaction of Nbn with CO + H2. Reaction mechanisms are discussed based on the experimental results in this work and those in the literature. Theoretical calculations are carried out to confirm our experimental results and suggested reaction mechanisms.

4:54PM L18.00013 Potential for Strong Pairing and High Transition Temperatures in Metallic Nanoclusters , AMBER POST, LOUIS BLOOMFIELD, University of Virginia — Studies of atomic clusters containing tens or hundreds of atoms have gained much interest in recent decades because of their potential to bridge the gap between isolated atoms and bulk systems. Notable results include the observation of a shell structure1 similar to that found in electronic shells of single atoms. Theoretical calculations2 show that certain levels within this shell structure allow for strong Cooper pairing. These calculations also show that the particular shell levels, which are realistically attainable, have high density of states in the HOS and LUS levels and could show substantially higher values of the superconducting transition temperature TC than are observed in the bulk material. At temperatures near TC , the onset of strong pairing can be experimentally observed by an increase in the minimum excitation energy of the particular cluster. Our group will first look for this energy increase in Al clusters at around 90K, the predicted TC for Al clusters of interest. Here we present a progress report on Al and describe future work. 1 W. Knight, K. Clemenger, W. de Heer, W. Saunders, M. Chou, and M. Cohen, Phys. Rev. Lett. 52, 2141 (1984). 2V. Z.Kresin and Y. N. Ovchinnikov, Phys. Rev. B 74, 024514 (2006). 5:06PM L18.00014 Electron pairing in pure Niobium and Niobium alloy clusters , ANTHONY LIANG, XIAOSHAN XU, SHUANGYE YIN, JOHN BOWLAN, WALT DE HEER, Georgia Institute of Technologies — Electrons in pure niobium and in niobium alloy clusters are ferroelectric at low temperatures. The ferroelectric effect is enhanced for niobium clusters doped with non-magnetic metals and reduced when doped with magnetic atoms. The effect is enhanced (reduced) for clusters with an even (odd) total number of valence electrons. For specific alloy clusters the ferroelectric state persists up to room temperature. Ferroelectricity in these clusters and superconductivity in the corresponding bulk appear to be related, with similar transitions temperatures and similar responses to specific impurities. The spontaneous polarization of a ground state involving a Cooper pair explains the observations.

5:18PM L18.00015 ABSTRACT WITHDRAWN —

Tuesday, March 6, 2007 2:30PM - 5:18PM — Session L19 DCP DCOMP: Frontiers in Electronic Structure Theory II Colorado Convention Center 104

2:30PM L19.00001 Many-Body Perturbation Theory and Density-Functional based approaches: successful combinations , LUCIA REINING, CNRS - Ecole Polytechnique - ETSF — Today, in the framework of solid state physics two main ab initio approaches are used to describe ground- and excited state properties of condensed matter: on one side, static ground state density functional theory (DFT) and its time-dependent extension (TDDFT) for the description of excited states; on the other side, Many-Boby Perturbation Theory (MBPT), most often used in Hedin s GW approximation [1] for the electron self-energy, or the Bethe-Salpeter equation for the calculation of response functions. Both approaches have led to breakthroughs, but suffer from different shortcomings: MBPT has a relative conceptual clarity and therefore allows one to find good approximations, but calculations are in general numerically very demanding. DFT-based approaches are in principle computationally more efficient, but a generally reliable and at the same time efficient description of exchange-correlation effects within TDDFT is difficult to obtain. In recent years a major effort has therefore been made in order to combine MBPT and TDDFT, searching for a formulation that would keep the advantages of both approaches (see e.g. [2,3]). In this talk we will discuss different ways to derive a linear response exchange-correlation kernel for TDDFT from MBPT. The strength of various approximations, that have been shown to reproduce continuum and bound excitons for a wide range of materials, as well as possible problems will be outlined, and the computational efficiency of the method examined. The question of how to use such a combination of MBPT and TDDFT in order to obtain vertex corrections to the self-energy [4] will also be addressed. [1] L. Hedin, Phys. Rev. 139, A796 (1965). [2]F. Sottile, V. Olevano, and L. Reining, Phys. Rev. Lett. 91, 056402 (2003) [3] S. Botti, F. Sottile, N. Vast, V. Olevano, L. Reining, H.-C. Weissker, A. Rubio, G. Onida, R. Del Sole, R.W. Godby, Phys. Rev. 69, 155112, (2004). [4] F. Bruneval, F. Sottile, V. Olevano, R. Del Sole and L. Reining, Phys. Rev. Lett. 94, 186402, (2005).

3:06PM L19.00002 Using Constrained DFT to Deﬁne a Diabatic Conﬁguration Space , TROY VAN VOORHIS — We show that several of the well-known shortcomings of approximate density functionals for treating electron transfer (ET) can be overcome by applying physically motivated constraints to the electron density. We summarize our implementation of this constrained density functional theory (CDFT) and present several illustrative applications that demonstrate the strengths of the new formalism: 1) CDFT allows charge transfer excitations to be treated accurately within a ground state formalism, including the long range -1/r interaction between the electron and the hole 2) One directly obtains diabatic states, which can be unambiguously associated with Marcus theory parameters and 3) Long-standing ground state electronic structure problems – such as the prediction of exchange couplings and certain reaction barrier heights – can be treated accurately in a rigorous fashion.

3:42PM L19.00003 Ab initio study of near-edge x-ray absorption fine structure of hexagonal ice and liquid water , WEI CHEN, Department of Physics, Princeton University, ROBERTO CAR, Department of Chemistry, Princeton University — We report first-principles calculations of near-edge x-ray absorption fine structure (NEXAFS) spectra of hexagonal ice and liquid water. Our work is motivated by the importance of accurately modeling NEXAFS spectra, which provide sensitive information on local molecular structures. In particular, we find a systematic improvement in the agreement of the calculated spectra with the experiment, by including excitonic effects, final state and self-interaction corrections. We correlate the calculated corrections to the degree of localization of the excited states.

3:54PM L19.00004 Going beyond the Tamm-Dancoff approximation in the Bethe-Salpeter approach to the optical properties of solids , PETER PUSCHNIG, CLAUDIA AMBROSCH-DRAXL, Atomistic Modelling and Design of Materials, University of Leoben — The solution of the Bethe-Salpeter equation (BSE) has turned out to be the method of choice for the ab-initio calculation of optical properties of semiconductors and insulators which is capable of correctly accounting for excitonic effects. Commonly, however, the coupling between the resonant and anti-resonant excitations is neglected, referred to as the Tamm-Dancoff approximation (TDA). This is well justified in many cases, in particular, for the working horses of theoretical solid state physics, such as bulk Si and GaAs. Here, we report on a first-principles investigation of the optical properties of organic semiconductors which are highly anisotropic systems. We find that the TDA no longer holds in such low-dimensional systems, where the exciton binding energies are no longer small compared to the band gaps. Going beyond the TDA leads to an increase of the exciton binding energy in the order of several tenths of an eV thereby considerably improving the agreement with experiment.

4:06PM L19.00005 Electron-atom scattering using time-dependent density-functional theory , META VAN FAASSEN, Dept Chemistry & Chem Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, KIERON BURKE, University of California, 1113 Natural Sciences II, Irvine, CA 92697 — We present a method to obtain single-channel elastic electron-atom scattering phase shifts from time-dependent density functional theory (TDDFT). The system is placed in a spherical box, and TDDFT is used to calculate its discrete spectrum, from which phase shifts are deduced. The inﬂuence of ground state Kohn-Sham potentials and exchange-correlation kernels on the results are discussed.

4:18PM L19.00006 Investigation of Bonding in the BF3-H2O Complex , ARCHANA DUBEY, H.P. SAHA, LEE CHOW, UCF Orlando, R.H. PINK, DIP N. MAHATO, M.B. HUANG, T.P. DAS1, SUNY Albany, R.H. SCHEICHER, MTU Houghton, MAHENDRA K. MAHANTI, NEHU, Shillong, India — The catalytic properties of BF3 involving its complexes with diﬀerent classes of molecules is of great current interest. As a typical system of complexes involving the B-O bond we have studied the BF3-H2O system using ﬁrst-principle Hartree-Fock-Roothaan procedure combined with many-body perturbation theory to include Van der Waals (VDW) interaction between BF3 and H2O molecules. From our results, the VDW contribution to the binding energy of the BF3-H2O complex comes out as 34.5% of the covalency, close to the 36.4% result from our earlier investigations on BF3-NH3 . The absolute values for the covalency and VDW contributions are both about 35% of the BF3-NH3result. Physical implications of these results will be discussed.

1Also UCF Orlando 4:30PM L19.00007 van der Waals coefficients in DFT: a simple approximation for the polarizability , STEFANO DE GIRONCOLI, SISSA and DEMOCRITOS, HUY VIET NGUYEN, SISSA, DEMOCRITOS and Hanoi University of Education — Long range van der Waals interaction plays a crucial role in many systems. Density functional Theory (DFT) within Local Density and Generalized Gradient Approximations for exchange-correlation energy is known to fail in describing properly this interaction, while direct calculations based on the exact Adiabatic Connection Formula are computationally impracticable, except for few simple systems. A simple and computationally fast scheme to calculate imaginary- frequency-dependent polarizability, hence asymptotic van der Waals interaction, within density functional theory is considered. The van der Waals coefficients for a large number of closed-shell ions and several molecules are calculated and compare well with available values obtained by more refined first-principle calculations. The success in these test cases shows the potential of the approximation in capturing the essence of long range correlations and may give useful information for constructing a functional which naturally includes van der Waals interaction in DFT.

4:42PM L19.00008 First-Principles Study of the Nature of Binding in BF3 Molecular Solids , DIP N. MAHATO, R.H. PINK, M.B. HUANG, T.P. DAS1, SUNY Albany, ARCHANA DUBEY, LEE CHOW, UCF Orlando, MAHENDRA K. MAHANTI, NEHU, Shillong, India, R. H. SCHEICHER, MTU Houghton — The binding of BF3 molecules in solid BF3 is studied by the Hartree-Fock Cluster Procedure, with Van der Waals interaction between the BF3 molecules included by the many-body perturbation theory procedure. The binding appears to be the result of strong cancellation between one-electron effects, represented by the covalent interaction between neighboring molecules combined with the coulomb interaction between the effective charges on the boron and fluorines in each of the neutral BF3 molecules and the many-body correlation effect between electrons on neighboring molecules leading to the Van der Waals interaction, the latter being the determining factor for the binding. Quantitative results will be presented for the binding energy in this solid state system which represents a class of molecular solids for which the neutral molecular units have substantial effective charges of different signs on the constituent atoms.

1Also UCF Orlando

4:54PM L19.00009 Optimized orbitals with second order opposite-spin correlation , MARTIN HEAD- GORDON, University of California, Berkeley — Despite tremendous progress, the most ubiquitous electronic structure methods, based on density functional theory (DFT), that can be applied to molecules ranging well over 100 atoms, exhibit failures for molecules with strong correlations, some types of radicals, and systems where dispersion interactions are important. At the same time, the most accurate electronic structure methods, based on coupled cluster theory, remain too computationally demanding to enable the routine treatment of molecules containing more than about 20 atoms. I will discuss a new self-consistent approach that correctly and inexpensively recovers dispersion interactions, without either excessive spin-contamination for radicals (as plagues traditional unrestricted Hartree-Fock-based methods), or the diﬃculties of self-interaction that can aﬀect DFT calculations of radicals. This approach yields optimized Breuckner-type orbitals. Its performance for relative energies, structures, and frequencies will be assessed, both for closed shell molecules, radicals, as well as some cases which exhibit pathological failures at both the DFT and MP2 levels of theory.

5:06PM L19.00010 On the dynamics of the spin-boson model: variational principle versus adiabatic approximation , TITUS SANDU, RADU IFTIMIE — The time-dependent variational principle is applied to the spin-boson model. We use two diﬀerent trial functions that exhibit various degrees of separation between the bosonic dynamics and the electronic dynamics. The equations of motion obtained for these two trial functions are shown to be equivalent with the equations of motions obtained with two diﬀerent adiabatic approximations of the dynamics.

Tuesday, March 6, 2007 2:30PM - 5:18PM — Session L26 DCP: Focus Session: Non-adiabatic Molecular Dynamics and Control at Conical Intersections III Colorado Convention Center 205 2:30PM L26.00001 Exploring conical intersections through high resolution photofragment translational spectroscopy1 , MICHAEL ASHFOLD, University of Bristol — High resolution measurements of the kinetic energies of H atom fragments formed during UV photolysis of gas phase imidazole, [1,2] pyrrole, [3] phenol [4] and thiophenol molecules show that: (i) X-H (X = N, O, S) bond ﬁssion is an important non-radiative decay process from the 1πσ* excited states in each of these molecules, and (ii) that the respective co-fragments (imidazolyl, pyrrolyl, phenoxyl and thiophenoxyl) are formed in very limited sub-sets of their available vibrational states. Identiﬁcation of these product states yields uniquely detailed insights into the vibronic couplings involved in the photo-induced evolution from parent molecule to ultimate fragments. [1] M.N.R. Ashfold, B. Cronin, A.L. Devine, R.N. Dixon and M.G.D. Nix, Science (2006), 312, 1637. [2] A.L. Devine, B. Cronin, M.G.D. Nix and M.N.R. Ashfold, J. Chem. Phys. (in press). [3] B. Cronin, M.G.D. Nix, R.H. Qadiri and M.N.R. Ashfold, Phys. Chem. Chem. Phys. (2004), 6, 5031. [4] M.G.D. Nix, A.L. Devine, B. Cronin, R.N. Dixon and M.N.R. Ashfold, J. Chem. Phys. (2006), 125, 133318.

1Contributions to this work from group members Brid Cronin, Mike Nix, Adam Devine, Graeme King and Professor Richard Dixon F.R.S are gratefully acknowledged, as is ﬁnancial support from the EPSRC via the pilot portfolio partnership LASER.

3:06PM L26.00002 Dynamic Stark Control of Photochemical Processes1 , BENJAMIN J. SUSSMAN, National Research Council of Canada & Queen’s University — A technique for controlling the outcome of photochemical reactions using the dynamic Stark effect due to a strong, nonresonant infrared field is demonstrated numerically and experimentally. A precisely timed infrared laser pulse is used to reversibly modify a potential energy barrier during a chemical reaction without inducing any real electronic transitions. Dynamic Stark control (DSC) is experimentally demonstrated during the nonadiabatic photodissociation of IBr. Significant modification of reaction channel probabilities are observed. The DSC process is nonperturbative, insensitive to laser frequency, and affects all polarizable molecules, suggesting broad applicability.

1In collaboration with Dave Townsend, Misha Yu. Ivanov, and Albert Stolow, National Research Council of Canada. 3:42PM L26.00003 Ab initio design of laser pulses to control molecular motion , GABRIEL BALINT- KURTI, QINGHUA REN, FREDERICK MANBY, University of Bristol, MAXIM ARTAMONOV, TAK-SAN HO, HERSCHEL RABITZ, University of Princeton, SHIYANG ZOU, University of Bristol, HARJINDER SINGH, IIIT Hyderabad, BRISTOL TEAM1, PRINCETON TEAM2 — Our recent attempts to design laser pulses entirely theoretically, in a quantitative and accurate manner, so as to fully understand the underlying mechanisms active in the control process will be outlined. We have developed a new Born-Oppenheimer like separation called the electric-nuclear Born-Oppenheimer (ENBO) approximation. In this approximation variations of both the nuclear geometry and of the external electric field are assumed to be slow compared with the speed at which the electronic degrees of freedom respond to these changes. This assumption permits the generation of a potential energy surface that depends not only on the relative geometry of the nuclei, but also on the electric field strength and on the orientation of the molecule with respect to the electric field. The range of validity of the ENBO approximation is discussed. Optimal control theory is used along with the ENBO approximation to design laser pulses for exciting vibrational and rotational motion in H2 and CO molecules. Progress on other applications, including controlling photodissociation processes, isotope separation, stabilization of molecular Bose-Einstein condensates as well as applications to biological molecules also be presented. *Support acknowledged from EPSRC.

1Group of G.G. Balint-Kurti 2Group of H. Rabitz

˜2 ˜ 2 3:54PM L26.00004 Probing NO2 close to the A B2/X A1 conical intersection by time-resolved imaging spectroscopy , BENJAMIN WHITAKER, NICK FORM, University of Leeds, UK, VALERIE BLANCHET, Universite Paul Sabatier, Toulouse, BEATRICE CHATEL, BERTRAND GIRARD, Universite Paul Sabatier, SCHOOL OF CHEMISTRY, UNIVERSITY OF LEEDS COLLABORATION, LCAR, IRSAMC, UNIVERSITE PAUL SABATIER COLLABORATION — Time-resolved imaging spectroscopy (TRIS) is emerging as a versatile technique with which to study the non-adiabatic coupling of vibrational and electronic degrees of freedom in molecules. The electronic predissociation of NO2 in the near UV 2 2 proceeds by internal conversion between the A˜ B2 and X˜ A1 states and is a benchmark example of such barrierless reactions. We have applied time-resolved + + imaging to measure the time-evolution, angular and kinetic energy distributions of NO , NO2 and photo electrons produced in pump-probe experiments using harmonics from a regeneratively ampliﬁed self-mode locked Ti:sapphire laser. Oscillations in the slow NO+ and photoelectron signals are observed and are 2 2 interpreted as measuring the energy level density of the coupled A˜ B2 and X˜ A1 states close to the conical intersection. By using an optical pulse shaper we are able to manipulate the spectrum of the ∼400 nm excitation to create pulse sequences with which we can exert partial control over the coupling between 2 2 the A˜ B2 and X˜ A1 states.

4:06PM L26.00005 The Jahn Teller and pseudo-Jahn Teller effect in the dark A˜ state of the nitrate radical NO3 , KANA TAKEMATSU, DAVID ROBICHAUD, MITCHIO OKUMURA, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, JOHN STANTON, Department of Chemistry, University of Texas, Austin, TX 78712 — Despite its apparent simple molecular structure, the lowest electronic states of the nitrate radical NO3 remain poorly understood. In particular, the three lowest states of the radical provide a benchmark for testing models of the Jahn-Teller (JT) and pseudo-JT effects. The dark A˜ state of NO3 undergoes strong JT distortion, suggesting that models with only linear and quadratic vibronic couplings are inadequate. We present cavity ringdown (CRD) and integrated cavity output (ICOS) ∼ ∼ 2 2 0 spectra of the forbidden A E” ← X A2 transition (preliminary report in Deev, et. al. J.Chem. Phys., 2005. 122:224305) and compare them to a simulation based on a model Hamiltonian developed by Koppel, Domcke and Cederbaum that incorporates both JT and PJT couplings. New insights into the pseudo-JT effect among the lowest states are gained by examination of intensity-borrowing mechanisms for the observed vibronic bands.

4:18PM L26.00006 Nonadiabatic Electronic and Rotational Energy Partitioning in F + H2O → HF + OH , MICHAEL ZIEMKIEWICZ, ALEX ZOLOT, DAVID NESBITT, JILA, University of Colorado — OH product state distributions from F + H2O → HF + OH have been carried out at a COM collision energy of 6(2) kcal/mol. These measurements complement earlier work on the dueterated version of the system (F + D2O → DF + OD) where extensive non-adiabatic interactions led to a population of spin-orbit excited OD products despite energetically inaccessible barriers on all but the ground electronic surface. In the present F + H2O measurements, the branching ratio is, within error bars, the same as in the deuterated case: 69(1)% of the molecules are found in the ground spin-orbit state, and 31(1)% are found in the excited (nonadiabatic) state. In contrast to this isotopomer-independent electronic branching ratio, the rotational distributions for this system are distinctly diﬀerent from the deuterated case. A detailed analysis of the rotational distributions for the title reaction leads to an estimate of the vibrational distribution of the unobserved HF fragment (v=2:v=1) of 3:1. The fact that isotoperization dramatically changes the rotational distributions while leaving electronic distributions unchanged sheds light on the important question of how and where nonadiabatic transitions take place in this four-atom system.

4:30PM L26.00007 Quantum State Resolved Reactive Scattering Near Conical Intersections: 2 2 2 2 F ( P ) + HCl → HF (v, J) + Cl( P ) and F ( P ) + H2O → HF (v, J) + OH( Π) via High Resolution IR Spectroscopy on Nascent HF Product , ALEXANDER ZOLOT, MICHAEL ZIEMKIEWICZ, MICHAEL DESKEVICH, DAVID NESBITT, JILA, National Institute of Standards and Tehcnology and University of Colorado — State resolved reaction dynamics of the reactionsF (2P )+HCl → 2 2 2 HF (v, J) + Cl( P )and F ( P ) + H2O → HF (v, J) + OH( Π)have been studied under rigorous single collision conditions in crossed molecular jets via IR absorbance of the HF product. Supersonic jet collision energies exceed the ground electronic state barrier height predicted by ab initio (DW-MCSCF) calculations, but can not overcome the larger barriers on excited state surfaces. The experimental results reveal highly vibrationally inverted nascent HF populations containing signiﬁcant population above the average energy available to products for both of the title reactions. Such excited products may be formed by the tail of the collision energy distribution, but may also be favored by the extra ∼1.1 kcal/mol available for reaction with spin-orbit excited ﬂuorine, previously observed in other systems. F+HCl product rotational distributions are found to be particularly non-statistical and are poorly modeled by single surface QCT.

4:42PM L26.00008 Optical control of dynamics in a simple chemical reaction: The cyclohexadiene ring-opening reaction , ROSEANNE SENSION, FOCUS Center, University of Michigan — UV excitation of 1,3-cyclohexadiene (CHD) results in an optically induced ring-opening reaction to form 1,3,5-cis-hexatriene (ZHT). The initial excited state wave packet accelerates away from the Frank- Condon region and is funneled through a conical intersection onto the 2A excited state where the nuclear ring-opening reaction occurs. Return to the ground state proceeds within a few hundred femtoseconds through two or more conical intersections between the 1A and 2A potential energy surfaces. Recent studies have demonstrated that multiphoton excitation of CHD can be used to influence the photochemical yield of ZHT. The multidimensional search of the control space for optimal pulses identified both the quadratic and cubic phase parameters of the pulse as important control parameters. These results are discussed in terms of potential physical models. 4:54PM L26.00009 Matching-pursuit/split-operator-Fourier-transform simulations of excited- state nonadiabatic quantum dynamics in pyrazine. , VICTOR BATISTA, XIN CHEN, Yale University — A simple approach for numerically exact simulations of nonadiabatic quantum dynamics in multidimensional systems is introduced and applied to the description of the photoabsorption spectroscopy of pyrazine. The propagation scheme generalizes the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)]. The time-evolution operator is applied, as defined by the Trotter expansion to second order accuracy, in dynamically adaptive coherent-state expansions. These representations are obtained by combining the matching-pursuit algorithm with a gradient- based optimization method. The accuracy and efficiency of the resulting computational approach are demonstrated in calculations of time-dependent survival amplitudes and photoabsorption cross sections, using a model Hamiltonian that allows for direct comparisons with benchmark calculations. Simulations in full-dimensional potential energy surfaces involve the propagation of a 24-dimensional wave packet to describe the S1 /S2 interconversion of pyrazine after after S0-S2 photoexcitation. The reported results show that the generalized MP/SOFT method is a practical and accurate approach to model nonadiabatic reaction dynamics in polyatomic systems.

5:06PM L26.00010 Femtosecond pump – shaped-dump – probe quantum control , PATRICK NUERN- BERGER, Physikalisches Institut, PHILIPP MARQUETAND, Institut fuer Physikalische Chemie, GERHARD VOGT, TOBIAS BRIXNER, Physikalisches Institut, VOLKER ENGEL, Institut fuer Physikalische Chemie, GUSTAV GERBER, Physikalisches Institut, Universitaet Wuerzburg, Am Hubland, 97074 Wuerzburg, Ger- many — We present a three pulse pump–shaped-dump–probe scheme for femtosecond spectroscopy. The objective is a reversion of regular control schemes for optimal excitation in which the pump pulse is shaped. Instead, we seek optimal de-excitation with a shaped dump pulse. Besides variation of the time delay between pump and dump pulses, the versatility of a femtosecond pulse shaper furthermore allows to record systematic ﬁtness landscapes as a function of selected pulse parameters, providing additional information on wave-packet evolution and the potential energy surfaces of the system under study. Since the dump pulse is independent from the pump pulse, the pump– shaped-dump–probe scheme facilitates control of molecular systems away from the initial Franck-Condon window in regions of the potential-energy landscape where the decisive reaction step occurs, e.g. near conical intersections. Experimental results on the retinal photoisomerization reaction in bacteriorhodopsin and exemplary model calculations demonstrate the potential of this new scheme.

Tuesday, March 6, 2007 2:30PM - 5:18PM — Session L35 DPB DCP DCOMP: Metalloproteins: Theory and Experiment Colorado Convention Center 405 2:30PM L35.00001 Hartree - Fock study of the Heme Unit of deoxy-hemoglobin for Hyperfine Interactions and Vibrational Properties. , T.P. DAS1, K. RAMANI LATA, R.H. PINK, DIP N. MAHATO, SUNY Albany, ARCHANA DUBEY, H.P. SAHA, A.F. SCHULTE, LEE CHOW, UCF, Orlando, R.H. SCHEICHER, MTU, Houghton, N.B. MAHARJAN, Tribhuvan University, Nepal, N. SAHU, U.T.M.D Anderson Cancer Center, Houston — The electronic structure of the Heme Unit of deoxy- Hemoglobin has been studied by the Hartree- Fock - Roothaan procedure for understanding the hyperfine interaction properties of the 57mFe nucleus and vibrational properties associated with Fe and proximal imidazole. Results will be presented for the 57mFe nucleus, including the isomer shift in Mossbauer spectroscopy, magnetic hyperfine and nuclear quadrupole interactions and for the Fe-Nε vibrational frequency. Comparisons will be made with available experimental data and possible further investigations will be discussed.

1Also UCF Orlando.

2:42PM L35.00002 DFT Studies of NO Activation of Heme Proteins. , A. BARABANSCHIKOV, J.T. SAGE, Northeastern University, N.J. SILVERNAIL, W.R. SCHEIDT, University of Notre Dame, J. ZHAO, WOLFGANG STURHAHN, E.E. ALP, Advanced Photon Source, Argonne, IL — Many important cardiovascular and neural system processes are triggered by activation of the enzyme soluble guanylate cyclase (sGC), a sensor of NO widely thought to be activated through binding of NO to heme. Our understanding of these processes will remain incomplete without knowing why NO activates sGC more eﬀectively than other diatomic ligands. We report DFT calculations on various porphyrins and heme protein active sites to test the hypothesis that activation of sGC is associated with disruption of the Fe-histidine bond to the protein. We demonstrate that NO binding signiﬁcantly weakens this bond. Also, comparing the predicted vibrational spectra of these compounds with nuclear resonance vibrational spectroscopy (NRVS) measurements allows us to identify the Fe- histidine stretching mode, a reaction coordinate for histidine dissociation in NO-ligated heme proteins. Comparison of 5-coordinate and 6-coordinate NO and CO compounds provides additional tests of the hypothesis.

2:54PM L35.00003 Ab-Initio-Based Approach to Study Complete Metalloproteins: Divide and Conquer Geometry Optimization of Nitric-Oxide Reductase , YUTAO YUE, TEEPANIS CHACHIYO, JORGE H. RODRIGUEZ, Department of Physics, Purdue University, West Lafayette, IN 47907-2036 — The direct application of ab-initio methods (Hartree-Fock or density functional theory) to study complete biomolecules has been impossible due to the huge computational cost of fully quantum mechanical calculations. As an initial step towards overcoming this problem, we implemented an ab-initio-based method to predict geometric structures of large metalloproteins using the principle of “divide and conquer.” The method has been applied to small test systems showing satisfactory agreement with all-atom ab initio calculations. We have successfully applied the divide and conquer approach to partially optimize the geometry of a ligand-enzyme system, namely NO binding to nitric-oxide reductases (NOR, P450nor). NOR is a metalloenzyme that catalyzes the reduction of NO to N2O. To compare our results with all atom calculations we studied a biochemically relevant subsystem (375 atoms) of the ligand-enzyme complex. The deviation between the divide and conquer geometry and the all atom partial geometry optimization is minor, on order of 10−1 A˚ for bond lengths. The computational cost of the method is moderately expensive making its application to large (bio) molecules plausible. Supported by NSF CAREER Award CHE-0349189 (JHR).

3:06PM L35.00004 Ab-Initio Based Computation of Rate Constants for Spin Forbidden Metalloprotein-Substrate Reactions1 , ABDULLAH OZKANLAR, JORGE H. RODRIGUEZ, Department of Physics, Purdue University, West Lafayette, IN 47907-2036, RODRIGUEZ RESEARCH TEAM — Some chemical and biochemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of ab-initio methods, such as spin density functional theory (SDFT), to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory (NA-TST) in conjuntion with SDFT to predict the rate constant of the spin- forbidden recombination of carbon monoxide with iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in very good agreement with experiment. In addition, we present results for the spin- forbidden ligand binding reactions of iron-containing heme proteins such as myoglobin.

1Supported by NSF CHE-0349189 (JHR) 3:18PM L35.00005 Dependence of Localized Electronic Structure on Ligand Configuration in ∗ the [2Fe] Hydrogenase Catalytic Core , CHRISTOPHER H. CHANG, KWISEON KIM, National Renewable Energy Laboratory — The [FeFe] hydrogenase enzyme is found in a variety of organisms, including Archaea, Eubacteria, and green algae1,2, and crystallographically determined atomic position data is available for two examples. The biologically unusual catalytic H-cluster, responsible for proton reduction to H2 in vivo, is conserved in the known structures and includes two bis-thiolato bridged iron ions with extensive cyano- and carbonyl ligation. To address the configurational specificity of the diatomic ligand ligation, density functional theoretical calculations were done on [2Fe] core models of the active center, with varying CO and CN− ligation patterns. Bonding in each complex has been characterized within the Natural Bond Orbital formalism. The effect of ligand configuration on bonding and charge distribution as well as Kohn-Sham orbital structure will be presented. [1] M. Forestier, P. King, L. Zhang, M. Posewitz, S. Schwarzer, T. Happe, M.L. Ghirardi, and M. Seibert, Eur. J. Biochem. 270, 2750 (2003). [2] Posewitz, M.C., P.W. King, S.L. Smolinski, R.D. Smith, II, A.R. Ginley, M.L. Ghirardi, and M. Seibert, Biochem. Soc. Trans. 33, 102 (2005). ∗This work was supported by the US DOE-SC-BES Hydrogen Fuels Initiative, and done in collaboration with the NREL Chemical and Biosciences Center.

3:30PM L35.00006 Ab Initio Computation of Spin Orbit Coupling Effects on Magnetic Prop- erties of Iron-Containing Complexes and Proteins , FREDY AQUINO, JORGE H. RODRIGUEZ, Department of Physics, Purdue University, West Lafayette, IN 47907-2036 — Zero-Field Splittings (ZFS) in metalloproteins and other metal complexes arise from the combined action of crystalline fields acting on the metal valence electrons and spin-orbit coupling (SOC), a relativistic effect. The ab-initio calculation of ZFS parameters of metal-containing (bio)molecules is a challenging computational problem of practical relevance to metalloenzyme biochemistry, inorganic chemistry, and molecular-based bio- nanotechnology. We have implemented a methodology which treats the nonrelativistic electronic structure of magnetic (bio) molecules within the framework of spin density functional theory (SDFT) and adds the relativistic effects of SOC via perturbation theory (PT). This combined SDFT-PT approach allowed us to compute the ZFS parameters of iron-containing complexes and non-heme iron proteins with a good degree of accuracy. We also developed a semiquantitative approach to elucidate the physico-chemical origin of the magnitudes of ZFS parameters. We present results for biochemically relevant iron complexes and for nitric oxide-containing non-heme iron proteins, such as isopenicillin N synthase, which have unusually large ZFS. The computed ZFS parameters are in good agreement with experiment. Supported by NSF CAREER Award CHE- 0349189 (JHR).

3:42PM L35.00007 Förster-type mechanism of the redox-driven proton pump , LEV MOUROKH, Queens College of CUNY, ANATOLY SMIRNOV, FRANCO NORI, Frontier Research System, RIKEN, Japan — We propose a model to describe an electronically-driven proton pump in the cytochrome c oxidase (CcO). We examine the situation when the electron transport between the two sites embedded into the inner membrane of the mitochondrion occurs in parallel with the proton transfer from the protonable site that is close to the negative (inner) side of the membrane to the other protonable site located nearby the positive (outer) surface of the membrane. In addition to the conventional electron and proton tunnelings between the sites, the Coulomb interaction between electrons and protons localized on the corresponding sites leads to so-called Förstertransfer, i.e. to the process when the simultaneous electron and proton tunnelings are accompanied by the resonant energy transfer between the electrons and protons. Our calculations based on reasonable parameters have demonstrated that the Försterprocess facilitates the proton pump at physiological temperatures. We have examined the effects of an electron voltage build-up, external temperature, and molecular electrostatics driving the electron and proton energies to the resonant conditions, and have shown that these parameters can control the proton pump operation.

3:54PM L35.00008 Investigation of copper(II) binding to the protein precursor of Non- Amyloid-Beta Component of Alzheimer Disease Amyloid Plaque , FRANCIS ROSE, MIROSLAV HODAK, JERRY BERNHOLC, N.C. State University — The Non-Amyloid-Beta Component Precursor (NACP) is a natively unfolded synaptic protein that is implicated in Alzheimers and Parkinsons diseases. Its aggregation into ﬁbrillar structures is accelerated by the binding of copper(II). Experimental studies suggest that the dominant copper binding site is located at the histidine residue in NACP. Based on this evidence we assembled a model fragment of the binding site and used DFT to analyze the conformational details of the most probable binding motifs. We investigated the overall conformational eﬀects with classical MD by constraining the copper binding site to the most energetically favorable geometry obtained from the DFT calculations. These results are compared and contrasted with those of the unbound NACP.

4:06PM L35.00009 Cooperative binding modes of Cu(II) in prion protein , MIROSLAV HODAK, North Carolina State University, ROBIN CHISNELL, WENCHANG LU, JERRY BERNHOLC — The misfolding of the prion protein, PrP, is responsible for a group of neurodegenerative diseases including mad cow disease and Creutzfeldt-Jakob disease. It is known that the PrP can efficiently bind copper ions; four high-affinity binding sites located in the octarepeat region of PrP are now well known. Recent experiments suggest that at low copper concentrations new binding modes, in which one copper ion is shared between two or more binding sites, are possible. Using our hybrid Thomas-Fermi/DFT computational scheme, which is well suited for simulations of biomolecules in solution, we investigate the geometries and energetics of two, three and four binding sites cooperatively binding one copper ion. These geometries are then used as inputs for classical molecular dynamics simulations. We find that copper binding affects the secondary structure of the PrP and that it stabilizes the unstructured (unfolded) part of the protein.

4:18PM L35.00010 Studies of myoglobin dynamics by dielectric relaxation spectroscopy , GUO CHEN, I. MIHUT, B. H. MCMAHON, A. MIGLIORI, P. W. FENIMORE, Los Alamos National Lab — Proteins are dynamic molecules and their motions are intimately linked to the fluctuations of their solvent environment. In this work we studied the protein-solvent interactions by measuring the dielectric response of horse myoglobin (Mb) in glycerol/H2O mixtures over a frequency range of 40Hz-110MHz. Two relaxation processes were observed at temperatures above 220K. The high frequency process corresponds to the α-fluctuations of the glycerol/H2O solvent and its rates were found to increase slightly at the presence of the Mb protein. The low frequency process, slower by roughly four orders of magnitude, is relevant to Mb motions and absent for the samples without Mb. The temperature dependence of the two processes can be approximated with the same Vogel-Tammann-Fulcher temperature dependence. Preliminary analyses suggest that the Mb-related process is associated with the conformational fluctuations of the whole Mb protein. Such fluctuations require the coordinated motions of surrounding solvent molecules and are thus an example of protein slaving to the solvent fluctuations.

4:30PM L35.00011 Vibrational Characterization of Myoglobin Compound II , W. ZENG, A. BARABAN- SCHIKOV, Y. ZHANG, J.T. SAGE, Northeastern University, E.E. ALP, W. STURHAHN, J. ZHAO, Argonne National Laboratory — Compound II intermediates are essential to oxygen activation by heme proteins. The protonation status of the FeIV oxo fragment is controversial. EXAFS and Raman spectroscopy have long suggested an FeIV =O group, but recent crystal structures show a long Fe-O distance more consistent with a protonated Fe-OH. We use nuclear resonance vibrational spectroscopy (NRVS) to probe the motion of 57Fe in compound II of horse heart myoglobin(Mb II). Although the NRVS signal is weaker than expected, we clearly identify the Fe-O stretch at 805 cm−1, in addition to previously unobserved in-plane Fe vibrations near 360 cm−1. Cryogenic Raman measurement on isotopically labeled Mb II reveals that the kinetic energy distribution (KED) of the Fe-O stretch is localized on the Fe-O fragment, with no significant involvement from the putative proton. Comparison with DFT vibrational predictions provide further insight into the character of the observed normal modes. We conclude that the oxo group is not protonated in Mb II. 4:42PM L35.00012 Investigations of the 40cm−1 mode in hexacoordinated ferric heme systems , FLAVIU GRUIA, XIONG YE, PAUL CHAMPION, Northeastern University — The 40cm−1 mode dominates the low frequency spectra of most hexacoordinated ferric heme systems investigated to date. For a better understanding and assignment of this mode we have measured the FCS excitation profile of cyanide bound myoglobin, which shows this feature particularly well. We observe a very interesting behavior of the initial phase and the amplitude of this mode which do not fit within the existent theoretical models. The experimental results could be explained if we postulate the existence of a fast non-radiative transition between the nuclear excited and the ground states. There are also arguments that support the existence of a charge transfer band that underlies the Soret band.

4:54PM L35.00013 Novel photo-protection mechanism in strongly coupled chlorophyll complexes: triplet excitons in chlorosomes and in artificial chlorophyll aggregates. , SERGEI SAVIKHIN, HANYOUP KIM, Purdue University, HUI LI, JULIA MARESCA, DONALD BRYANT, The Pennsylvania State University — Bacteriochlorophyll (BChl) and chlorophyll (Chl) molecules are known to produce highly toxic singlet oxygen due to energy transfer from their excited triplet states to oxygen molecules. The monomeric (B)Chl molecules in a solution photo-degrade within minutes under sunlight. In (B)Chl pigment-protein complexes of photosynthesis, a carotenoid is typically positioned within a distance of 4 A˚ of individual (B)Chl or antenna arrays, allowing rapid triplet energy transfer from (B)Chl to the carotenoid. Our time resolved and steady state optical experiments reveal that strongly coupled BChl arrays of pigments are inherently protected due to the formation of triplet excitonic states. According to model simulations, the energy of the triplet exciton is substantially lower than that of the triplet state of an individual BChl, dropping below that of singlet oxygen, and blocking the triplet energy transfer to both carotenoid and to oxygen. This effect is observed experimentally in photosynthetic chlorosomes and in artificial BChl complexes.

5:06PM L35.00014 Transport dynamics in membranes of photosynthetic purple bacteria1 , FELIPE CAYCEDO, FERNEY RODRIGUEZ, LUIS QUIROGA, Universidad de los Andes, FRANCESCA FASSIOLI, NEIL JOHNSON, University of Oxford — Photo- Syntethic Unit (PSU) of purple bacteria is conformed by three basic constituents: Light Harvesting Complex 2 (LH2) antenna complexes, where chromophores are distributed in a ring in close contact with caroteniods with a function of collecting light; LH1s, ring shaped structures of chromophores which harvest and funnel excitations to the Reaction Centre (RC), where phtosynthesis takes place. Studies concerning a single PSU have been capable of reproducing experimental transfer times, but incapable of explaining the fact that architecture LH2-LH1-RC of phototosynthetic membranes changes as light intensity conditions vary. The organization of antenna complexes in the membranes that support PSU seems to have its own functionality. A hopping model where excitations are transferred within a membrane is used, and populations of RC, LH1 and LH2 are investigated. Diﬀerent statistics concerning arrival times of excitations that excite a single PSU are considered and compared with the global model where coordinates of a great portion of a membrane are included. The model permits in a classical basis to understand which parameters make photosynthesis in purple bateria eﬃcient and reliable.

1Facultad de Ciencias-Uniandes(2006)

Tuesday, March 6, 2007 5:45PM - 6:45PM — Session M19 DCP: DCP Business Meeting Colorado Convention Center 104

5:45PM M19.00001 DCP Business Meeting —

Wednesday, March 7, 2007 8:00AM - 11:00AM — Session N19 DCP DCOMP: Focus Session: Frontiers in Electronic Structure Theory III Colorado Convention Center 104 8:00AM N19.00001 A New View of the Kondo Effect from an Ab Initio Embedded Configura- tion Interaction Theory , EMILY CARTER, Princeton University — Over the past decade, we have been developing an ab initio theory to describe localized correlated many-electron states in condensed matter. This theory embeds a correlated quantum chemistry description into surroundings described by periodic density functional theory (DFT). Recent technical advances in the theory include: (i) implementation of ultrasoft pseudopotentials (USPPs) in a consistent manner across all levels of theory (periodic DFT, CASSCF, and CI), (ii) self-consistent updates of the density of the total system, thereby allowing a fully-self-consistent embedding operator, and (iii) a multi-reference singles and double excitation CI (MRSDCI) treatment of electron correlation in the embedded region. Our current embedded configuration interaction (ECI) theory is now more efficient (via USPPs), less approximate (by use of self-consistent embedding potentials), as well as more accurate (via MRSDCI) than earlier versions that were based either on many-body perturbation theory or valence CI/CASSCF wavefunctions. The current version is now being used to study a variety of systems/phenomena where DFT is known to fail, due to either neglect of many-body effects or self-interaction artifacts. Time permitting, more than one example will be given of how the embedding theory is able to give a qualitatively (as well as quantitatively) different view of these systems/phenomena. We will focus on the Kondo effect, a long standing problem in condensed matter physics, which has not had a first principles solution until now. The Kondo effect refers to the observation of an anomalous resistivity minimum at low temperatures for materials containing magnetic transition metal impurities in nonmagnetic host metals. We will show that the ECI theory is able to capture the physics and offer a new view of this phenomenon, while periodic DFT and finite cluster quantum chemistry calculations do not.

8:36AM N19.00002 First-principles calculations of nanoscale capacitors at finite bias potential , MASSIMILIANO STENGEL, UC Santa Barbara — When the thickness of an oxide film is reduced to few unit cells, its dielectric properties (which are relevant, e.g., for nonvolatile ferroelectric memories and as gate oxides in MOSFET transistors) start to deviate from those predicted by macroscopic models, and cannot be disentangled from the metallic or semiconducting contacts. One particularly important issue related to interfacial effects is the “dielectric dead layer”, which plagues the performance of thin-film perovskite capacitors by substantially reducing the effective permittivity (κ) of the active high-κ material. The microscopic origins of this reduced permittivity, and in particular whether it stems from defects or from the fundamental properties of a metal/insulator interface, are not well understood. To address this problem from first principles, we will first show how the macroscopic polarization (and the coupling to an external field) can be rigorously defined for a periodic metal-insulator heterostructure, by using techniques and ideas borrowed from Wannier-function theory [1]. We will then demonstrate our new method by calculating the dielectric properties of realistic SrRuO3/SrTiO3/SrRuO3 nanocapacitors [2]. In particular, we demonstrate the existence of an intrinsic dielectric dead layer and analyze its origin by extracting the ionic and electronic contributions to the electrostatic screening. We establish a correspondence between the dead layer and the hardening of the collective SrTiO3 zone-center polar modes, and determine the influence of the electrode by repeating our calculations for Pt/SrTiO3/Pt capacitors. Our results provide practical guidelines for minimizing the deleterious effects of the dielectric dead layer in nanoscale devices.

[1] M. Stengel and N. A. Spaldin, Origin of the dielectric dead layer in nanoscale capacitors, Nature (London) 443, 679 (2006).

[2] M. Stengel and N. A. Spaldin, Ab-initio theory of metal-insulator interfaces in a finite electric field, cond-mat/0511042 (2005). 9:12AM N19.00003 Ab Initio Quantum Simulations of Liquid Water1 , JOHN GERGELY, DAVID CEPERLEY, University of Illinois Urbana - Champaign, FRANCOIS GYGI, University of California Davis — Some recent efforts at simulating liquid water have employed “ab initio” molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT)2 and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods.

1Supported by DOE SCIDAC DE-FC02-06ER25794 2E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).

9:24AM N19.00004 Adaptive multilevel Finite Element Method for Solving the Electronic Schrödinger Equation1 , ERIC BYLASKA, PNNL, MIKE HOLST, JOHN WEARE, UCSD — It is widely appreciated that to use computational methods for the design of materials encompassing a wide assortment of elements from the Periodic Table, highly efficient methods based as closely as possible on accurate quantum mechanics are needed. We have developed an O(N) ab initio molecular dynamics method based on an adaptive multilevel finite element first principles solver with an efficacious implementation of hybrid functionals . The matrix representations of the discrete Hamiltonian operator in the finite element basis are always sparse due to the local support nature of finite element basis functions. As a result, application of the Hamiltonian operator to a discrete function has complexity which is linear in the number of discretization points. This development also makes use of completely unstructured simplex meshes that have the advantage of giving resolution of the near singular features around atomic nuclei using minimal computational resources. Various aspects of the implementation and computational efficiencies will be discussed. This method has been applied to several systems including excitons in quartz, transition metal dimers, and aqueous complexes.

1support from the Advanced Scientiﬁc Computing Research program of the U.S. Department of Energy, Oﬃce of Science

9:36AM N19.00005 GW calculations of large model structures , PAOLO UMARI, STEFANO BARONI, DEM- OCRITOS, Elettra Theory Group, Trieste Italy — We introduce a novel approach for performing ﬁrst-principles GW calculations of large model structures. A description of the valence and conduction manifolds in terms of non-orthogonal generalized Wannier functions permits to minimize the dimension of the basis set required for describing the space of single electron transitions. This dimension scales linearly with the size of the system. Then a space-time approach is used to calculate the self-energy operator in the space of Kohn-Sham eigenstates. Ultrasoft pseudopotentials are straightforwardly implemented within this scheme.We validate our approach by calculating the vertical ionization energies of small molecules and ﬁnd excellent agreement with the experiment. Then we shows its potentiality by addressing a model structure of vitreous silica.

9:48AM N19.00006 Toward an accurate and practical description of Xe/Cu(111) physisorption , GAROLD MURDACHAEW, SISSA, STEFANO DE GIRONCOLI, SISSA and DEMOCRITOS, PATRICK HUANG, EMILY CARTER, Princeton University, GIACINTO SCOLES, SISSA and Princeton University — The physisorption of rare gases on metal surfaces has often been described by density functional theory. However, standard DFT has shown very limited success due to its well-known shortcomings when applied to weak interactions. A possible approach which at least includes the relevant missing physics is to use a blend of “corrected” DFT coupled with a damped-dispersion interaction. Alternatively, one may model the surface by a cluster since it is possible to apply highly accurate quantum chemical methods to small clusters. Unfortunately, cluster model approximations do not give a good description of the physisorption process on the surface. In particular, the site preference of Xe/Cu(111) physisorption as given by cluster models is qualitatively incorrect. For this reason, an approach which better simulates the surface is required. Some recent results obtained using the embedded cluster approach of E. A. Carter, P. Huang, and coworkers [P. Huang and E. A. Carter, J. Chem. Phys. 125, 084102 (2006)] will be presented.

10:00AM N19.00007 Boundary Conditions for States with Maximally Broken Time-Reversal Symmetry1 , ROGER HAYDOCK, C.M.M. NEX, University of Oregon — For non-crystalline materials, electronic states can only be calculated for finite clusters, and the results are sensitive to the boundary conditions. States which go to zero on the boundary have infinite life-times, appropriate for isolated clusters, but not for macroscopic materials whose states have finite life-times. Instead, we chose a boundary condition for which the states have minimal life-times, in other words, one for which the states have maximally broken time-reversal symmetry. This approach is tested for a variety of systems and compared with its close relative, the maximum entropy approximation.

1Work supported by the Richmond F. Snyder Fund.

10:12AM N19.00008 Importance of second neighborhood ensembles on PdAu bimetallic surfaces1 , DINGWANG YUAN, RUQIAN WU, XINGAO GONG — Atomic configurations of two or three Pd substituents on the Au(111) and Au(001) surface are investigated using the first-principles pseudopotential plane wave approach. Pd atoms are found to form second neighborhoods on PdAu surfaces. The Pd-d band becomes narrow and well below the Fermi level, very different from those in a Pd film or bulk Pd. Yet the surface Pd atoms are still active and serve as independent attractive centers towards adsorbates. Through studies of example reactions such as CO oxidation, ethylene dehydrogenation and vinyl acetate synthesis, we demonstrate the importance of special ensembles in catalyzing reactions by confining reactants in a small region.

1Supported by DOE-BES, grant No: DE-FG02-04ER15611.

10:24AM N19.00009 Dielectric function by FLAPW method. , TATSUYA SHISHIDOU, TAMIO OGUCHI, Hiroshima University — Response functions, which describe how electrons respond to external fields, are the central quantity in solid state physics. Many physical properties, such as optical spectra, phonon spectra, dielectric constant, magnetic and structural instabilities, and so on, are accessible if one can calculate the corresponding response function. Moreover, the response functions play important role in the application of many-body perturbation theory. In this paper, we present a way to calculate dynamical inverse dielectric function ε−1(r, r0, ω) within the framework of the all-electron full-potential linearized augmented plane wave (FLAPW) method. We work with the random phase approximation (RPA) instead of the plasmon pole approximation. Local field effects are taken into account. Details of our method and implementation will be given, focusing on its efficiency and the treatment of the Coulomb singularity at Γ point. Calculations for semiconductors, ferromagnetic 3d transition metals, and insulating antiferromagnetic transition-metal oxides will be presented and compared with available experiments and theories. 10:36AM N19.00010 State-of-the Art Procedure for the Calculation of Quartic Force Fields: + Application to HO2 , TIMOTHY LEE, XINCHUAN HUANG, NASA Ames Research Center — In the 1990’s, ab initio methods began to yield quartic force fields for use in the calculation of ro-vibrational spectra with an accuracy that previously had been unimaginable. The main reason for this advance was the development of efficient computer programs for calculating singles and doubles coupled-cluster energies that included an estimate for connected triple excitations, denoted CCSD(T). Thus the advent of CCSD(T) quartic force fields computed with large one-particle basis sets changed the paradigm for the ab initio calculation of ro-vibrational spectra. Small correction terms have now been successfully incorporated into these procedures, including core-correlation, scalar relativistic, and others. Previously, we investigated procedures where all of these correction terms are appended in one way or another to a base calculation. In the current work, we develop a new procedure where most of these correction terms are included from the beginning, while still minimizing the overall + computational cost. Our new procedure is detailed and its application to the lowest triplet and singlet states of HO2 presented.

10:48AM N19.00011 A Correct, Density Functional Description of Semiconductors1 , D. BAGAYOKO, G. ZHAO, L. FRANKLIN, H. JON, Southern University and A&M College — The profusely reported inability of some density functional calculations to describe correctly the band gaps of semiconductors has been ascribed to the derivative discontinuity of the exchange correlation energy, the self-interaction associated with approximate potentials, and other factors, i.e., pd repulsion in the case of wurtzite InN. From 1998 to present, we have studied several semiconductors with local density approximation (LDA) and generalized gradient approximation (GGA) potentials. Upon applying the Bagayoko, Zhao, and Williams (BZW) method to the implementation of the linear combination of atomic orbital (LCAO) formalism, we have obtained band gaps and electron effective masses in excellent agreement with experiment for BaTiO3, GaN, GaAs Si, Ge, 3C-SiC, 4H-SiC, ZnSe, ZnO, carbon nanotubes, InN, and AlAs among others. This ab-initio method avoids a basis set and variational effect inherently associated with LCAO calculations – irrespective of the selected potential. We present a summary of the BZW method and of the aforementioned results, including the correct description of low-lying conduction bands as verified by agreements with measured optical transition energies and dielectric functions. These results clearly point to an urgent need to revisit (a) the above presumed causes of reported failures of DFT and (b) computational methods suffering from the identified and well-defined basis set and variational effect.

1Funded in part by the Dept. of the Navy, Oﬃce of Naval Research (Grant No. N00014-5-1-0009) and by NASA (Grant Nos. NCC 2-1344 and NAG 5-10253).

Wednesday, March 7, 2007 8:00AM - 11:00AM — Session N26 DCP: Focus Session: Non-adiabatic Molecular Dynamics and Control at Conical Intersections IV Colorado Convention Center 205

8:00AM N26.00001 Coherent 2D Spectroscopy and Control of Molecular Complexes , TOBIAS BRIXNER, Physikalisches Institut, Universitaet Wuerzburg — Coherent two-dimensional femtosecond spectroscopy is used to investigate electronic couplings within molecular complexes. Third-order optical response functions are measured in a non-collinear three-pulse photon echo geometry with heterodyne signal detection. In combination with suitable simulations this allows recovering the delocalization of excited-state wavefunctions, their coupling, and the corresponding energy transport pathways, with nanometer spatial and femtosecond temporal resolution. Examples of multichromophoric systems are the FMO and the LH3 light-harvesting complexes from green sulfur bacteria and purple bacteria, respectively, for which energy transfer processes have been determined. Additional challenges arise if one is interested in the spectroscopy of photochemical rather than photophysical processes in molecular complexes: The product yields attained by a single femtosecond laser pulse are often very small, and hence time-dependent signals are hard to measure with good signal-to-noise ratio. In the context of coherent control, this implies that bond-breaking photochemistry in liquids is still difficult despite the many successes of optimal control in gas-phase photodissociation. In a novel accumulative scheme, macroscopic amounts of stable photoproducts are generated in an optimal fashion and with high product detection sensitivity. In connection with time-resolved spectroscopy, the accumulative scheme furthermore provides kinetic information on the pathways of low-efficiency chemical reaction channels. This was applied to investigate the photoconversion of green fluorescent protein.

8:36AM N26.00002 Watching the electronic motions driven by a conical intersection , DAVID JONAS, University of Colorado at Boulder — In chemistry, the fastest electronic rearrangements proceed through “conical intersections” between electronic potential energy surfaces. With suﬃciently short pulses, the electronic motion can be isolated by polarized excitation of aligned electronic wavepackets at a conical intersection. Polarized femtosecond probing reveals signatures of electronic wavepacket motion (due to the energy gaps) and of electron transfer between orbitals (due to the couplings) driven by the conical intersection. After exciting a D4h symmetry silicon naphthalocyanine molecule onto a Jahn-Teller conical intersection in the ﬁrst excited state, electronic motions cause a ∼100 fs drop in the pump-probe polarization anisotropy. The polarized vibrational modulations of the signal can be used to deduce the symmetry and stabilization energies for each vibration. The initial decay of the polarization anisotropy can be quantitatively predicted from these vibrational parameters. Both coupling and energy gap variations are important on the ∼100 fs timescale. A 1 meV stabilization drives electrons from orbital to orbital in 100 fs, and the theory indicates that a chemically reactive conical intersection with 1000x greater stabilization energy could cause electronic equilibration within 2 fs. We have recently carried out experiments on a nominally D2h symmetry free-base naphthalocyanine for which the splitting between x and y polarized transitions is not resolved in the linear spectrum. For this molecule, the anisotropy also decays on a similar timescale and exhibits damped modulations whose origin (vibrational or electronic) has not yet been determined. The role of the central protons and nominal D2h symmetry in the electronic dynamics will be discussed.

− − 9:12AM N26.00003 Electronic relaxation dynamics in (water)n (n=25-100) and (CH3OH)n (n ∼140-530) clusters via femtosecond photoelectron imaging , ASTER KAMMRATH, GRAHAM GRIFFIN, UC Berkeley, JAN VERLET, University of Durham, ART BRAGG, UC Los Angeles, DANIEL NEUMARK, UC Berkeley and Lawrence Berkeley National Laboratory — Large − − − clusters of (H2O)n (n=25-50), (D2O)n (n=25-100) and (CH3OH)n (n ∼140-530) are studied with femtosecond time-resolved photoelectron imaging. For all three systems, the excess electron is promoted to an excited state with a pump laser pulse at 1.55 eV. Subsequent dynamics are monitored by observing photoelectrons detached after a variable delay with a probe pulse at 3.1 eV. For all three systems the excess electron is seen to decay via internal conversion − − − back to the ground state with lifetimes of 190-130 fs for (H2O)n , 360-150 fs for (D2O)n and 260-170 fs for (CH3OH)n . For all three systems, lifetime of the excited state decreases with increasing cluster size and is found to vary linearly with 1/n. Extrapolation to the bulk yields lifetimes of 54±30 fs for H2O, 72±22 fs for D2O and ∼150 fs for CH3OH.

9:24AM N26.00004 ABSTRACT WITHDRAWN — 9:36AM N26.00005 Quantum dynamics and photochemistry of negative ions via photoelectron imaging and photofragment spectroscopy. , ANDREI SANOV, EMILY GRUMBLING, RICHARD MABBS, TEREFE HABTEYES, KOSTYA PICHUGIN, LUIS VELARDE — Photochemistry of molecular and cluster anions is studied using photoelectron imaging and photofragment spectroscopy. Photoelectron imaging is used to observe interference eﬀects in electron photoemission and monitor the transformations of the electronic structure in chemical reactions. The transformations of electronic energy levels and the corresponding wavefunctions are studied in the solvent and reaction-coordinate domains. Time-resolved results reﬂect the electron emission dynamics, establishment of the reaction product electronic identity and provide dynamical tests of the anion electronic potentials and exit-channel interactions in chemical reactions. Photofragment spectroscopy in the solvent domain reveals solvent-enabled and solvent-controlled bond dissociation and ion-molecule association reactions in anionic environments, including state-crossings and Renner-Teller interactions.

9:48AM N26.00006 Conformationally controlled chemistry: Excited state dynamics dictate ground state dissociation , ARTHUR SUITS, Wayne State Univ, MYUNG-HWA KIM, UC Santa Barbara, LEI SHEN, BAILIN ZHANG, Wayne State Univ, HONGLI TAO, TODD MARTINEZ, UIUC — Ion imaging results show distinct photodissociation dynamics for propanal cations initially prepared in either the cis- or gauche- conformation, even though these diﬀer only slightly in energy and there is a small barrier between them. The product kinetic energy distributions for the H elimination channels are bimodal, and the two peaks are readily assigned to propanoyl cation + H and hydroxyallyl cation + H. Ab initio multiple spawning dynamical calculations show that distinct ultrafast dynamics in the excited state leads to internal conversion to the ground state in isolated regions of the potential surface for the two conformers, and from these distinct regions, conformer interconversion does not eﬀectively compete with dissociation.

10:00AM N26.00007 Conformer-selected photodissociation: Ab Initio Multiple Spawning Dy- namics of Excited Propanal Cation , HONGLI TAO, Univiersity of Illinois at Urbana-Champaign, TODD MARTINEZ, University of Illinois at Urbana-Champaign — Recent experiments have shown that pure cis and gauche propanal cations can be prepared using REMPI (Resonance Enhanced Multiphoton Ionization Spectroscopy). The H elimination pathway which results when these conformer-selected cations are photoexcited was found to depend on the conformer (cis vs. gauche). This dependence is very surprising since the interconversion barrier of the two conformers is small compared to the excited energy. We use the ab initio multiple spawning (AIMS) method developed in our group to model the conformer-speciﬁc photodissociation and to elucidate its origins.

10:12AM N26.00008 A Numerical Study of Pulse-Shape Control of Non-Adiabatic Electron Excitation in the Strong-Field Regime , STANLEY SMITH, Temple Uinversity Chemistry Department, XIAOSONG LI, University of Washington Chemistry Department, ALEXEI MARKEVITCH, Temple University Chemistry Department, DMITRI ROMANOV, Temple University Physics Department, H. BERNHARD SCHLEGEL, Wayne State University Chemistry Department, ROBERT LEVIS, Temple University Chemistry Department — The electron optical response of several molecular monocations to short strong-field laser pulses was studied using time-dependent Hartree-Fock theory. In addition to the carrier frequency and maximum amplitude (up to 3.75 x 1013 W/cm2), the short pulses were characterized by pulse shape parameters: the amplitude profile (trapezoidal and gaussian) and the carrier phase shift. The electron response was traced by the evolution of the excited states occupation numbers and by the instantaneous dipole moment of the molecule. In the molecular monocations studied, butadiene, naphthalene, and anthracene, we observed significant modifications in the dipole moment response and in the corresponding excited state spectra, controlled by intensity, frequency, phase, and shape of the laser pulse.

10:24AM N26.00009 Adaptive Control Goal Selection for Strong-Field Dissociative Ionization of Polyatomic Molecules , DMITRI ROMANOV (1,3), HUYEN TRAN (2,3), ROBERT LEVIS (2,3), (1) Department of Physics, (2) Department of Chemistry, and (3) Center for Advanced Photonics Research, Temple University, Philadelphia PA — In many settings (for instance, in strong-field mass- spectral sensing technologies) improving control efficiency is more important than achieving specific control goals. In this case, control goals may be adaptively formulated in the process of a strong-field experiment. To determine the pairs of fragment ions in a mass spectrum that are most susceptible to control by adaptive optimization of the laser pulse shapes in the strong-field regime, a statistical method is proposed that is based on covariance analysis of the mass spectral fragmentation patterns generated by a set of random shaped pulses. As a test, the method was applied to fragmentation of a large organic molecule dimethylmethylphosphonate, (CH3O)-PO-(OCH3)-(CH3). All possible pairs of the ionized fragments in tof mass spectrum were ranked by the value of their correlation coefficients ranging from +1 to –1. A genetic-algorithm based adaptive control was then used to optimize the ion peak ratios in these pairs. Convincingly, the pairs of fragment ions that have higher negative covariances possess a correspondingly higher degree of controllability, while the pairs that have higher positive covariances possess correspondingly lower controllability.

10:36AM N26.00010 Probing Strong-Field Electron-Nuclear Dynamics of Polyatomic Mole- cules Using Proton Motion , ROBERT LEVIS (1,3), ALEXEI MARKEVITCH (1,3), DMITRI ROMANOV (2,3)1, STANLEY SMITH (1,3), (1) Department of Chemistry, (2) Department of Physics, and (3) Center for Advanced Photonics Research, Temple University, Philadelphia, PA 19122 USA — Protons ejected from a large polyatomic molecule during its Coulomb explosion can carry information about the dynamics of explosion and pre-explosion processes related to specific molecular structure. To extract this information, the proton kinetic energy distributions were derived from the shape or the time-of-flight proton peak for three structure-related molecules, anthracene, octohydroanthracene, and anthraquinone, subjected to intense 800 nm, 60 fs laser pulses. The kinetic energy distributions are found to be markedly molecular-specific, providing insight into similarities and differences in the nonadiabatic electron-nuclear dynamics in these molecules during the laser pulse. In particular, analysis of the proton energy distributions reveals molecular specificity of non-adiabatic charge localization and field-mediated restructuring of polyatomic molecules polarized by strong laser fields.

[email protected]

10:48AM N26.00011 Toward Coherent Control of Cis-Stilbene Photodynamics , JASON QUENNEVILLE, Los Alamos National Laboratory, TODD J. MARTINEZ, University of Illinois at Urbana-Champaign — Stilbene can undergo photoisomerization between its cis and trans isomers. Non-radiative quenching of excited state population to the ground state can occur at a twisted and pyramidalized conical intersection of S0 and S1 that is remarkably similar to that found for ethylene. In addition, photo-excited cis-stilbene can undergo a cyclization reaction giving 4a,4b- dihydrophenanthrene. Here, population decay occurs through a conical intersection in the cis-stilbene configuration. Both competing reaction pathways give appreciable reactant recovery. The product branching ratios can be directly related to the location of the conical intersections in nuclear coordinate space and also, more specifically, to the wavepacket dynamics in the nonadiabatic region. A significant effort is currently underway at Los Alamos to achieve coherent control of photo-excited cis-stilbene. The goal will be to design a shaped femtosecond laser pulse that will control photo-product yield. More importantly, we hope to gain an understanding of the important features of the optimized electric field and thus insight into the prospects for more complicated materials. We will detail the potential surfaces of photo-excited cis-stilbene, the initial S1 dynamics, as well as opportunities for quantum control. Wednesday, March 7, 2007 8:00AM - 10:48AM — Session N35 DBP DCP: Focus Session: Time Resolved Structural Investigations on Protein Folding and Function Colorado Convention Center 405

8:00AM N35.00001 Correlating folding and signaling in a photoreceptor by single molecule measurements and energy landscape calculations1 , WOUTER HOFF, Dept of Microbiology and Molecular Genetics, Oklahoma State University — Receptor activation is a fundamental process in biological signaling. We study the structural changes during activation of photoactive yellow protein (PYP). This is triggered by photoisomerization of the p-coumaric acid (pCA) chromophore of PYP, which converts the initial pG state into the activated pB state. Mechanical unfolding of Cys-linked PYP multimers probed by atomic force microscopy (AFM) in the presence and absence of illumination reveals that the core of the protein is extended by 3 nm and destabilized by 30 percent in pB. These results establish a generally applicable single molecule approach for mapping functional conformational changes to selected regions of a protein and indicate that stimulus-induced partial protein unfolding can be employed as a signaling mechanism. Comparative measurements, Jarzynski-Hummer-Szabo analysis of the data, and steered MD simulations of two double-Cys PYP mutants reveal strong anisotropy in the unfolding mechanism along the two axes defined by the Cys residues. Unfolding along one axis exhibits a transition-state-like feature where six hydrogen bonds break simultaneously. The other axis displays an unpeaked force profile reflecting a non-cooperative transition, challenging the notion that cooperative unfolding is a universal feature in protein stability. MD simulations with a coarse-grained protein model show that the folding of pG is two-state, consistent with experimental observations. In contrast, the folding free energy surface of a coarse-grained model of pB involves an on-pathway partially unfolded intermediate that closely matches experimental data. The results reveal that interactions between the pCA and its binding pocket can switch the energy landscape for PYP from two- to three-state folding, and show how this can be exploited to trigger large functionally important protein conformational changes.

1WDH is supported by NIH grant MG063805

8:36AM N35.00002 Spectroscopic probes of enzyme-ligand interaction dynamics1 , CHRISTOPHER CHEATUM, JIGAR BANDARIA, SAMRAT DUTTA, SARAH HILL, AMNON KOHEN, University of Iowa, Department of Chemistry — Formate dehydrogenase catalyzes the NAD-dependent oxidation of formate to carbon dioxide. The intrinsic chemical step involves hydride transfer from formate to the nicotinamide ring of NAD. As with several other NAD-dependent dehydrogenases, kinetic measurements suggest that thermal fluctuations of the enzyme are important in the hydride-transfer reaction. We have measured the dynamics of enzyme-inhibitor interactions in binary and ternary complexes of formate dehydrogenase with pseudohalides using infrared photon-echo spectroscopy. The pseudohalides are excellent vibrational chromophores that are known to be sensitive reporters of interactions with their local environments. They are also excellent inhibitors for formate dehydrogenase. Our measurements reveal significant differences in the dynamics of the different binary and ternary complexes. By comparing and contrasting the dynamics for different complexes we gain insight into the active-site components that make the most important contributions to the observed dynamics.

1Supported by the Roy J. Carver Charitable Trust

8:48AM N35.00003 Shallow Free Energy Landscapes Remodelled by Ligand Binding1 , TROY MESSINA, DAVID TALAGA, EMILIO GALLICHIO, RONALD LEVY, Rutgers University, Department of Chemistry and Chemical Biology — Glucose/galactose binding protein (GGBP) functions as part of a larger system of proteins for molecular recognition and signalling in enteric bacteria. Here we report on the thermodynamics of conformational equilibrium distributions of GGBP from both time-resolved fluorescence experiments and computational umbrella sampling molecular dynamics analyzed by the weighted histogram analysis method (WHAM). Three conformations appear at zero glucose concentration and systematically transition to three conformations at high glucose concentration. Fluorescence anisotropy correlations, fluorescent lifetimes, thermodynamics, computational structure minimization and molecular dynamics, and previous work were used to identify the three components as open, closed, and twisted conformations of the protein. The existence of three states at all glucose concentrations indicates that the protein continuously fluctuates about its conformational state space via thermodynamically driven state transitions, and the glucose biases the populations by reorganizing the free energy profile. These results and their implications are discussed in terms specific and non-specific interactions GGBP has with cytoplasmic membrane proteins.

1supported by NIH Ruth L. Kirschstein NRSA Post Doctoral Fellowship F32GM072328

9:00AM N35.00004 High-throughput biophysics of functional tuning in photoactive yellow protein1 , WOUTER HOFF, Dept of Microbiology and Molecular Genetics, Oklahoma State University, ANDREW PHILIP, GEORGE PAPADANTONAKIS, Dept of Biochemistry and Molecular Biology, University of Chicago, OSU TEAM, UOFC TEAM — The relationship between the structure of a protein and its function is a central unresolved problem in biology. We use photoactive yellow protein (PYP) to develop quantitative high-throughput methods to study this problem. PYP is a small bacterial photoreceptor with rhodopsin-like photochemistry based on its p-coumaric acid (pCA) chromophore. The absorbance maximum and pKa of the pCA in the active site of native PYP are shifted from 400 nm and 9.0 in water to 446 nm and 2.8 in the protein. Thus, PYP offers a unique model system to probe protein-ligand interactions. Here we show that high-throughput microscale methods can be used for quantitative biophysical studies of the absorbance spectrum PYP, its fluorescence quantum yield, apparent pKa of the pCA, protein stability against chemical denaturation, and kinetics of the last PYP photocycle step. A wide range of properties was observed among the mutants, and structural features that tune functional properties were identified. These results open the way for high-throughput quantitative biophysical studies of PYP.

1WDH is supported by NIH grant MG063805

9:12AM N35.00005 Probing protein dynamics using Fluorescence Resonance Energy Transfer with donors of different lifetimes , WEIQUN PENG, George Washington University, TANIA CHAKRABARTY, University of Chicago, PAUL GOLDBART, University of Illinois at Urbana Champaign, PAUL SELVIN, University of Illinois at Urbana Champaign — Fluorescence resonance energy transfer (FRET), using nanosecond dyes, and its derivative, Lanthanide-based resonance energy transfer (LRET), using millisecond-lifetime lanthanide chelates, are methods to measure distances on the 2-10 nm length-scale. It has been found that in certain systems energy transfer efficiency E for FRET and LRET measurements can be dramatically different [Chakrabarty et al., PNAS, 99: 6011-6016 (2002)]. Here we develop a theoretical model that shows that the dramatic difference can be explained by the presence of intrinsic dynamics of the system. Furthermore, we quantitatively investigate how information about the time-scale and distance-scale associated with the intrinsic dynamics can be inferred, by comparison of FRET and LRET results. 9:24AM N35.00006 Advanced Infrared Spectroscopy for Time-Resolved Structural Investiga- tion of Protein Structure and Function1 , AIHUA XIE, Department of Physics, Oklahoma State University — The human genome encodes approximately 30,000 different proteins. A single mutation at a critical site of one protein can cause serious diseases, such as cardiac failure and cancer. This illustrates the significant role of protein structures in protein functions. In order to obtain a fundamental understanding of protein structure-function relation, we must develop and employ both physical theories and experimental techniques. In my talk, I will report both experimental and computational studies on vibrational structural markers for advanced infrared spectroscopy, slaved protein structural dynamics, and “electrostatic epicenter” model as a general mechanism for activation of receptor proteins in cell signaling.

1In collaboration with Anupama Thubagere, Lorand Kelemen, Beining Nie, Sandip Kaledhonkar, and Edward Manda, Oklahoma State University.

10:00AM N35.00007 Channel noise reduction due to gating charge effects , GERHARD SCHMID, IGOR GOYCHUK, PETER HANGGI,¨ University of Augsburg, Germany — We investigate the influence of gating charge effects on the channel noise-induced spontaneous spiking activity of excitable membrane patches [1] within a stochastic Hodgkin-Huxley model [2]. The random switching of the channel gates between an open and a closed configuration is always connected with movement of gating charge within the cell membrane. At the beginning of an action potential the gating current is opposite to the direction of the ion current through the membrane. Therefore, the excitability is expected to become reduced due to the influence of gating current. Our study revealed that while the deterministic modelling with gating charge effects does not differ dramatically from the original Hodgkin-Huxley model for the standard set of parameters, the corresponding stochastic model which takes into account the channel noise – i.e. the fluctuations of the number of open ion channels – does behave very differently for intermediate-to-large membrane patch sizes. A main finding is that spontaneous spiking activity becomes drastically reduced [1]. [1] G. Schmid, I. Goychuk, and P. Hänggi, Phys. Biol., in press (2006); (arXiv:abs/q-bio.NC/0611040). [2] G. Schmid, I. Goychuk, and P. Hänggi, Europhys. Lett. 56, 22 (2001)

10:12AM N35.00008 A Molecular Dynamics-Decorated Finite Element Method (MDeFEM) Framework for Simulating the Gating of Mechanosensitive Channels , XI CHEN, YUYE TANG, GUOXIN CAO, JEJOONG YOO, ARUN YETHIRAJ, QIANG CUI, Columbia University — The gating pathways of mechanosensitive channels of large conductance (MscL) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness. The interactions between various continuum components are derived from atomistic energy calculations. The structural variations along the gating pathway are consistent with previous analyses based on structural models and biased molecular-dynamics simulations. Upon membrane bending, there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation. Compared to popular all-atom simulations, the MDeFEM framework offers a unique alternative to bridge detailed intermolecular interactions and biological processes occurring at large spatial and timescales. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction.

10:24AM N35.00009 Develop vibrational structural makers for probing the protonation state and hydrogen bonding interactions of tyrosine in proteins and their functional intermediates , AIHUA XIE, BEINING NIE, EDWARD MANDA, ANUPAMA THUBAGERE, Oklahoma State University — Proteins are dynamic in nature. In order to understand how a protein performs its function based on laws of physics, it is critical to probe and investigate functionally important structural transitions of the protein. Time-resolved infrared spectroscopy oﬀers excellent time resolution (picoseconds to seconds), and contains extensive structural information. The real challenge is how to extract structural information from time-resolved infrared data. We will report computational methods for developing vibrational structural markers of tyrosine. Using density function theory (DFT) based ﬁrst principle computational studies combined with experimental data, we found that it is possible to unambiguously determine if the phenolic ring in Tyrosine is neutral or negatively charged based on the frequency of one ring vibrational mode. In addition, we show that it possible to determine the number and nature of hydrogen bonding interactions of a phenolic group in proteins using a combination of C-O stretching and O-H stretching frequencies (2D vibrational spectroscopy).

10:36AM N35.00010 Correlated Fluorescence Parameters of Single Molecules , CLAUDIU GRADINARU, University of Toronto, DAVID CHANDLER, CARL HAYDEN, Sandia National Labs — A novel detection system is used in a confocal optical microscope for measuring correlated fluorescence lifetimes and spectra. Fluorescence photons emitted from a sample are imaged through a dispersive optical system onto a time- and position-sensitive detector. For each photon the apparatus records the wavelength, the emission time relative to the laser excitation pulse and the absolute detection time, so that correlations among all the fluorescence properties are maintained. A histogram over many photons can generate a full fluorescence spectrum and a correlated decay plot at every pixel in a fluorescence image. The complex data structure allows mapping the time-dependent distribution of multiple fluorescent species in a sample and enables monitoring the dynamics of single molecules on a time scale that spans from picoseconds to minutes. Unique correlations between intensity, spectrum and lifetime prove useful for tracking changes in the nanoenvironment of fluorescent probes. The detection method also provides a more complete description of the fluorescence resonance energy transfer (FRET) than conventional microscopy techniques, as demonstrated by single-pair FRET experiments between dyes spaced apart by short peptides and by dsDNA chains.

Wednesday, March 7, 2007 11:15AM - 2:15PM — Session P18 DCP: Condensed Phase Dynamics, Structure and Thermodynamics Colorado Convention Center 103

11:15AM P18.00001 First-principles study of molecular point defects in ice Ih , MAURICE DE KONING, ALEX ANTONELLI, Universidade Estadual de Campinas, ANTONIO J.R. DA SILVA, ADALBERTO FAZZIO, Universidade de Sao Paulo — We present a first-principles study of the structure and energetics of molecular point defects in ice Ih [1]. Our approach is based on a DFT-GGA description, utilizing a periodic supercell containing 96 water molecules. We compute the formation free energies and corresponding thermal equilibrium concentrations as a function of temperature for the molecular vacancy and 3 different interstitial structures: the Tc, Tu and Bc configurations. The latter involves bonding to the surrounding lattice, whereas the first two do not. The results indicate that, due to its bonding to the surrounding lattice, the equilibrium concentration of the Bc interstitial is larger than that of the Tc and Tu structures, suggesting that the Bc structure is the preferred interstitial configuration in ice Ih. Comparison with the molecular vacancy, on the other hand, indicates that the vacancy is expected to be the overall dominant molecular point defect in ice Ih, at least for temperatures below T ≈ 200 K. Due to the elevated formation entropy of the Bc interstitial, however, a crossover scenario in which the Bc interstitial becomes favored at temperatures below the melting point, as has been suggested experimentally, is conceivable. [1] M. de Koning, A. Antonelli, A.J.R. da Silva and A. Fazzio, Phys. Rev. Lett. 97, 155501 (2006). 11:27AM P18.00002 Size- and Temperature- Dependent Crystal Growth Rates , XIAN-MING BAI, MO LI, Georgia Institute of Technology — Using molecular dynamics simulations and a crystal/melt coexistence model, we have calculated the size-dependent crystal growth rates of a Lennard-Jones system over a wide range of undercooling temperatures. Our results show that the growth rate or interface moving velocity decreases substantially with the increasing system size. It is found that the system fluctuations are related to the finite-size effects. By treating the atomic site acceptance ratio as a function of temperature and system size rather than a constant, we modified the collision-controlled model which fits the simulation results well.

11:39AM P18.00003 ESR Studies of a Reorienting Nickel Complex , BRUCE KOWERT, St. Louis University — Electron spin resonance spectra of the planar bis(maleonitriledithiolato)nickel anion radical (BMNT) in the intermediate motional region have been simulated in several polar solvents using axially symmetric reorientation. The rotational diffusion about the long in-plane axis is three to four times faster than that about the two axes perpendicular to it. The reorientational model needed to produce agreement with experiment is either in or close to the Brownian rotational diffusion limit. The solvents are 4-allyl-2-methoxyphenol (eugenol), dimethyl phthalate, tri-n-butyl phosphate, tris(2-ethyl-hexyl)phosphate, and 2-methoxyethyl ether (diglyme), ethyl alcohol, and a dimethylformamide-chloroform mixed solvent. The reorientational rates from the simulations are in general agreement with those from line width analyses carried out from the fast to the slow motional regions. The temperature dependence of the diffusion rates is discussed in terms of the Stokes-Einstein-Debye (SED) model and the Vogel-Tammann-Fulcher equation.

TM 11:51AM P18.00004 Low coverage Neon adsorption on HiPCo nanotube bundles1 , SUBRA- MANIAN RAMACHANDRAN, OSCAR VILCHES, University of Washington, Dept of Physics, Seattle — We present heat capacity measurements of Ne adsorbed on single-walled closed-end carbon nanotube bundles (HiPCoTM ) between 2 and 20 K. Limited adsorption isotherms measurements for 17K

1This research is supported by NSF DMR 0606078.

12:03PM P18.00005 Structure and dynamics of levitated liquid aluminates , LOUIS HENNET, IRINA POZDNYAKOVA, CRMHT, 1d avenue de la Recherche Scientifique, 45071 Orléans,France, MARIE-LOUISE SABOUNGI, CRMD, 1b rue de la Férollerie, 45071 Orléans, France, DAVID L. PRICE, CRMHT, 1d avenue de la Recherche Scientifique, 45071 Orléans, France — We have used the aerodynamic levitation technique combined with CO2 laser heating to study the structures of liquid CaAl2O4 and MgAl2O4 with x-ray and neutron diffraction. We determined the structure factors and corresponding pair correlation functions describing the short-range order in the liquids. The combination of the two scattering techniques makes it possible to derive information not accessible with a single measurement. We have also obtained information on the dynamics of liquid MgAl2O4 with inelastic x-ray scattering.

12:15PM P18.00006 Thermal Fluctuations and Excitonic Interactions in Polyadenosine , JOHN JEAN, Regis University — Interest in the electronic structure and photophysics of DNA has been sparked in recent years by increased awareness of the biological effects of non–ionizing UV radiation as well as the possibility of using short DNA oligomers as molecular conduits for efficient charge or energy transport in nanoscale devices. The optical properties of DNA in the near UV region are governed by dipole-allowed transitions localized on the aromatic bases, which have excited state lifetimes on the order of a few hundred femtoseconds. Recent time-resolved experiments on polyadenosine oligomers, however, provide clear evidence for stacking-induced long-lived, stacking-induced states and spectral shifts compared to those of the monomer bases. The origin of these states and their relation to stacking dynamics is still largely unknown. DNA is a highly dynamic structure undergoing large-amplitude structural fluctuations on timescales spanning many orders of magnitude and spatial correlation lengths, thus characterization of the excitonic states requires understanding how nearest-neighbor Coulombic and exchange interactions couple to picosecond motions of the bases. In this paper, we present results from hybrid QM/MD simulations of polyadenosine in solution that provide detailed insight into the time-dependent stacking interactions in these systems and the effects of dynamic disorder on the temporal and spatial properties of the low-lying excitons.

12:27PM P18.00007 The activation of phosphoramide mustard anticancer drugs from ab initio simulations. , MARKUS ALLESCH, Graz University of Technology, Austria, and Lawrence Livermore National Laboratory, ERIC SCHWEGLER, Lawrence Livermore National Laboratory, MIKE COLVIN, University of California, Merced, FRANCOIS GYGI, GIULIA GALLI, Lawrence Livermore National Laboratory and University of California, Davis — The nitrogen mustard based DNA alkylating agents were the first nonhormonal drugs to be used effectively in the treatment of cancer and remain one of the most important drugs for the chemotherapeutic management of many common malignancies today. An understanding of the activation of these compounds is, in itself, of scientific interest, but also critical in designing improved analogs of greater selectivity and efficacy. We have investigated the activation pathways of one of the most active metabolites, phosphoramide mustard (PM), and its methylated ester (PMME). In particular, we have examined the activation barrier and reaction free energy for the intramolecular cyclization reaction using first principles molecular dynamics simulations with explicit and continuum solvation models. Structural, dynamical and electronic properties along the reaction path have been computed mainly to address the question why de-esterification is required to activate these drugs. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48.

12:39PM P18.00008 Use of light scattering data to determine free energies of ternary mixtures , GEORGE THURSTON, DAVID ROSS, CARL LUTZER, Rochester Institute of Technology, SETH FRADEN, Brandeis University — We demonstrate a method that uses light scattering data to determine the free energy of ternary liquid mixtures, through solving a second-order nonlinear partial differential equation appropriate for single isotropic phases. We show that forward light scattering efficiency data, together with boundary condition data, permit integration of the second derivative of the intensive free energy along curves tangent to the local dielectric coefficient gradient vector. With suitable information about phase boundaries the method also accommodates the presence of phase-separated regions next to single-phase regions in which the governing equation is an appropriate model. In the presence of composition-dependent optical dielectric dispersion, light scattering at more than one wavelength can help augment and check such free energy determination. In summary, light scattering provides a non-invasive method of determining ternary liquid mixture free energies without adopting specific free energy models in advance. 12:51PM P18.00009 Proton momentum distributions in water: A path integral molecular dynamics study , VARADHARAJAN SRINIVASAN, JOSEPH A. MORRONE, Dept. of Chemistry, Princeton University, Washington Road, NJ 08544, DANIEL SEBASTIANI, Dept. of Spectroscopy, Max-Planck-Institut fuer Polymerforschung, ROBERTO CAR, Dept. of Chemistry/ PRISM, Princeton University — Recent neutron Compton scattering experiments have detected the proton momentum distributions of water. This density in momentum space is a quantum mechanical property of the proton, due to the confining anharmonic potential from covalent and hydrogen bonds. The theoretical calculation of this property can be carried out via “open” path integral expressions. In this work, we present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize the SPC/F2 empirical force field to model the system’s interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.

1:03PM P18.00010 Calculation of Proton Transfer Rates in Liquids Using Molecular Dynamics Simulations , YIN GUO, Department of Physics, Oklahoma State University — We have been investigating a computational method that incorporates WKB tunneling calculations within the framework of classical molecular dynamics (MD) simulations. The computational cost is at the same level as the usual MD simulation, thus providing a practical and efficient dynamical approach for treating quantum tunneling. Building upon the earlier gas-phase studies, we extend the method to condensed phase materials. As a test case, the method is applied to a model system that represents proton transfer AH–B↔A−–H+B in liquid methyl chloride, where AH–B is a linear complex with parameters chosen to model a typical phenol-amine complex. The calculated results are compared with those of earlier studies on the same system by Azzouz and Borgis and by Hammes-Schiffer and Tully using different methods.

1:15PM P18.00011 Local structure and the intermediate-energy fine structure in x-ray Raman scattering from ice Ih , G.T. SEIDLER, T.T. FISTER, C. HAMNER, F.D. VILA, University of Washington, J.O. CROSS, Advanced Photon Source, Argonne National Laboratory — The structure of the various different equilibrium and nonequilibrium phases of water ice is a topic of considerable interest, with strong relevance for geophysics, atmospheric sciences, and space sciences. Recent advances in non-resonant x-ray Raman scattering (XRS) provide a new method for studying local structure of water ices in extreme environments including especially in high-pressure cells. Here, we investigate two pragmatic issues: the optimum choice of momentum transfer q for these measurements and the usefulness of the intermediate-energy fine structure as a strong fingerprint of local atomic structure out to several coordination shells. To this end, we present new XRS measurements of ice Ih with greatly improved statistics over earlier work, and also present extensive full-multiple calculations of the dependence of the intermediate-energy fine structure on local structure. We find that XRS measurements at high q, where the XRS cross-section is largest but where multipole transitions can be important, show little difference from dipole-limited soft x-ray absorption studies. In addition, our calculations predict significant sensitivity of the XRS intermediate-energy fine structure to different ice structures.

1:27PM P18.00012 Covalency in Actinide and Lanthanide Hexachloride Anions , PING YANG, ENRIQUE BATISTA, RICHARD MARTIN, Los Alamos National Laboratory, CHRISTIN CARLSON, DAVID CLARK, STEVEN CONRADSON, DANIEL SCHWARZ, MARINNE WILKERSON, Seaborg Institute, Los Alamos National Laboratory — Whether actinide atoms form covalent or ionic bonds is still a matter of debate after many years of study and it remains a challenge for experimentalists and theoreticians. From the experimental side, synchrotron-based ligand K-edge X-ray absorption spectroscopy appears as a promising technique for probing this issue. From the theoretical perspective, quantum chemical simulations should be able to add on a ﬁrst principle understanding. To tackle this problem, we have applied these techniques on a series of octahedral uranium and lanthanide chloride n− salts, MCl6 (M= U, Ce, Pr) in various oxidation states (n=1, 2, 3). We will show hybrid density functional theory calculations that give evidence of the covalent nature of the M-Cl bond in a quantitative manner. This covalency was found to increase for higher oxidation states.

1:39PM P18.00013 Site Sensitivity and local electronic symmetries in carboranes , T.T. FISTER, G.T. SEIDLER, F.D. VILA, University of Washington, J.O. CROSS, Advanced Photon Source, Argonne National Laboratory, J.C. LINEHAN, Pacific Northwest National Laboratory — Icosohedral carboranes containing ten boron and two carbon atoms are seeing renewed interest because of their potential use in new cancer and AIDS therapies. These molecules have flexible geometries which allow bonding to three types of carbon sites (e.g. ortho-, para-, and meta- configurations). Using a new multielement spectrometer, we present the first x-ray Raman scattering (XRS) study on each isomer with excited state spectra taken from the both the carbon and boron 1s states. The change in the electronic structure between the isomers is most pronounced in the carbon spectrum, where the position in the edge confirms prior density functional theory calculations. With the boron spectra, we used the unique momentum transfer dependence of XRS to extract the symmetry components of the density of unoccupied states, i.e. the l-DOS. These results give an improved picture of the local electronic properties of the carboranes.

1:51PM P18.00014 The electronic structure of Co and Ni tetraazaannulenes , JING LIU, JIE XIAO, P. JEPPSON, P.A. DOWBEN, Department of Physics and Astronomy, University of Nebraska-Lincoln, SEOK-BONG CHOI, L. JARABEK, A.N. CARUSO, Center for Nanoscale Science and Engineering, North Dakota State University, YA.B. LOSOVYJ, Center for Advanced Microstructures and Devices, Louisiana State University — We compare two metal centered tetraazaannulene (TMTAA) macrocyclic complex molecules: 5,7,12,14- tetramethyl -2,3:9,10- dibenzo [b,i] -1,4,8,11- tetraazacyclotetradecine nickel (II) and 5,7,12,14- tetramethyl -2,3:9,10- dibenzo [b,i] -1,4,8,11- tetraazacyclotetradecine cobalt (II). The highest occupied molecular orbital to the lowest unoccupied molecular orbital gap, obtained from combined ultraviolet photoemission and inverse photoemission studies, is close to the expected value of 6.6 eV expected from simple model calculations. While both the Co(II) (s=1/2) and Ni(II) (s=0) tetramethyldibenzo- tetraazaannulene molecular electronic structures are very similar, the Ni(II) adopts a high symmetry molecular conﬁguration upon adsorption, with a strong preferential orientation. The role of an unpaired electron upon molecular symmetry and stability is discussed.

2:03PM P18.00015 Pump-Probe Photoionization Spectroscopy of penta methyl cyclopentadiene , PETER WEBER, FEDOR RUDAKOV, Brown University — The ultrafast curve crossing from the excited electronic state to the ground state in cyclic dienes often proceeds via conical intersections. Time-resolved experiments were performed by exciting the ﬁrst excited state of pentamethylcyclopentadiene, as well as other methylated cyclopentadiene derivatives, with femtosecond pulses at 260 nm. Photoionization with a time-delayed probe pulse yields delay-time dependent mass and photoelectron spectra that reveal the ultrafast character of the curve crossing dynamics.

Wednesday, March 7, 2007 11:15AM - 2:15PM — Session P19 DCP DCOMP: Focus Session: Frontiers in Electronic Structure Theory IV Colorado Convention Center 104 11:15AM P19.00001 Ab-initio DMRG and Canonical Transformation Theories of Electronic Structure , GARNET CHAN, Cornell University — I will talk about two complementary methods that are under development in our group: (1) Ab-initio Density Matrix Renormalization Group: The Density Matrix Renormalization Group (DMRG) is a natural multireference method. Recently, we have implemented a quadratic-scaling DMRG algorithm which opens up the description of multireference (strongly interacting) correlation in large quasi-one-dimensional systems [1]. I will report calculations using this technique on conjugated oligomers correlating exactly, in the sense of Full-CI, complete pi-active spaces with up to 100 electrons in 100 orbitals (100, 100). (2) Canonical Transformation Theory: We have been developing a canonical transformation method to incorporate dynamical correlation on top of a multireference starting point. Our theory, termed Canonical Transformation Theory (CT) [2] is based on an exponential ansatz and is size-consistent. It retains the accuracy of coupled cluster theory at equilibrium bond geometries, but extends this accuracy to the full potential energy surface. The cost of the calculation is the same as for single-reference coupled cluster theory. I will report calculations using this technique for bond-breaking and excited states. I will also describe our recent eﬀorts in developing a reduced-scaling version of the theory for large molecules. [1] J. Chem. Phys. 125, 144101 (2006) [2] J. Chem. Phys. 124, 194106 (2006)

11:51AM P19.00002 Real-time ab initio simulations of excited-state dynamics in nanostructures1 , DAVID TOMANEK, Michigan State University — Combining time-dependent ab initio density functional calculations for electrons with molecular dynamics simulations for ions, we investigate the effect of excited-state dynamics in nanostructures. In carbon nanotubes, we find electronic excitations to last for a large fraction of a picosecond.2 The de-excitation process is dominated by coupling to other electronic degrees of freedom during the first few hundred femtoseconds. Later, the de-excitation process becomes dominated by coupling to ionic motion. The onset point and damping rate in that regime change with initial ion velocities, a manifestation of temperature dependent electron-phonon coupling. Considering the fact that the force field in the electronically excited state differs significantly from the ground state, as reflected in the Franck-Condon effect, atomic bonds can easily be broken or restored during the relatively long lifetime of electronic excitations. This effect can be utilized in a “photo-surgery” of nanotubes, causing structural self-healing at vacancy sites3 or selective de-oxidation processes induced by photo-absorption.4 Also, electronic excitations are a key ingredient for the understanding of sputtering processes in nanostructures, induced by energetic collisions with ions.5

1In collaboration with Yoshiyuki Miyamoto, Angel Rubio, and Arkady Krasheninnikov. Supported by NSF NSEC grant EEC-425826 and NSF NIRT grant ECS-0506309. 2Yoshiyuki Miyamoto, Angel Rubio, and David Tomanek, Phys. Rev. Lett. 97, 126104 (2006). 3Yoshiyuki Miyamoto, Savas Berber, Mina Yoon, Angel Rubio, and David Tomanek, Chem. Phys. Lett. 392, 209 (2004). 4Yoshiyuki Miyamoto, Noboru Jinbo, Hisashi Nakamura, Angel Rubio, and David Tomanek, Phys. Rev. B 70, 233408 (2004). 5Yoshiyuki Miyamoto, Arkady Krasheninnikov, and David Tomanek (in preparation).

12:27PM P19.00003 First principles spectroscopy of confined water. , MANU SHARMA, GIULIA GALLI, Department of Chemistry, University of California, Davis — In order to characterize the changes in hydrogen bonding in water confined at the nanoscale, and to understand the effect of the interface between water and the confining medium, we carried out a spectroscopic investigation using first principles calculations. In particular, we computed the infrared (IR) spectrum of liquid water confined between two sheets of graphite. While the far IR region of the spectrum contains features characterizing the H-bond dynamics in water, we find a significant overlap of this region with the vibrational modes of graphite. We also find modes in the near IR region ∼2500 cm−1, associated to the OH stretching mode, which while present in the kinematical (power) spectrum are absent from the computed IR spectrum. We demonstrate that these modes arise due to a dynamical charge transfer between water molecules and the p – orbitals of the graphite surface.

12:39PM P19.00004 Quadratic Scaling Local Canonical Transformation Method. , DEBASHREE GHOSH, TAKESHI YANAI, GARNET KIN-LIC CHAN, Cornell University — Canonical transformation theory [1] can be used to describe the detailed dynamic correlation in bonding situations where there is signiﬁcant non-dynamic, i.e. multireference character. This theory uses an exponential ansatz and is size- consistent. The computational cost of this method scales as N6 which is about the same as in a single reference coupled cluster theory. We have devised a local Canonical transformation method for large systems. For large systems, we have been able to obtain quadratic scaling with the size of the system. Reduced and linear scaling algorithms for methods like MP2 and coupled cluster are well known. However, all these reduced scaling algorithms have been primarily developed for single reference correlation calculations. By combining the local canonical transformation method with, e.g. the quadratic scaling ab-initio Density Matrix Renormalization Group theory, we can now obtain a reduced-scaling description of dynamical and non-dynamical correlation in large multireference problems. [1] Takeshi Yanai, Garnet K.L. Chan, J. Chem. Phys. 124, 194106, 2006.

12:51PM P19.00005 Representing molecules as atomic-scale electrical circuits with fluctuating- charge models , JIAHAO CHEN, TODD MARTÍNEZ, University of Illinois at Urbana-Champaign — Fluctuating-charge models (FCMs), also known as chemical potential equilibration models, can describe charge transfer in molecular mechanics (MM). Examples of FCMs are QEq [1], fluc-q (FQ) [2], and our recently proposed PE-CC-QVB2 [3] and QTPIE [4]. FCMs describe the accumulation and depletion of atomic charges with electronegativities and chemical hardnesses. We show that this description of atoms maps molecular systems onto electrical circuits. Unlike other models [1, 2], our models correctly model a diatomic molecule in the dissociation limit; we explain how this is reflected in its circuit representation. FCMs hence establish a new connection between the statistical mechanics of molecular electronic structure [5] and classical circuit theory. [1] A. K. Rappe, and W. A. Goddard III, J. Phys. Chem. 95, 3358 (1991). [2] S. W. Rick, S. J. Stuart, and B. J. Berne, J. Chem. Phys. 101, 6141 (1994). [3] J. Morales, and T. J. Mart´ınez, J. Phys. Chem. 108A, 3076 (2004). [4] J. Chen, and T. J. Mart´ınez, Chem. Phys. Lett. submitted (2006). [5] J. Morales, and T. J. Mart´ınez, J. Phys. Chem. 105A, 2842 (2001).

1:03PM P19.00006 Partition-of-unity finite element method for large, accurate electronic- structure calculations1 , JOHN PASK, Lawrence Livermore National Laboratory, NATARAJAN SUKUMAR, University of California, Davis — Over the past few decades, the planewave pseudopotential (PW) method has established itself as the method of choice for large, accurate, density-functional calculations in condensed matter. However, due to its global Fourier basis, the PW method suffers from substantial inefficiencies in parallel implementation and problems involving localized states. Modern real-space approaches, such as finite-difference (FD) and finite-element (FE) methods, resolve these problems but have until now required much larger bases to attain the required accuracy. Here, we present a new real-space FE based method which employs modern partition-of-unity FE techniques to substantially reduce the number of basis functions required. Initial results show order-of-magnitude improvements relative to current state-of-the-art PW and adaptive-mesh FE methods for systems involving localized states such as d- and f-electron metals.

1This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48. 1:15PM P19.00007 Anti-Hermitian Contracted Schrödinger Equation for the Determination of Ground-state Energies and Two-electron Reduced-density-matrices without Wavefunctions1 , DAVID MAZZIOTTI — A recent advance in the theory of the contracted Schrödingerequation (CSE), in which only the anti-Hermitian part of the equation is solved, permits the direct determination of ground-state two-electron reduced density matrices (2-RDMs) that yield 95-100% of the correlation energy of atoms and molecules [Mazziotti, Phys. Rev. Lett. 97, 143002 (2006)]. Here we discuss in detail the anti-Hermitian contracted Schrödingerequation (ACSE) and its comparison to the CSE with regard to cumulant reconstruction of RDMs, the role of Nakatsuji’s theorem, and the structure of the wavefunction. The ACSE is also formulated in the Heisenberg representation and related to canonical diagonalization. The solution of the ACSE is illustrated with a variety of molecules. The computed 2-RDMs very closely satisfy known N-representability conditions.

1Support from NSF, David-Lucile Packard Foundation, and Dreyfus Foundation.

1:27PM P19.00008 A Near Linear-Scaling Smooth Local Coupled Cluster Algorithm for Elec- tronic Structure , JOSEPH SUBOTNIK, ALEX SODT, MARTIN HEAD-GORDON, UC Berkeley, PITZER CENTER TEAM — We demonstrate near linear-scaling of a new algorithm for computing smooth local coupled-cluster singles-doubles (LCCSD) correlation energies of quantum mechanical systems. Full CCSD provides an excellent, size-consistent treatment of electron correlation, but is computationally expensive, scaling formally as O(n6); by contrast, our LCCSD algorithm recovers more than 99% of the CCSD correlation energy, while achieving near linear-scaling. Furthermore, previous domain-based LCCSD models had discontinuous potential-energy curves, with correspondingly infinite nuclear forces; by contrast, our domain-free algorithm’s correlation energy is a rigorously differentiable function of nuclear coordinates, with correspondingly finite nuclear forces. Thus, our algorithm should allow, in the future, for the propagation of quantum dynamics on a highly correlated electron surface. We present applications to small polypeptide conformational energies, and demonstrate how one may smoothly dissociate two benchmark molecules (ethane and ketene) at the LCCSD level of electronic correlation using our algorithm.

1:39PM P19.00009 Linear scaling integral fitting , ALEXANDER SODT, MARTIN HEAD-GORDON, University of California, Berkeley and LBNL Chemical Sciences Division — In density (or integral) fitting methods, the density (or an orbital product) is replaced with a sum of atom- centered “auxiliary” functions, which are used to efficiently compute Coulomb interactions. In this work, we present a method for computing localized fit coefficients that scales linearly with system size, and introduces only extremely modest errors. We apply the algorithm to a variety of methods, including the J piece of the Fock matrix.

1:51PM P19.00010 New many-body approach to photoemission and spectral functions1 , CARL- OLOF ALMBLADH, CLAUDIO VERDOZZI, Mathematical Physics, Lund University (Sweden) — A new method for the description of photoemission and other spectra is presented. The key idea is to expand the transition amplitudes rather than the spectral function themselves. This leads to spectral intensities of a Golden-rule-like form. In the language of Keldysh path-ordered technique, contributions to “lesser” functions such as G< are classified into loss and no-loss diagrams, and in each diagram transition amplitudes can be identified. Conserving theories in the sense of Kadanoff and Baym exactly fulfill macroscopic conservation laws but may violate the positiveness of spectral functions. In contrast, the present scheme may violate conservation laws but it will always give positive spectra, thus being especially suitable for photoemission and other processes where spectral shapes are of primary interest. As examples, we will discuss the one-electron spectral function beyond GW theory and in presence of phonons. In both cases we find subtle interference effects between self-consistency and vertex corrections and a marked improvement of satellites. As a final example, photoemission beyond the sudden approximation will be discussed.

1Work supported by the EU’s 6th Framework Programme through the NANOQUANTA Network of Excellence (NMP4-CT-2004-500198)

2:03PM P19.00011 Targeting individual excited states in DMRG. , JONATHAN DORANDO, JOHANNES HACHMANN, GARNET KIN-LIC CHAN, Cornell University — The low-lying excited states of π-conjugated molecules are important for the development of novel devices such as lasers, light-emitting diodes, photovoltaic cells, and field-effect transistors [1,2]. The ab-intio Density Matrix Renormalization Group (DMRG) provides a powerful way to explore the electronic structure of quasi-one-dimensional systems such as conjugated organic oligomers. However, DMRG is limited to targeting only low-lying excited states through state-averaged DMRG (SDMRG). There are several drawbacks; state-averaging degrades the accuracy of the excited states and is limited to at most a few of the low-lying states [3]. In this study, we present a new method for targeting higher individual excited states. Due to progress in the field of numerical analysis presented by Van Der Horst and others [4], we are able to target individual excited states of the Hamiltonian. This is accomplished by modifying the Jacobi-Davidson algorithm via a “Harmonic Ritz” procedure. We will present studies of oligoacenes and polyenes that compare the accuracy of SDMRG and Harmonic Davidson DMRG. [1] Burroughes, et al. , Nature 347, 539 (1990). [2] Shirota, J. Mater. Chem. 10, 1, (2000). [3] Ramasesha, Pati, Krishnamurthy, Shuai, Bredas, Phys. Rev. B. 54, 7598, (1997). [4] Bai, Demmel, Dongarra, Ruhe, Van Der Horst, Templates for the Solution of Algebraic Eigenvalue Problems, SIAM, 2000.

Wednesday, March 7, 2007 11:15AM - 2:15PM — Session P26 DCP: Focus Session: Electron & Ion Solvation in Clusters & the Condensed Phase I Colorado Convention Center 205 11:15AM P26.00001 How do solvent structure and counterion distribution control quantum solvation in liquids? , BENJAMIN SCHWARTZ, Dept. Chem. & Biochem., UCLA — Molecular liquids differ from each other not only in their polarity or their ability to make or accept hydrogen bonds but also in their intrinsic packing. Here, we show that the way a solvent packs can have dramatic effects on the dynamics of electron transfer reactions. Using a combination of nonadiabatic mixed quantum/classical molecular dynamics simulations and ultrafast pump-probe spectroscopy, we show that the presence of intrinsic cavities in liquid THF makes charge transfer dynamics in this solvent different from that in other solvent such as water. For example, we find that photoexcitation can cause solvated electrons in THF to transfer from one cavity to another, providing a mechanism for light-induced electron relocalization. We also find that the way a solvent distributes counterions around a reacting solute can dramatically alter not only the rate but even the products of charge transfer reaction. For example, following excitation of the charge-transfer-to-solvent (CTTS) band of iodide in THF, we find that for soft counterions such as tetrabutylammonium, roughly 10% of the ejected electrons form a loose complex with the counterion within a few ps of excitation. For harder counterions such as sodium, however, we find that there can be photoinduced transfer of the CTTS electron from the of I¯ anion to the Na+. If the sodium cations are complexed into crown ethers, however, electron transfer to Na+ is shut off. Finally, we also investigate electron solvation and the CTTS dynamics of I¯ in THF/water mixtures. We find that CTTS excitation leads to ejection of the electron in an initially THF-rich environment characteristic of the I¯ solvation structure, but that the electrons subsequently become hydrated on a tens to hundreds of ps time scale. 11:51AM P26.00002 Dynamics in the First Hydration Shell of Anions1 , JAMES HYNES, Univ. Colorado, Boulder — We will describe our recent efforts to elucidate theoretically the vibrational and reorientation dynamics of water molecules in the first hydration shells of anions in aqueous solution, to assist in the interpretation of recent ultrafast infrared spectroscopic experiments on this issue. In particular, we will discuss (a) OH vibrational frequency dephasing for an iodide ion dilute in a solution of HOD in D2O and (b) the reorientation dynamics for an HOD in the first hydration shell of a chloride ion dilute in a solution of HOD in D2O. This work has been performed in collaboration with Damien Laage, Suyong Re and Bruno Nigro of the Dept. de Chimie, Ecole Normale Superieure, Paris.

1Suppported in part by a grant from NSF.

12:27PM P26.00003 Electronic Excitation in Aqueous Anions , STEPHEN BRADFORTH, University of Southern California — Anions when hydrated in water exhibit new features in their electronic absorption spectrum. In the completely hydrated medium of bulk water, charge transfer bands are fully developed and valence transitions exhibited in vacuum can also lead to production of solvated electrons. Using broadband femtosecond transient absorption spectroscopy, we have recorded two-photon absorption spectra that characterize the spectrum of electronic states of aqueous organic and inorganic anions and explored the electronic relaxation dynamics occurring after excitation of valence and charge-transfer-to-solvent states. The detachment dynamics typically are strongly dependent on the excitation energy. The overall solvated electron yields can be understood in terms of competing non-adiabatic, solvation and vibrational relaxation pathways in the excited state. Understanding these electronic states and pathways provides several critical tests for solution electronic structure theories.

1:03PM P26.00004 Infrared spectroscopy of hydrated sulfate dianions , JIA ZHOU, GABRIELE SANTAMBRO- GIO, MATHIAS BRUMMER, DAVID MOORE, LUDGER WOSTE, GERARD MEIJER, DANIEL NEUMARK, KNUT ASMIS, University of California, Berkeley 2− — The ﬁrst infrared spectra of a multiply-charged anion in the gas phase are presented. The spectra of SO4 ·(H2O)n, with n=3 to 24, show four main bands 2− assigned to two vibrations of the dianionic core, the water bending mode, and solvent libration. The triply degenerate SO4 antisymmetric stretch vibration probes the local solvent symmetry, while the solvent librational band is sensitive to the solvent hydrogen bonding network. The spectra and accompanying electronic structure calculations indicate a highly symmetric structure for the n =6 cluster and closure of the ﬁrst solvation shell at n =12.

1:15PM P26.00005 Charge-transfer (CT) dynamics of iodide salts in tetrahydrofuran (THF) and THF-water mixtures. , ARTHUR BRAGG, BENJAMIN SCHWARTZ, Department of Chemistry and Biochemistry, UCLA — We have used the spectral sensitivity of the solvated electron to its local environment to probe counterion and cosolvent effects on ultrafast CT dynamics in THF and THF-water mixtures following 1-photon excitation of the I¯ CTTS band. We find that dynamics in pure THF are dramatically influenced by the presence of the counterion, such that CTTS-generated electrons associate strongly with nearby cations and recombine negligibly with the geminate iodine radical. Studies in solvent mixtures aim to examine preferential ion solvation according to its effects on CT, focusing on THF-rich mixtures, in which water is thought to preferentially solvate equilibrated electrons. Results demonstrate that electrons are initially introduced into water-deficient regions of these solutions, subsequently hydrating over 10’s-100’s of picoseconds. Trends in the CT and hydration dynamics of electrons generated near various counterions and in solutions of varied water content are used to develop an understanding of the local solvent environments of these ion pairs.

1:27PM P26.00006 Density Functional Theory calculations of energies of ions in water and in nanopores1 , KEVIN LEUNG, Sandia National Laboratories, MARTIJN MARSMAN, Universitat Wien — Accurate estimates of ion hydration and electrostatic energies are critical for predicting the permeation or rejection of ions in water-ﬁlled nanopores. Ab initio Molecular Dynamics methods (AIMD), based on Density Functional Theory (DFT), accounts for the electronic properties and polarizability of materials, water molecules, and ions, and it may appear to be the method of choice for predicting accurate ion energies in water and in nanopores. In practice, applying DFT coupled with the use of periodic boundary conditions in a charged simulation cell leads to anomalous shifts in the electrostatic potential. Using the projector augmented-wave (PAW) method, Wannier functions, and appropriate corrections, we report energies of ions in several systems that can be referenced to interfaces or unambiguous (“vacuum”) values.

1 Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. Department of Energy’s National Nuclear Security Administration, under contract DE-AC04-94AL85000.

1:39PM P26.00007 Hydrogen bonding and coordination in normal and supercritical water from X-ray inelastic scattering , P. H.-L. SIT, DMSE, MIT, CHRISTOPHE BELLIN, Institut de Minèralogie et de Physique des Milieux Condensès,UniversitèPierre et Marie Curie, BERNARDO BARBIELLINI, Department of Physics, Northeastern University, D. TESTEMALE, J.-L. HAZEMANN, Laboratoire de Cristallographie, CNRS, T. BUSLAPS, European Synchrotron Radiation Facility, NICOLA MARZARI, DMSE, MIT, ABHAY SHUKLA, Institut de Minèralogie et de Physique des Milieux Condensès,UniversitèPierre et Marie Curie — A direct measure of hydrogen bonding in water under conditions ranging from the normal state to the supercritical regime is derived from the Compton scattering of inelastically-scattered X-rays. First, we show that a measure of the number of electrons ne involved in hydrogen bonding at varying thermodynamic conditions can be directly obtained from Compton profile differences. Then, we use first-principles simulations to provide a connection between ne and well-defined structural measures for the number of hydrogen bonds nHB . Our study shows that over the broad range studied the relationship between ne and nHB is linear, allowing for a direct experimental measure of bonding and coordination in water. In particular, the transition to supercritical state is characterized by a sharp increase in the number of water monomers, but also by a significant number of residual dimers and trimers.

1:51PM P26.00008 Binding Energies between Guest Atoms in Clathrate II , HIDEKAZU TOMONO, KAZUO TSUMURAYA, Meiji University, JAPAN — The guest atom displacements in clathrates II have been reported on experimental and theoretical points of views. The recent papers on the displacements are given in the reference [1]. The displacements are found to be about 0.6 A˚ from the center of the Si28 cage to the hexagonal ring between the Si28 cages. The binding energies between the guest atoms however have been unknown so far. In the present work we calculate the energies between Na atoms in clathrates II Na2@Si136 and Na24@Si136 with a density functional analysis. We will discuss the cohesion mechanism of the clathrates based on the binding nature between the cations in Zintl phase. [1] H. Takenaka and K. Tsumuraya, Mater. Trans., 47, 63 (2006).

2:03PM P26.00009 Solvation of anions by aromatic molecules probed by infrared spectroscopy , J. MATHIAS WEBER, HOLGER SCHNEIDER, KRISTEN M. VOGELHUBER, JILA — We have studied the interaction of chloride ions with partially fluorinated benzenes by gas phase infrared photodissociation spectroscopy. Our studies were motivated by the fact that fluorination changes the charge distribution in a benzene molecule. While C6H6 has a negatively charged carbon ring and a positively charged hydrogen periphery, C6F6 has a positively charged carbon ring and a negatively charged fluorine periphery. If the interaction between a closed-shell anion (such as Cl−) and the aromatic molecule were based mostly on electrostatic interaction, such an ion would bind to C6HnF6−n via the π system for small n and via H bonds to the periphery for large n. We have used IR − spectroscopy of Ar solvated Cl ·C6HnF6−n complex anions to investigate if this paradigm holds, using the red shift and intensity increase of CH stretching modes for H-bonded CH oscillators to discern whether Cl− binds to the π system rather than to the periphery at different levels of F substitution. Wednesday, March 7, 2007 11:15AM - 1:51PM — Session P35 DBP DCP: Focus Session: Protein Motin Vibrations to Conformational Changes Colorado Convention Center 405 11:15AM P35.00001 Dose and exposure requirements for the protein x-ray serial crystallography. , DMITRI STARODUB, Department of Physics, Arizona State University, Tempe, AZ 85287-1504 — We have proposed spraying proteins (aligned by a laser) across a synchrotron beam to solve proteins which cannot be crystallized.1 A single-file stream of ice-jacketed proteins is considered. We compute diffraction patterns for the GroEL at the incident x-ray flux predicted for a new coherent scattering beamline at the Advanced Photon Source. Using iterative phasing of the data, we determine the relationship between the count rate at a reconstructed pixel (or 3D voxel) of a given size in the real-space charge-density map and number N of proteins in the 10-µm 2 kV x-ray beam at any instant. A modulation transfer function estimates resolution for various exposure times. With the incident flux of 106 photons/s/nm2 and N=10, over 5,000 counts/s are distributed over the entire diffraction pattern, which is sufficient for a nm resolution with 200 s exposure. We compare the results of this numerical lensless imaging experiment with a simple theoretical treatment of image formation in the dark and bright field phase contrast. Supported by ARO, NSF and co-workers.1 1J. Chem Phys. 123, 244304 .

11:27AM P35.00002 Crystallization media inhibit protein structural dynamics , ANUPAMA THUBAGERE, LORAND KELEMEN, SANDIP KALEDHONKAR, AIHUA XIE, Oklahoma State University — The ﬁrst role of any crystallization solution is to reduce the solubility of proteins, so that it induces protein precipitation. Most times, protein precipitation does not lead to protein crystallization. Do crystallization solutions play any other roles that are crucial for protein crystallization? Here we report our studies that crystallization solutions suppress or inhibit protein structural dynamics. Photoactive yellow protein (PYP), a bacterial blue light photoreceptor protein, is employed as a model system in our study. We use time-resolved FTIR spectroscopic technique to probe the structural dynamics of proteins, including the proton transfer process and global conformational motions. We found that high concentration crystallization solutions (NH4)2SO4 strongly inhibit the structural dynamics of PYP upon blue light excitation. We will examine and discuss the mechanism in which crystallization solutions inhibit protein structural dynamics. The results are expected to provide insights to fundamental understanding of protein crystallization of water-soluble proteins. In addition, the data clearly demonstrates that the structural dynamics observed in crystalline conditions may be far from their natural structural dynamics for studies of protein structure-function relations.

11:39AM P35.00003 ABSTRACT HAS BEEN MOVED TO D26.00011 — 11:51AM P35.00004 Conformational dependence of a protein kinase phosphate transfer reaction , MONTIAGO LABUTE, Theoretical Division, Los Alamos National Laboratory, GRAEME HENKELMAN, Department of Chemistry and Biochemistry, University of Texas, Austin, CHANG-SHUNG TUNG, PAUL FENIMORE, BEN MCMAHON, Theoretical Division, Los Alamos National Laboratory — Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005).

12:03PM P35.00005 Interaction of Receptors and GTPase-Activating Proteins in a G Protein Signaling Module1 , MARC TURCOTTE, WEI TANG, ELLIOTT M. ROSS, University of Texas Southwestern Medical Center — We have developed a model of the interactions of proteins involved in G protein signaling using steady-state data from reconstituted vesicles. The model includes receptor, G protein (G), GTPase activating protein (GAP), GTP and GDP. Implementation is done using coupled ordinary differential equations. We performed a global fit to the model parameters against enzymologic and nucleotide-binding data using simulated annealing constrained by thermodynamics. Validation was done using Monte Carlo data. Fit parameters uncertainties were obtained via multiple repeats of stochastic searches. We studied fit parameter correlations near a solution by local thermal sampling of the cost manifold. The best fit parameters agree with values derived from dynamic data not used in our fit. We used our model to study signaling in familiar regimes and to predict new, testable behaviors in others. Signal output is a complex function of the inputs: receptor and GAP at physiologic and experimental concentrations of GTP and GDP. We studied the shape of the activation surface. Its complexity derives from stoichiometric relationships among protein concentrations. Our model predicts signaling pathways and dynamical response in G protein modules.

1NIH RO1GM30359, NIH K25GM071957, Welch Foundation I-0982

12:15PM P35.00006 Fast motion of the surface alcohol molecules deduced from sum-frequency vibrational spectroscopy , JAEHO SUNG, Department of Physics, Sogang University, DOSEOK KIM, Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University — Sum-frequency generation (SFG) vibrational spectroscopy was used to investigate the surface of the homolog series of alcohols from methanol to octanol. It was found that SFG signal strengths from the terminal methyl group of short-chain alcohols cannot be explained by assuming the surface molecules were ﬁxed in time. Introduction of the rotational motion with time scale comparable to the dephasing time of the vibrational mode of the terminal methyl group (∼0.7 picosecond) was able to explain the reduction of the SFG signal by motional averaging eﬀect. This timescale of motion increased with the increase in the molecule size and bulk viscosity. Our result also suggests that surface alcohol molecules move faster as compared to the same molecules in the bulk liquid.

12:27PM P35.00007 Effect of molecular vibrations on charge transfer in polypeptide chains , NIKOLAI SERGUEEV, ALEXANDER DEMKOV, University of Texas at Austin — We present first principles framework suitable for analyzing and understanding the effect of molecular vibrations on charge transfer in polypeptide chains. Our approach is based on density functional theory and Keldysh nonequilibrium Green’s function formalism. This method allows us to treat both electrons and molecular vibrations (phonons) on equal footing in a self-consistent manner. The salient feature of our technique is that we consider the vibration of the whole polypeptide bridge. We present a numerical results for a charge transfer through alanine polypeptide chains of the various length and show that the electron tunneling is greatly affected when the interaction between electrons and molecular vibrations is taken into account. We also present a vibrational spectroscopy analysis and identify those vibrational modes of the alanine polypeptides involved into the inelastic charge transfer.

12:39PM P35.00008 No Long-Lived Coherent Oscillations in Proteins at Room Temperature , ROBERT AUSTIN, MICHAEL WHITE, Princeton University — A recent PRL (PRL 95, 253601 (2005)) suggested that proteins could have very narrow holes (Hz wide) burnt into their electronic spectra at 300K, and suggested that “snail-paced” light group velocity light could result. We will show that the authors mistook conformational diffusion phase shifts for narrow lines and show that there are no narrow long-lived holes in a protein spectra at 300 K nor is there any snail-paced light. 12:51PM P35.00009 Slow light with bacteriorhodopsin solutions , CHANDRA YELLESWARAPU, FRANCISCO ARANDA, REJI PHILIP, RAO DEVULAPALLI, University of Massachusetts - Boston — Slow light in gases and solids has been studied in recent years. Various applications are possible depending on the modulation frequency and the amount of delay that can be induced in the traveling wave. Recently we demonstrated ultra slow light in the biological photo-membrane bacteriorhodopsin (bR) polymer film at room temperature [Phy. Rev. Lett., 95, 2536011, 2005]. By exploiting the photoisomerization property of bR for coherent population oscillation, the group velocity is controlled from about 0.1 mm/sec to the speed of light. But as bR is embedded in a polymer matrix, the isomerization rates are slow and hence limited to low modulation frequencies. On the other hand bacteriorhodopsin solution can be used for obtaining slow light at higher modulation frequencies. Studies in solution also offer the advantage of changing the optical density at ease resulting in longer pulse delays. Detailed results on slow light where the delay is varied with modulation frequency, optical density and all-optical control with a blue laser beam will be presented.

1:03PM P35.00010 Physical basis for membrane-charge selectivity of cationic antimicrobial peptides , BAE-YEUN HA, SATTAR TAHERI-ARAGHI, University of Waterloo — Antimicrobial peptides are known to selectively disrupt (highly- charged) microbial membranes by asymmetrical incorporation into the outer layers. We present a physical basis for membrane-charge selectivity of cationic antimicrobial peptides. In particular, we provide a clear picture of how peptide charge, Q, inﬂuences the asymmetrical insertion – one salient feature is the existence of an optimal peptide charge, at which selective insertion is optimized. Our results suggest that large Q is required for antimicrobial selectivity, consistent with experiments.

1:15PM P35.00011 Investigating Potential Surfaces with QM/MM Methods , THOM VREVEN, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492 — Geometry optimization of large QM/MM systems is not trivial, especially when transition states or higher order saddle points are desired. The optimization can be carried out with a macro/micro scheme, which alternates (internal coordinate) geometry steps in the QM region with full (cartesian) minimizations of the MM region. This significantly reduces the number of QM calculations, and avoids bottlenecks associated with coordinate transformation and Hessian manipulation. This standard macro/micro scheme, however, suffers from numerical instability and compromised convergence behavior. This affects particularly the optimization of transition states, which is therefore not often successful. To address these problems we present extensions to the macro/micro scheme, which have been implemented in the ONIOM framework for hybrid methods. In the standard scheme, the QM and MM regions are coupled only through first order terms. We now include second order coupling using analytical MM contributions, employing linear scaling methods. We show how this improves convergence and allows for the optimization and characterization of saddle points in very large systems. We demonstrate our methods using various examples, such as the hydrogen peroxide reduction by Selenoprotein Glutathione Peroxidase, proton transfer in H-Y zeolite, and thermal isomerization of retinal in Bacteriorhodopsin.

Wednesday, March 7, 2007 2:30PM - 5:30PM — Session S19 DCP: Mesoscopic Systems, Clusters, and Nanoscale Systems Colorado Convention Center 104

2:30PM S19.00001 First principles study of adsorption and dissociation of H2,O2, and CO on 1 α-Al2O3 (0001) supported Pt-Co alloy , T.J. DHILIP KUMAR, C. ZHOU, B. NADUVALATH, Department of Chemistry, University of Nevada Las Vegas — Recently, there has been several investigations carried out to improve the electro-catalytic activity of Pt and Pt based alloys for the oxygen reduction reaction in fuel cell electrodes. In particular, Pt-Co alloy systems have been often employed. To gain physical insight into the catalytic properties of these systems we have performed a systematic study of the electronic structures, bonding and growth patterns of nanoclusters of Pt-Co alloy using ﬁrst principles density functional calculations. The 3:1 ratio of Pt-Co alloy has been constructed as nanoclusters and thin ﬁlm supported on α-Al2O3. The geometry optimized tetrahedron, and the square planar structures of Pt3Co are placed over the slabs of six layers α-Al2O3(0001) surface. Activity of H2,O2 and CO on these structures from various approaches has been explored. In all our calculations the non-locality in the exchange correlation functional is taken into account by considering spin polarized generalized gradient approximation as proposed by Perdue and Wang. Brillouin zone integrations have been performed using Monkhorst-Pack grids with (2 X 2 X 1) k-point meshes. The electronic structures of these systems have been analyzed by computing the electronic density of states.

1This work is supported by DOE Grant DE-FG36-05GO85028.

+/− 2:42PM S19.00002 Influence of Charge State on the Reaction of FeO3 with Carbon Monoxide , J.U. REVELES, S.N. KHANNA, Virginia Commonwealth University, N.M. REILLY, G.E. JOHNSON, A.W. CASTLEMAN JR., Penn State University — A synergistic study combining experiments in molecular beams and first principles electronic structure calculations within a gradient corrected density functional approach is used to investigate the reactivity of charged FeO3 clusters with CO. It is shown that highly oxidized iron clusters are able to readily effect the oxidation of CO to CO2 at ambient temperature. Calculated energy profiles of the reaction demonstrate that the oxidation efficiency is governed by the strength +/− of oxygen binding to the iron atom. Results for FeO3 are presented and reveal that cation clusters are more efficient than the corresponding anion clusters at effecting the oxidation reaction due to different bond energies resulting from charge distribution.

2:54PM S19.00003 Atomic-scale Characterization of Free Radical Adsorption to the Si(111)-7 x 7 Surface , NATHAN GUISINGER1, SHAUN ELDER, NATHAN YODER, MARK HERSAM, Northwestern University — Ultra-high vacuum (UHV) scanning tunneling microscopy (STM) was employed to investigate free radical chemistry on the Si(111)-7 × 7 surface with atomic-scale spatial resolution. In particular, the nitroxyl free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) was explored, due to its single-site binding mechanism. UHV STM imaging of isolated molecules revealed that TEMPO covalently reacts with adatom dangling bonds with high affinity, while exhibiting a preference towards center adatom sites during the initial stages of adsorption. Adsorption to center and corner adatoms approached a ratio of 1:1 with increased surface coverage. Upon saturation, the surface exhibited long-range ordering. Following adsorption to a center adatom site, significant charge transfer occurred between TEMPO and a neighboring adatom. Scanning tunneling spectroscopy was utilized to investigate this delocalized effect by spatially mapping the local density of states. This study provides fundamental insight into free radical surface chemistry and suggests a direct pathway for forming nearly perfectly ordered organic adlayers on the Si(111)-7 × 7 surface.

1Present Aﬃliation: NIST 3:06PM S19.00004 CO2 Sensing and CO and H2O Interactions on Mats of Gold Nanoparticle Decorated GaN Nanowires.1 , C.A. BERVEN, R. ABDELRAHAMAN, W. BARREDO, D.N. MCILROY, Dept. of Physics, University of Idaho — We report on the use of mats of gold-nanoparticle-decorated GaN nanowires for the detection of CO2 and the possible generation of CO2 and H2 by interactions of CO and H2O on the surfaces of the gold nanoparticles. The sensor was constructed from a 10-20 µm thick mat of GaN nanowires grown on a 1 cm diameter sapphire substrate followed decoration of the nanowires with gold nanoparticles. Selective wet etching was then used to reduce the amount of gold on the nanowires. Electrical measurements were made of the mat under various atmospheres. When exposed to just water vapor, CO or H2 the current-voltage curves were similar to those when in vacuum. However, when the device was exposed to CO followed by H2O, we saw a signiﬁcant reduction in the current at all values of applied voltage. Exposure to just CO2 showed a similar response to that of mixing CO and H2O implying that CO2 is being generated and that what is being sensed is the product of the reaction of CO + H2O creating CO2. As a consequence of CO2 being detected after the mixing of CO and H2O, we speculate that H2 is being generated giving a possible new mechanism for H2 generation.

1Reserach supported by NSF (EPS-0447689 and PHY-0453253) and the W M Keck Foundation

3:18PM S19.00005 Sorption and condensation of Neon in MCM48 as monitored by X-ray diffraction. , PAUL SOKOL, DUNCAN KILBURN, Indiana University Cyclotron Facility — In this submission we report on experiments that simultaneously measure adsorption isotherms and X-ray diffraction measurements on Neon in the mesoporous silica glass MCM 48. The isotherms are similar to those reported previously in the literature. Simultaneous X-ray measurements allow the variation of adsorbate structure to be monitored as the sorption progresses. We observe that the most rapid increase in the intensity of the first peak in the scattered spectrum occurs during the initial sorption of Neon layers, but before capillary condensation. We show that this can be explained via conventional scattering theory and that it provides a new perspective on the processes of monatomic gas sorption. We also report on modified phase transitions and structures for the confined Neon.

3:30PM S19.00006 Water in Carbon Nanotubes:A New Quantum Phase of Water1 , GEORGE REITER, University of Houston, CHRISTIAN BURNHAM, DIRAR HOMOUZ, University of Houston, PHILIP PLATZMAN, JEREMY MAYERS, TYNO ABDUL-REDAH, ISIS, Rutherford-Appleton Laboratory, ALEXANDER MORAVSKY, MER Corporation, JICHEN LI, University of Manchester, C.-K. LOONG, ALEXANDER KOLESNIKOV, Argonne National Laboratory — The momentum distribution of the protons in ice Ih, ice VI, high density amorphous ice and water in carbon nanotubes has been measured using deep inelastic neutron scattering. We ﬁnd that, at low temperatures, the momentum distribution for the water in the nanotubes is qualitatively unlike that in any other phase of water or ice. The kinetic energy of the protons is 35mev less than that in ice Ih at the same temperature, and the high momentum tail of the distribution, characteristic of the molecular covalent bond and the stretch mode of the proton in the molecule, is not present. We observe a phase transition between 230K and 268K in the nanotube data. The high momentum tail is present in the higher temperature measurement, which resembles that of ice Ih at the same temperature. Molecular dynamics simulations show the phase transition to be associated with the reordering of the hydrogen bonds of the 2-D ice layer, coating the interior of the nanotube at low temperatures, into a 3-D structure at 268K. Although there is yet no model for water that explains the low temperature momentum distribution, our data reveals that the protons in the hydrogen bonds in the 2-D ice layer are coherently delocalized, and that the 2-D ice layer is a qualitatively new phase of ice.

1The work of G. Reiter, C. Burnham, D. Homouz and P. Platzman was supported by DOE Grant DE-FG02-03ER46078

1 3:42PM S19.00007 Bulk vs. Nanoscale WS2: Finite Size Effects and Solid State Lubrication , S. BROWN, J.L. MUSFELDT, University of Tennessee, I. MIHUT, J.B. BETTS, A. MIGLIORI, Los Alamos National Laboratory, R. ROSENTSVEIG, R. TENNE, Weizmann Institute of Science — Metal dichalcogenide nano-structures have recently attracted attention due to their unique closed cage structures, hierarchy of length scales, and outstanding solid-state lubrication behavior. In order to understand the bulk vs. nanoscale effects, we measured the low temperature specific heat of layered and nano-particle WS2. Below 9 K, the specific heat of the nano-particles deviates from that of the bulk counterpart. Further, it deviates from the usual T3 dependence below 4 K, due to both finite size effects and inter-particle interactions. This separation of nanoscale effects from T3 dependence can be modeled by assuming that the phonon density of states is flexible, changing with size and shape of the nanoparticle. We invoke relationships between low temperature T3 phonon term, Young’s modulus, and friction coefficient to assess the difference in the tribological properties. Based on this analysis, we conclude that the improved lubrication properties of the nanoparticles are extrinsic in origin.

1This work is supported by the U.S. Department of Energy.

3:54PM S19.00008 Theory of surface enhanced Raman scattering from a molecule adsorbed on a chain-like cluster of metallic nanoparticles and nanoshells , JEANNE BONNER, KARAMJEET ARYA, San Jose State University, San Jose — The Raman cross-section from a molecule is believed to enhance by more than 10 orders of magnitude when it is adsorbed on a cluster of silver nanoparticles. These large enhancements are attributed to the resonant excitation of the surface plasmon modes of the cluster those have very large localized electric field near its surface. The resonant position and the electric field of these modes are very sensitive to the structure of metal particles and the size and shape of the cluster. Using multiple scattering in the wave-vector space between the individual particles in the cluster we have calculated the resonant position of these modes and their enhanced electric field for clusters of different shape formed from two, three, and four nanospheres and nanoshells. We find the maximum enhancement in the cross-section can reach up to 10 orders of magnitude for silver particle clusters. We also find important new results for the chain like clusters of three or more particles where there is a dramatic increase in the enhancement due to very sharp resonant features of the modes. These features may be helpful in identifying the cluster shape and size in the surface enhanced Raman scattering experiments.

4:06PM S19.00009 ABSTRACT WITHDRAWN —

4:18PM S19.00010 ABSTRACT WITHDRAWN —

4:30PM S19.00011 Assembly and Interaction of Au/C Core-Shell Nanoparticles , PETER SUTTER, ELI SUTTER, YIMEI ZHU, Brookhaven National Laboratory — The encapsulation of metal nanoparticles in fullerene cages has attracted much interest recently due to the expected novel and exotic properties. Despite the interest in these nanostructures, important properties, such as the thermal stability and interactions of encapsulated nanoparticles as well as the process of encapsulation itself are not entirely understood. Using real-time transmission electron microscopy we study the formation of Au/C core-shell structures from C-supported Au nanoparticles, and their thermally and electron beam induced interactions [1, 2]. At temperatures below 400C no C-shell is assembled, and closely spaced Au nanoparticles interact by coalescence. At high temperatures (400C - 800C) the Au particles are transformed into Au/C core-shell structures via encapsulation into curved, fullerene-like C shells. The shells initially passivate the Au cores and inhibit their coalescence. But under electron irradiation, the Au cores can break free from their shells, and hence can coalesce. Surprisingly, at this stage the assembled C-sheets may actually enhance the coalescence process by driving the directed motion of Au/C particles and causing the efficient contraction of widely spaced particle ensembles. [1] E. Sutter, P. Sutter, Y. Zhu, Nano Lett. 5, 2092 (2005). [2] E. Sutter, P. Sutter, Y. Zhu, Surf. Sci. 600, 3654 (2006). 4:42PM S19.00012 DFT study on the charge density shift bucky-ferrocene vs. bucky- ruthenocene , TUNNA BARUAH, RAJENDRA ZOPE1, University of Texas at El Paso, MARK PEDERSON, Naval Research Laboratory — Iron and ruthenium atoms have similar valence electron configurations. Ferrocene and ruthenocene are stable metallocenes that satisfy the 18-electron rule. Re- cently, Sawamura et al. [J. Am. Chem. Soc. vol. 124, pp. 9354 (2002)] have succeeded in synthesizing fused complexes of ferrrocene and ruthenocene with fullerene, known as bucky-ferrocene and bucky-ruthenocene, respectively. The experiments show shift in charge density from ferrocene to fullerene in the ground state. However, no charge transfer from ruthenocene to fullerene is observed in case of the bucky-ruthenocene. We have performed all electron density functional calculations to obtain the equilibrium structures of the bucky-ferrocenes and bucky-ruthenocenes. Both, the staggered and eclipsed geometries are examined. The differences in the electronic structure and nature of bonding in these two systems are studied by analyzing the frontier orbitals, dipole moments, and charge density in their ground and singlet excited states.

1also at Howard university

4:54PM S19.00013 Temperature-dependent properties of SiC Clusters1 , C. GHOSH, M. YU, S. SHEN, C.S. JAYANTHI, S.Y. WU, University of Louisville — Using a semi-empirical quantum mechanics based molecular dynamics simulation [Phys. Rev. B, 74, 155408 (2006)], SinCm clusters were shown to exhibit several types stable structures corresponding to different compositions and distributions of Si and C but a fixed total number of atoms [Ming Yu et al. – APS March 2007]. Specifically, it was shown that an almost uniform admixture of Si and C atoms in a 147-atom SiC cluster exhibited a bucky diamond structure, while the Si-rich and the C-rich stable structures for the same fixed number of total atoms (n+m= 147) exhibited totally different structures with different co-ordinations, bonding, etc. In the present work, we will investigate how equilibrium structures of these different structures evolve with the increase of the temperature from 0K to the melting temperature, and quantities such as pair-distribution functions, electronic density of states, etc. will be calculated up to the melting temperature. This study will provide characterizations of both ordered and disordered SiC clusters, as well as SiC “liquids” in reduced dimensions.

1Funding Support: Honda Research Grant and KSEF.

5:06PM S19.00014 Thermodynamic Properties and Grain Growth in Pt Nanoparticles1 , KATHER- INE SLOYAN, Imperial College London, THOMAS EKIERT, KARL UNRUH, University of Delaware — The evolution in the structural and thermodynamic properties of chemically prepared Pt nanoparticles has been studied by x-ray diﬀraction (XRD), transmission electron microscopy (TEM), diﬀerential scanning calorimetry (DSC), and ac magnetic susceptibility measurements. Depending on the synthesis conditions, the XRD and TEM measurements indicated that nanoparticles could be prepared with mean diameters between about 5 and 10 nm. A combination of XRD, TEM, and DSC measurements also indicated that the as-prepared nanoparticles were stable with respect to grain growth to temperatures of about 300 ˚C. Above this temperature, grain growth resulted in an increase in the mean particle size and a slight increase in the Pt lattice parameter as well. AC susceptibility measurements as a function of the temperature indicate that with decreasing grain size there is an increase in the real part of the susceptibility and a corresponding decrease in the imaginary susceptibility.

1This work was supported by the Undergraduate Research Oﬃce at the University of Delaware

5:18PM S19.00015 Ligand control of solubility and capping structure of colloidal CdSe nanorods , WEI WANG, SARBAJIT BANERJEE, SHENGGUO JIA, MICHAEL STEIGERWALD, IRVING HERMAN, Materials Research Science and Engineering Center at Columbia University — The length and functional group of the organic capping ligands of colloidal CdSe nanorods play a critical role in determining their solubility in chloroform. Optical transmission spectroscopy shows decreased solubility of CdSe nanorods capped by relatively long ligands, and increased solubility of CdSe nanorods capped by alkyl phosphonate ligands. 1H and 31P nuclear magnetic resonance (NMR) and inductively coupled plasma-atomic emission spectroscopy (ICP-AES) studies indicate that when mixtures of phosphonic acids with different lengths are used in synthesis, the shorter ligands selectively remain on the inorganic surface, but the overall number of ligands on the surface is smaller than that of the nanorods capped by long ligands. The proposed capping structure of colloidal CdSe nanorods is that there is a shell of ligands bound to the core of the nanorods and additional ligands can be trapped by this shell. The bound and the trapped ligands can strongly affect the solubility of the individual nanorods and the interactions between the nanorods that lead to aggregation. This work is supported by the MRSEC program of the National Science Foundation under Award No. DMR-0213574 and by the New York State Office of Science, Technology, and Academic Research (NYSTAR).

Wednesday, March 7, 2007 2:30PM - 5:18PM — Session S26 DCP: Focus Session: Electron & Ion Solvation in Clusters & the Condensed Phase II Colorado Convention Center 205

2:30PM S26.00001 Spectroscopy and Dynamics of Excess Electrons in Clusters , DANIEL NEUMARK, University of California, Berkeley — Clusters in which excess electrons are bound to solvent molecules can provide important links with electrons solvated in liquids, most notably the hydrated electron in aqueous solution. These considerations have motivated a series of studies in our group on the spectroscopy and dynamics of excess electrons in water and methanol clusters, which have been investigated using a combination of one-photon and time-resolved photoelectron − − imaging and infrared photodissociation spectroscopy. Salient results are as follows. (i) Both (H2O)n and (CH3OH)n show evidence for multiple isomers with very diﬀerent vertical detachment energies, suggesting multiple electron binding motifs to these clusters. (ii) The time-resolved experiments yield direct measurements of excited state lifetimes in these clusters. Extrapolation to the inﬁnite-size limit yields lifetimes of 50 fs for the hydrated electron and 150 fs for electrons dissolved in methanol. These ultrafast lifetimes are in good agreement with so-called non-adiabatic solvation models for bulk solvated electrons. − (iii) Recent infrared spectroscopy experiments on (H2O)n (n≤50) clusters obtained using a tunable free-electron laser have provided new insights into how the electron binding in these clusters evolves with size.

3:06PM S26.00002 Theoretical Studies of Negatively Charged Water Clusters: The Role of Polarization and Dispersion for Electron Binding1 , KENNETH D. JORDAN, University of Pittsburgh — A quantum Drude − oscillator model is used to characterize negatively charged water clusters as large as (H2O)24. The Drude model allows for inclusion of electron correlation eﬀects between the excess electron and the electrons of the water molecules, at a fraction of the computational cost of all-electron ab initio methods. Application of − the Drude model to (H2O)6 demonstrates that there are many isomers with small electron binding energies that are more stable than the species with double acceptor water monomers that dominate under experimental conditions and that have electron binding energies near 0.45 eV. The talk will also explore the connection between the Drude model and more traditional polarization models used in describing the interaction of excess electrons with water. We show that a series of “polarization” models can be derived from the Drude model, by carrying out an adiabatic separation between the excess electron and the Drude degrees of freedom. It is found that the polarization and Drude models give similar electron binding energies for species in which the excess electron experiences large electrostatic attraction, but that the polarization models signiﬁcantly overbind the excess electron in cases where the electrostatics play only a small role.

1In collaboration with Albert DeFusco, University of Pittsburgh and Thomas Sommerfeld, Southeastern Louisiana University. 3:42PM S26.00003 Excess Electrons in Water: Clusters, Interfaces, and the Bulk , LASZLO TURI, Eotvos Lorand University, Department of Physical Chemistry, Budapest 112, P. O. Box 32, H-1518, Hungary — The presence of charged species at interfaces plays a central role in a wide range of physical processes. Heterogeneous electron transfer is among the most notable examples with implications in electrochemistry, atmospheric chemistry, heterogeneous catalysis, or from a more general viewpoint, in biological through-space electron transfer reactions. An excess electron in an aqueous environment may be considered as a useful model for studying key energetic, structural and dynamic aspects of these complex phenomena. Excess electrons are known to stabilize in bulk water, as hydrated electrons. Hydrated electron systems with reduced dimensionality, such as negatively charged, finite size water clusters, and excess electrons at aqueous interfaces of infinite size, have also been studied for a while. In the present work we will overview the results of a series of mixed quantum-classical molecular dynamics simulations aimed to examine the physical properties of various aqueous excess electron systems. The investigated systems include finite size water cluster anions, infinite ambient water/air, supercooled water/air, Ih ice/air, amorphous ice/air interfaces, and the fully hydrated electron. The discussion will focus on the critical issue whether the excess electron localizes in interior-bound states completely surrounded by water molecules, or on the water surface (interface) with significant electronic amplitude appearing outside the molecular frame (surface-bound states). Correlations of the excess electron state with the size, internal energy, and the local molecular structure of the environment will be illustrated. We will also demonstrate the dramatic influence of the excess electron state on the observable physical properties. The possible interconnections of the finite size cluster anions, the electrons at the infinite size water/air interfaces, and the three-dimensional, fully hydrated electron are also explored in comparison with available experimental data.

4:18PM S26.00004 Optical Spectrum of the Hydrated Electron in Supercooled and Super- critical Water and Ice , DAVID BARTELS, ERICA PRICE, YIQUI DU, Notre Dame Radiation Laboratory — Simulation of the hydrated electron optical spectrum has been the goal of a generation of researchers, and was apparently achieved within the last decade using a one-quantum- electron/pseudopotential/classical water MD modeling strategy. The temperature dependence of the spectrum (red shift at elevated temperature) was reported to be actually the eﬀect of water bulk density. The red shift in simulation was linear in the inverse density. Spectra of the hydrated electron recorded in our laboratory in supercritical water strongly disagree with the simulation result, in that there is very little spectral change for a factor of six change in water density, from 0.1 to 0.6 g/cc at 375◦C. A new result presented here concerns the spectra in supercooled water, which can be compared with spectra in water at higher temperature at the same bulk density. In this comparison, density of the water very clearly does not determine the position of the absorption maximum—the temperature does. The one-quantum-electron/pseudopotential/classical water MD methodology clearly lacks some critical aspects of the real water-electron interaction. A comparison of the electron solvated in supercooled water or in ice at the same temperature shows virtually the same shape on the blue side, but a much narrower bandwidth on the red side in ice relative to water.

4:30PM S26.00005 Evidence for the Formation and Solvation of the (Na+,e¯) Complex Pairs in Tetrahydrofuran (THF) , MOLLY CAVANAGH, ROSS LARSEN, BENJAMIN SCHWARTZ, University of California, Los Angeles — Using ultrafast spectroscopy, we monitor the spectral relaxation of the solvated sodium atom created following the ultrafast excitation of the sodium anion (sodide) charge-transfer-to-solvent band in THF. Immediately following excitation, a sodium atom that has the characteristic gas-phase 590-nm D-line absorption is formed. By untangling the overlapping spectral dynamics of the sodide bleach and solvated electron, we are able to cleanly elucidate the dynamics of the Na atom, whose absorption spectrum eventually shifts to ∼900 nm. We observe a fast, ∼300 fs solvation of the immediately formed gas-phase-like Na atom species followed by a chemical interconversion in ∼800 fs, as characterized by an isosbestic point, into a new species. The new species, which we assign as a (Na+;e¯) contact pair, undergoes slow solvation in ∼10 ps to ultimately form the equilibrium 900-nm absorber. In combination, our data oﬀers the most complete picture of the dynamics of the sodide CTTS reaction and its spectral intermediates.

4:42PM S26.00006 Single and Double Excess Electrons in Water Clusters1 , YING LI, ROBERT BARNETT, UZI LANDMAN, School of Physics, Georgia Institute of Technology — Excess electrons in polar solvents is a topic of continuing interest. Early theoretical research on this subject predicted formation of surface and internal hydrated electron states, depending on the size of the water cluster and the state of the cluster [1]. Evidence for these modes of electron hydration has been reported in recent experiments. We discuss here theoretical investigations of excess electrons states in water clusters as a function of cluster size and state (liquid and frozen) using hybrid quantum (DFT)/classical simulations. In addition we discuss dielectron hydration in clusters [2]. [1] R. N. Barnett, C. L. Cleveland, U. Landman, J. Jortner, J. Chem. Phys. 88, 4429 (1988). [2] H.-P. Kaukonen, R. N. Barnett, U. Landman, J. Chem. Phys. 97, 1365 (1992).

1Supported by the US D.O.E. (FG06-86ER-45234)

4:54PM S26.00007 Charge-transfer reactions, energy gaps, and electron-transfer diabatic surfaces , NICOLA MARZARI, P. H.-L. SIT, Department of Materials Science and Engineering, MIT — Density-functional theory in the LDA or GGA approximation has become the widely-used standard model of condensed matter theory. I will discuss shortcomings and solutions to some of the problems that arise when addressing complex chemical reactions. These challenges include the correct description of electron-transfer processes, where electrons become delocalized and shared between ions that should be in diﬀerent oxidation states. An eﬀective solution can be obtained by introducing a penalty functional that imposes the correct charge state on the ions involved in the reaction [1]. This approach is validated in a model system, showing that the ground state and the charge-transfer excited state can be calculated with negligible errors, and then applied to the determination of the diabatic free-energy surfaces for ferrous and ferric ions in solution. [1] P. H.-L. Sit, Matteo Cococcioni and Nicola Marzari, Phys. Rev. Lett. 97, 028303 (2006).

5:06PM S26.00008 Isomers and the correlation between excess electron binding and the local H-bonding motif in hydrated electron clusters.1 , MARK JOHNSON2, Yale University — We describe a series of experimental results that address the origin of the isomeric classes of negatively charged water clusters that differ according to their electron binding energies. The molecular structure of the local electron binding site is revealed through the isomer-specific vibrational spectra in the intramolecular HOH bending and OH stretching regions for both H and D isotopomers. Isomer selection is accomplished with a photochemical population modulation scheme in which low electron binding isomers are sequentially and systematically removed from the mixed isomer ensembles created in free jet ion sources. The class of clusters (type I) that most strongly binds an excess electron exhibits a characteristic red-shifted band in the bending region that is assigned, based on the behavior of very small clusters, to electron attachment to a single water molecule held to the supporting network by a double H-bond acceptor (AA) motif. Isomers that bind the electron more weakly do not display this spectral signature, indicating that local H-bonding topology is a significant factor in controlling the overall work functions of the clusters. Isomer interconversion and growth mechanisms will also be addressed using Ar-mediated incorporation of hetero-isotopes and surface electron scavenging by reactive charge-transfer collisions.

1Department of Chemsitry, Yale University 2submtted to chemical physics electron and ion solvation (Rossky)

Thursday, March 8, 2007 8:00AM - 11:00AM — Session U6 DCOMP DCP: Recent Progress in Computational Approaches for Rare Events Colorado Convention Center 207 8:00AM U6.00001 Transition Path Sampling and Rare Events in Complex Fluids , PETER BOLHUIS, University of Amsterdam — The transition path sampling technique has matured to a universal tool for the study of rare events in the decade since its development. In this presentation I will give a brief overview of current progress. As an example I will discuss an application to micelle formation, ﬁssion and fusion in surfactant solutions.

8:36AM U6.00002 Phase transformations and transition path sampling methods , CHRISTOPH DELLAGO, University of Vienna — Under pressure, CdSe-nanocrystals transform from the four-coordinated wurtzite structure to the six-coordinated rocksalt structure. The transformation is a rare event that is strongly inﬂuenced by the size and the shape of the crystallite. Using this example, we will discuss how the transition path sampling methodology provides a framework for the study of the mechanism and the kinetics of phase transformations.

9:12AM U6.00003 Computational techniques for the description of rare events , PHILL GEISSLER, University of California, Berkeley — No abstract available.

9:48AM U6.00004 Theory and modeling of rare events , ERIC VANDEN-EIJNDEN, Courant Institute of Mathematical Sciences — No abstract available.

10:24AM U6.00005 Metadynamics for the description of rare events , MICHELE PARRINELLO, ETH, Zurich — No abstract available.

Thursday, March 8, 2007 8:00AM - 10:48AM — Session U18 DCP: Spectroscopy and Dynamics of Single Molecules and Nanoparticles Colorado Convention Center 103 8:00AM U18.00001 Single-Molecule Spectroscopic Investigations of RNA Structural Dynamics , JULIE L. FIORE, DAVID J. NESBITT, JILA, National Institute of Standards and Technology and University of Colorado — To function properly, catalytic RNAs (ribozymes) fold into specific three-dimensional shapes stabilized by multiple tertiary interactions. However, only limited information is available on the contributions of individual tertiary contacts to RNA conformational dynamics. The Tetrahymena ribozymes’s P4–P6 domain forms a hinged, “candy-cane” structure with parallel helices clamped by two motifs, the GAAA tetraloop-tetraloop receptor and adenosine (A)-rich bulge–P4 helix interactions. Previously, we characterized RNA folding due to a tetraloop-receptor interaction. In this study, we employ time-resolved single-molecule FRET methods to probe A-rich bulge induced structural dynamics. Specifically, fluorescently labeled RNA constructs excited by a pulsed 532 nm laser are detected in the confocal region of an inverted microscope, with each photon sorted by arrival time, color and polarization. We resolve the kinetic dependence of A-rich bulge-P4 helix docking/undocking on cationic environment (e.g. Na+ and Mg2+ concentration.) At saturating [Mg2+], the docked structure appears only weakly stabilized, while only 50% of the molecules exhibit efficient folding.

8:12AM U18.00002 Addressed Grids for Single-Nanoparticle Studies1 , W.D. TENNYSON, C.E. ALLEN, D.S. HARTNETT, M.E. CURTIS, A.R. DEDIGAMA, D.J. WASIELEWSKI, M.D. MCCUTCHEN, D.H. DAHANAYAKA, M.B. JOHNSON, L.A. BUMM, Center for Semiconductor Physics in Nanostructure, Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma, Norman, OK 73019, USA — We have developed a grid structure with a simple and robust address system to assist in locating and relocating individual substrate-supported nanoparticles. We demonstrate application of our addressed grids for facile characterization of the SAME nanoparticles in multiple instruments. Our grids can be prepared on a variety of substrates using lift-oﬀ photolithography. We will show addressed grids of Cr/Au on silicon, fused silica, and ITO coated glass as well as application to multiple measurements of the same nanoparticles by scanning electron microscopy, optical microscopy, atomic force microscopy, and single nanoparticle spectroscopy.

1This work has been supported by NSF CAREER grant No. CHE-0239803, NSF MRSEC No. DMR-0080054, and AFSRO No. FA9550-06-1-0365.

8:24AM U18.00003 Eﬀect of Environment on Single-Photochromic-Molecule , SATOSHI YOKOJIMA, Mitsubishi Chemical Group Science and Technology Research Center, INC. and CREST-JST, YASUTAKA FUJIU, MASANORI TACHIKAWA, Quantum Chemistry Division, Graduate School of Science, Yokohama-city University, JUN-WEI SHEN, QI GAO, PAUL TCHOUPE, TAKAO KOBAYASHI, AKINORI MURAKAMI, MITSURU YONEYAMA, KATSUYA KANDA, SHINICHIRO NAKAMURA, Mitsubishi Chemical Group Science and Technology Research Center, INC. and CREST-JST, TOSHIKAZU EBISUZAKI, Riken, TUYOSHI FUKAMINATO, MASAHIRO IRIE, Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University — Recent experimental results on the photochromic reactions of diarylethene derivatives at the single-molecule level by using a ﬂuorescence technique [T. Fukaminato, T. Sasaki, T. Kawai, N. Tamai, and M. Irie, J. Am. Chem. Soc. 126 (2004) 14843; M. Irie, T. Fukaminato, T. Sasaki, N. Tamai, and T. Kawai, Nature 420 (2002) 759.] is analyzed by the quantum chemical calculations and the molecular dynamics calculations.

8:36AM U18.00004 Single-molecule fluorescence quenching near small nanoparticles , V. N. PUS- TOVIT, T. V. SHAHBAZYAN, Jackson State University — We study theoretically radiative and nonradiative decay of a single molecule near small gold nanoparticle. The local field enhancement leads to an increased radiative decay rate while the energy transfer from molecule to optically-inactive electronic states in nanoparticle results in a decrease in fluorescence quantum efficiency for small molecule-nanoparticle distances. We performed a DFT-TDLDA calculation of both the enhancement and the quenching for small nanometer-sized gold nanoparticles. We found that in a close proximity to the surface, the non-radiative decay rate is dominated by generation of electron-hole pairs out of the Fermi sea resulting in a significantly lower quantum efficiency as compared to that obtained from electromagnetic calculations. For large distances, the efficiency is maximal for molecule polarized normal to the surface, whereas for small distances it is maximal for parallel orientation.

8:48AM U18.00005 Atomic-Scale Coupling of Photons to Single-Molecule Junctions , SHIWEI WU, Department of Physics and Astronomy, University of California, Irvine, CA 92697-4575, NAOKI OGAWA, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan, WILSON HO, Department of Physics and Astronomy and Department of Chemistry, University of California, Irvine, CA 92697-4575, USA — The study of optical phenomena at the atomic scale is expected to provide new understanding of molecules and their chemical dynamics. The combination of lasers with a low temperature scanning tunneling microscope (STM) has led to the observation of photo-induced resonant tunneling with sub-molecular spatial resolution for single molecules adsorbed on a solid surface [Science 312, 1362, (2006)]. Furthermore, the irradiation of femtosecond laser pulses into this single-molecule junction defined by STM results in non-linear coupling by two-photon excitation, rather than the single-photon coupling in the case of continuous wave (CW) lasers. These experiments lead to new opportunities by tapping into the unique properties of lasers and the STM. 9:00AM U18.00006 Energy Spectra of Individual Gold Monolayer Protected Clusters Mea- sured by Single Electron Tunneling Force Microscopy , NING ZHENG, JON JOHNSON, GANGLI WANG, CLAYTON WILLIAMS, University of Utah — Monolayer Protected Clusters (MPCs) exhibit strong quantum confinement effects and size dependent electronic, optical and chemical properties. The energy levels of individual gold MPCs (Au38 & Au140) have been directly measured by Single Electron Tunneling Force Microscopy at room temperature in UHV.[1,2] Single electrons, tunneling between a probe tip and individual gold MPCs are detected using a novel surface potential measurement technique.[2] Tunneling events to and from the MPCs are recorded as a function of the applied bias voltage. A clear electronic spectrum is obtained, showing a HOMO-LUMO gap for Au38 but not for Au140. For both MPCs the single electron charging energy is measured. Spectral differences from particle to particle are observed. The energy spectra obtained by this method are directly compared with existing electrochemical data,[3] showing good agreement. The methodology will be described and the measured electronic spectra for Au38 and Au140 will be presented and discussed. 1. E. Bussmann, D. J. Kim, and C.C. Williams, Appl. Phys. Lett. 85, 2538 (2004) 2. E. Bussmann, N. Zheng, and C. C. Williams, Nano Lett.; 2006; 6(11) 3. Lee, D el at, J. Am. Chem. Soc. 2004, 126, 6193

9:12AM U18.00007 On the reactivity of neutral metal oxide clusters in the gas phase: Detec- tion through 118 nm single photon ionization , SHENG-GUI HE, YAN XIE, ELLIOT BERNSTEIN, Department of Chemistry, Colorado State University — Single photon ionization by a vacuum ultra-violet (VUV, 118 nm) laser is successfully employed for the study of reactions of neutral metal oxide clusters (TimOn, FemOn, ComOn) with various simple molecules (CO, NO, SO2,H2O) in the gas phase. Neutral clusters are generated by reaction of laser ablation generated metal plasma with O2 in a supersonic expansion. Clusters are reacted with reactant gases in a ﬂow tube reactor. Detection of neutral clusters and products is through ionization with 118 nm laser radiation and time of ﬂight mass spectroscopy. Rich neutral cluster chemistry is observed: (1) TimO2m and TimO2m+1 absorb one or more H2O molecules for m ≥ 2 and m ≥ 1, respectively; (2) FeO2, FeO3, and possibly FeO are reactive with CO while Fe2O4 and Fe2O5 are less reactive; (3) Fe2O5 is reactive with NO and SO2, but FeO2 is much less reactive with them; and (4) small ComOn clusters (m ≤ 4 and n ≤ 6) are more reactive than large clusters (6 ≤ m ≤ 12 and 8 ≤ n ≤ 17) with CO, and among these small clusters, Co3O4 is particularly reactive. A detailed quantum chemistry study of FemOn reactions with CO is in progress. Preliminary calculations indicate that reactions of FeO and FeO2 with CO to produce CO2 are overall barrierless, in agreement with the experimental observations.

9:24AM U18.00008 ABSTRACT WITHDRAWN —

9:36AM U18.00009 ABSTRACT WITHDRAWN — 9:48AM U18.00010 Structures and energetics of hydrocarbon molecules in the full hydrogen chemical potential range , YONGXIN YAO, TZU-LIANG CHAN, CAI-ZHUANG WANG, KAI-MING HO, Iowa State University — Hydrocarbons, especially polycyclic aromatic hydrocarbons (PAH), attract much interest as candidates for the unidentiﬁed infrared bands (UIRs), UV extinction curve and diﬀuse interstellar bands in the interstellar medium. While many experiments and quantum chemical calculations of the infrared spectra on human-selected hydrocarbons have been done, it remains an open question. A key reason may be the complicated phase space of hydrocarbons originated from the enormous bonding ability of carbon. Here we present a series of unbiased global search for hydrocarbon molecules (CnHm, 1

10:00AM U18.00011 Structural evolution of Au nanoclusters: From planar to cage to tubular motifs1 , BOKWON YOON, Georgia Institute of Technology, XIAOPENG XING, Rowland Institute at Harvard, UZI LANDMAN, Georgia Institute of − Technology, JOEL H. PARKS, Rowland Institute at Harvard — The evolution of structural motifs of gold cluster anions, Aun , in the size range n = 11 − 24 has been determined through a comparison of electron diﬀraction data with density functional calculations. The results provide clear evidence for a transformation from planar to three-dimensional structures in the range n = 12 − 14, the development of cage structures for n = 16 and 17, the appearance of a tetrahedral structure at n = 20, and the emergence of a highly symmetric tubular structure for n = 24.

1supported by the AFOSR and the U. S. DOE

10:12AM U18.00012 Bulk Quantities of Noble Gas Nanoclusters with Five-Fold Symmetry Stabilized in Superfulid Helium , V. KIRYUKHIN, Rutgers Univ, E.P. BERNARD, V.V. KHMELENKO, R.E. BOLTNEV, D.M. LEE, Cornell Univ., N.V. KRAINYUKOVA, Inst. Low Temp. Phys., Kharkov, Ukraine — Bulk quantities (volume∼cm3, atomic density∼1019-1020 cm−3) of noble gas nanoclusters (size∼5-6 nm) were produced in superfluid helium by injection technique. X-ray diffraction measurements show that the samples consist of weakly interacting nanoclusters with five-fold symmetry axes, such as icosahedra and decahedra. These results open new opportunities for fundamental research of nanoclusters of noble gases and other materials in well-controlled environments using experimental techniques requiring bulk samples.

10:24AM U18.00013 Support-induced Catalytic Activity of Gold Nanocluster , CHUN ZHANG, BOK- WON YOON, UZI LANDMAN, School of Physics, Georgia Institute of Technology — The catalytic activity of gold nanoclusters supported on metal-oxide surfaces is a topic of active research efforts. Recently, a dimensionality crossover of gold clusters, adsorbed on a metal-supported thin film of MgO(100), has 1 been predicted . We present here a first- principles study of the catalytic activity of a planer Au20 cluster on two- layer MgO(100) film supported by a Mo surface. Both Langmuir-Hinshelwood (LH) and Eley–Rideal (ER) mechanisms of CO oxidation are investigated. The barrier of the LH mechanism is found to be 0.15 eV. For the ER mechanism, the barrier depends on the direction of approach of the CO molecule to the preadsorbed oxygen molecule, varying between a vanishing barrier height and 0.2 eV. Charge transfer from the Mo surface to the cluster supported on the thin MgO(100) film plays a key role in the catalyzed CO oxidation process.

10:36AM U18.00014 The Electronic Structure of Diamondoids: When does a Molecule Become a Nanoparticle? , TREVOR WILLEY, Lawrence Livermore National Laboratory, CHRISTOPH BOSTEDT, T. MOLLER, Technische Universitat, Berlin, Germany, J. E. DAHL, S. G. LIU, R. M. K. CARLSON, MolecularDiamond Technologies, Chevron, Richmond, CA, T. VAN BUUREN, R. W. MEULENBERG, E. NELSON, L. J. TERMINELLO, Lawrence Livermore National Laboratory — Methane and diamond are common materials with well-known, but extremely diﬀerent properties. Fundamental, compelling questions then arise: with sp3 bound carbon molecules/clusters, at what sizes do diamond-like properties emerge? Pure, defect-free, perfectly hydrogen-terminated diamondoids, from ∼0.5 nm to ∼1 nm, bridge the gap between molecules and nanoparticles. Furthermore, experiments in the gas phase eliminate particle-particle interaction and ensure measurement of pure, pristine, and undamaged molecules. X-ray absorption probes the unoccupied electronic states; the carbon K-edge reveals rich electronic structure in the series methane, cyclohexane, adamantane, diamantane, through to hexamantane. Diamondoids show the emergence of a diamond-like band structure. Using x-ray absorption and soft x-ray emission, we will compare our experimental LUMO/conduction band and HOMO/valence band positions with predicted changes in HOMO-LUMO gap from several calculations. Thursday, March 8, 2007 8:00AM - 11:00AM — Session U19 DCP: Focus Session: Ultrafast Dynamics using X-rays and Electrons I Colorado Convention Center 104

8:00AM U19.00001 Ultrafast X-ray Science at SLAC and LCLS1 , PHILIP BUCKSBAUM, PULSE Center, Stanford Linear Accelerator Center — Hard x-rays (E greater than 1 keV) can probe the structure of matter on the length scale of a chemical bond. Ultrafast lasers (t less than 1 ps) can capture the quantum dynamics of single vibration in a crystal lattice or in a molecule, and they have also been used to view the transient molecular-scale transformations of chemical reactions. Until recently, only laser-induced plasma radiation was capable of capturing these ultrafast dynamics and also viewing them on the scale of a single chemical bond. The recent Sub-Picosecond Pulse Source experiment at SLAC was the first instrument based on synchrotron radiation from an undulator that could do both. During its two-year run, its 8 keV, 80 fs x-ray pulses were the brightest ultrafast x-rays in the world. This is just the beginning. The planned X-ray free electron laser at SLAC (LCLS) will generate focused x-ray fields as strong as atomic binding fields, comparable to today’ highest intensity lasers. These new tools are creating some special opportunities for new science, and also some challenges. I will discuss these, and present recent progress in ultrafast x-ray sources and science.

1This work is supported by the U.S. Department of Energy, Oﬃce of Basic Energy Sciences

8:36AM U19.00002 Ultrafast lattice dynamics in laser-excited solids probed with femtosecond X-ray diffraction , KLAUS SOKOLOWSKI-TINTEN, University of Duisburg-Essen, Germany — Ultrafast pulsed excitation of solids provides a unique way of depositing energy into materials and to create states of strong electronic excitation and high temperature and pressure. With the initial deposition of energy a complex chain of elementary physical processes is triggered which can lead to structural changes on very rapid time-scales, and often along unusual, non-equilibrium pathways. Due to the unique combination of atomic-scale spatial and temporal resolution, the recent progress in the development of ultrafast X-ray sources has provided new opportunities for studying such processes. This talk will discuss our recent work on ultrafast time-resolved X-ray diffraction using laser-driven as well as accelerator-based femtosecond X-ray sources. Examples include the non-thermal melting transition in semiconductors, the direct observation of large-amplitude coherent optical phonons, and studies of the energy relaxation in optically excited solids through measurements of the transient Debye-Waller effect.

9:12AM U19.00003 Non-Thermal Liquid Formation Dynamics Studied with Ultrafast Diffuse X-Ray Scattering , KELLY GAFFNEY, PULSE Center, SLAC, CHRISTIAN BLOME, DESY, SIMON ENGEMANN, PULSE Center, SLAC, DAVID FRITZ, LUSI, SLAC, PATRICK HILLYARD, Stanford University, Department of Chemistry, JORGEN LARSSON, Lund University, AARON LINDENBERG, PULSE Center, SLAC, MATTHIEU NICOUL, University Duisburg-Essen, DAVID REIS, FOCUS Center, University of Michigan, KLAUS SOKOLOWSKI- TINTEN, University of Duisburg-Essen, JERRY HASTINGS, LUSI, SLAC, THE SUB-PICOSECOND PULSE SOURCE COLLABORATION — The ultrafast melting dynamics of a laser excited semiconductor crystal have been studied with femtosecond x-ray scattering. We have used diffuse x-ray scattering to determine that a liquid structure appears within 2 ps of laser excitation. This structure preserves the density of the crystal, and can be well fit with a hard sphere structure factor, unlike equilibrium liquid InSb. At a delay time of 100 ps, an under-dense liquid structure forms with large amplitude scattering at intermediate momentum transfer. A concurrent rise in small angle scattering intensity suggests that voids form in this under-dense liquid. Cooling and contraction leads to the formation of a dense liquid structure on the ns time scale distinct from that of the equilibrium liquid InSb. The equilibrium liquid structure does not appear until delay times of 20 ns and longer.

9:24AM U19.00004 Laser-induced phonon-phonon interaction in bismuth , MARTIN GARCIA, EEUWE ZIJLSTRA, Physics Department, Universität Kassel — We demonstrate that the coupling between laser-induced coherent phonons in bismuth leads to the appearance of mixing signals in the isotropic reflectivity. As a consequence modes that cannot usually be detected by means of the isotropic reflectivity show up. We further demonstrate that this interaction is strongly dependent on the laser fluence and is for that reason only observable when sufficiently intense laser pulses are used. In addition, we demonstrate that the coupling between phonons of the same symmetry leads to the appearance of higher harmonics in the isotropic reflectivity.

9:36AM U19.00005 Magnetic field effects on ultrafast lattice compression dynamics of Si(111) crystal when excited by linearly-polarized femtosecond laser pulses , KOJI HATANAKA, HIDEHO ODAKA, KIMITOSHI ONO, HIROSHI FUKUMURA, Tohoku University — Time-resolved X-ray diffraction measurements of Si (111) single crystal are performed when excited by linearly-polarized femtosecond laser pulses (780 nm, 260 fs, negatively-chirped, 1 kHz) under a magnetic field (0.47 T). Laser fluence on the sample surface is 40 mJ/cm2, which is enough lower than the ablation threshold at 200 mJ/cm2. Probing X-ray pulses of iron characteristic X-ray lines at 0.193604 and 0.193998 nm are generated by focusing femtosecond laser pulses onto audio-cassette tapes in air. Linearly-polarized femtosecond laser pulse irradiation onto Si(111) crystal surface induces transient lattice compression in the picosecond time range, which is confirmed by transient angle shift of X-ray diffraction to higher angles. Little difference of compression dynamics is observed when the laser polarization is changed from p to s-pol. without a magnetic field. On the other hand, under a magnetic field, the lattice compression dynamics changes when the laser is p-polarized which is vertical to the magnetic field vector. These results may be assigned to photo-carrier formation and energy-band distortion.

9:48AM U19.00006 X-ray studies of acoustic vibrations from semiconductor superlattices. , MARIANO TRIGO, YU-MIIN SHEU, DAVID REIS, ROBERTO MERLIN, MATTHEW REASON, RACHEL GOLDMAN, University of Michigan — We present ultrafast X-ray studies of acoustic phonons transmitted from a GaAs/AlAs superlattice. An ultrafast laser pulse impulsively excites coherent acoustic waves in the superlattice which subsequently transmit into the GaAs substrate. A short x-ray pulse can be used to probe the wave packet traveling in the bulk material, without the need of a transducer such as a second SL by detecting sidebands of Bragg diffraction. Unlike optical probes, the short wavelength of the x-rays allows momentum resolved detection over a wide range of wavevectors. This method should in principle be able to detect the whole spectrum of the generated excitations. Furthermore, the coherent part of the excitation is followed by a much slower thermal diffusion which, as we will show, can also be studied by time resolved x-ray scattering. [1] R. Merlin, Solid State Comm. 102, 207 (1997). [2] D. A. Reis et al., Phys. Rev. Lett. 86, 3072 (2001) 10:00AM U19.00007 Ultrafast X-Ray Diffraction Study of Potential Energy Surface Evolution in InSb Under Intense Laser Excitation , PATRICK HILLYARD, Stanford University, Department of Chemistry, KELLY GAFFNEY, AARON LINDENBERG, SIMON ENGEMANN, PULSE Center, Stanford Linear Accelerator Center, DAVID REIS, FOCUS Center, University of Michigan, ANIRUDDHA DEB, PULSE Center, Stanford Linear Accelerator Center, DREW MEYER, Stanford University, Department of Chemistry, JEROME HASTINGS, PULSE Center, Stanford Linear Accelerator Center — Ultrafast time-resolved x-ray diffraction has been used to directly monitor atomic disordering in InSb as a function of carrier density. The carrier dependent curvature of the potential energy surface has been determined from the time evolution of the atomic structure. Three regimes have been identified. At low carrier densities, atomic disordering occurs via a thermal mechanism with an exponential time constant determined by the electron-phonon coupling constant. Upon increasing excited carriers to roughly 5% of the valence band electron population, a sharp transition is observed and the predominant disordering mechanism is inertial motion on a softened potential energy surface with a Gaussian time constant of ∼400 fs. For a carrier density above ∼20%, accelerated atomic motion on an inverted potential energy surface is observed. This inverted regime was previously predicted by theory but had been unobserved until now.

10:12AM U19.00008 Transient Lattice Deformation in Laser-Irradiated Semiconductor Studied by Picosecond Time-Resolved X-ray Diﬀraction , KAZUTAKA NAKAMURA, HIROAKI KISHIMURA, YOICHIRO HIRONAKA, KEN-ICHI KONDO, Tokyo Institute of Technolgy, TOSHIYUKI ATOH, Tohoku University — The transient lattice behavior of Si(111) single crystal under 300-ps laser irradiation has been studied by using picosecond time-resolved X-ray diﬀraction. When the laser is irradiated, the rocking curves of the laser-irradiated Si(111) have a higher-angle-shifted component due to lattice compression by laser ablation. The maximum lattice strain is estimated at 5.6 %, which is larger than the Hugoniot elastic limit for Si (111). After 1000 ps, a broadening of the main peak is observed. In addition, the rocking curve of the recovered sample is clearly broader than that of a pristine sample. Reciprocal space mapping for the recovered sample shows that the lattice spacing of the recovered sample does not change from that of the pristine sample, whereas lattice planes are misoriented. The results of the time-resolved measurement and the assessment of the recovered sample indicate that mosaic blocks with inclined orientations are induced by laer-driven elastic compression and the subsequent pressure release within 1000 ps, rather than plastic deformation.

10:24AM U19.00009 ABSTRACT WITHDRAWN — 10:36AM U19.00010 Ultrafast Photoinduced Solid State Phase Transitions Probed by Fem- tosecond Electron Diffraction , R. ERNSTORFER, M. HARB, C.T. HEBEISEN, T. DARTIGALONGUE, R.E. JORDAN, G. SCIAINI, R.J.D. MILLER, INSTITUTE FOR OPTICAL SCIENCES AND DEPARTMENTS OF CHEMISTRY AND PHYSICS, UNIVERSITY OF TORONTO TEAM — Fem- tosecond Electron Diffraction harbors great potential for providing atomic resolution of structural changes as they occur, essentially watching atoms move in real time. It combines temporal resolution on the hundreds of femtoseconds scale – a time scale typically only accessible by time-resolved optical spectroscopy – with real-space structural information on the atomic scale. We applied this technique to study the structural response of thin free-standing metal and semiconductor [1] films upon ultrafast electronic photo-excitation within a wide range of excitation levels. These studies distinguish the different mechanisms, thermal vs. non-thermal, of energy transfer from electronic to vibrational degrees of freedom resulting in different melting mechanisms for both classes of materials. In addition, we discuss a technique we recently established to determine the duration of the electron pulses by using the ponderomotive force of an intense femtosecond laser pulse to sequentially scatter parts of the electron pulse and found the electron pulse duration to be about 400 fs [2]. [1] M. Harb et.al., J. Phys. Chem. B, in print. [2] C.T. Hebeisen et al., Opt. Lett 31, 3517 (2006).

10:48AM U19.00011 Ultrafast Time-resolved Electron Diffraction with Megavolt Electron Beams1 , JEROME HASTINGS, Stanford Linear Accelerator Center, FEDOR RUDAKOV, DAVID DOWELL, JOHN SCHMERGE, STEPHEN GIERMAN, PETER WEBER — An rf photocathode electron gun is used as an electron source for ultrafast time-resolved pump-probe electron diffraction. We observed single-shot diffraction patterns from a 160 nm Al foil using the 5.4 MeV electron beam from the Gun Test Facility at the Stanford Linear Accelerator. Excellent agreement with simulations suggests that single-shot diffraction experiments with a time resolution approaching 100 fs are possible. Details of the measurements and applications will be discussed

1DD, JH, JS, SG are supported by Stanford University for the Department of Energy under contract number DE-AC03-76SF00515. PMW funded by Army Research Oﬃce, contract number DAAD19-03-1-0140, and Department of Energy, contract number DE-FG02-03ER15452.

Thursday, March 8, 2007 8:00AM - 10:48AM — Session U26 DCP: Focus Session: Charge Transport in Nanostructures I Colorado Convention Center 205 8:00AM U26.00001 Transport in nanoscale systems: hydrodynamics, turbulence, and local electron heating , MASSIMILIANO DI VENTRA, UC San Diego — Transport in nanoscale systems is usually described as an open-boundary scattering problem. This picture, however, says nothing about the dynamical onset of steady states, their microscopic nature, or their dependence on initial conditions [1]. In order to address these issues, I will first describe the dynamical many-particle state via an effective quantum hydrodynamic theory [2]. This approach allows us to predict a series of novel phenomena like turbulence of the electron liquid [2], local electron heating in nanostructures [3], and the effect of electron viscosity on resistance [4]. I will provide both analytical results and numerical examples of first-principles electron dynamics in nanostructures using the above approach. I will also discuss possible experimental tests of our predictions. Work supported in part by NSF and DOE. [1] N. Bushong, N. Sai and M. Di Ventra, “Approach to steady-state transport in nanoscale systems” Nano Letters, 5 2569 (2005); M. Di Ventra and T.N. Todorov, “Transport in nanoscale systems: the microcanonical versus grand-canonical picture,” J. Phys. Cond. Matt. 16, 8025 (2004). [2] R. D’Agosta and M. Di Ventra, “Hydrodynamic approach to transport and turbulence in nanoscale conductors,” cond-mat/05123326; J. Phys. Cond. Matt., in press. [3] R. D’Agosta, N. Sai and M. Di Ventra, “Local electron heating in nanoscale conductors,” cond-mat/0605312; Nano Letters, in press. [4] N. Sai, M. Zwolak, G. Vignale and M. Di Ventra, “Dynamical corrections to the DFT-LDA electron conductance in nanoscale systems,” Phys. Rev. Lett. 94, 186810 (2005).

8:36AM U26.00002 Molecular conductance simulations with a ‘hybrid’ DFT-NEGF approach , ALEXANDER PROCIUK, BARRY DUNIETZ, University of Michigan — A time propagated DFT-NEGF methodology for describing molecular conductance through extended metal-molecule-metal systems is developed. This innovative method calculates transient currents in the presence of time dependent perturbations applied to the molecular junction. Steady state currents can be calculated in the presence of finite temporal perturbations. The electronic density, represented by the lesser GF, is recast into a form that expresses the temporal propagation of the energy spectrum. The effects of the potential biased metal electrodes are expressed with energy dependent ‘self-energy’ terms. This results in a manageable and compact expression for the electron density. This density can be propagated by a specialized scheme that elucidates the transport properties of the system. Propagation, in the absence of an applied temporal perturbation, reduces to an alternative and novel NEGF transport methodology. In addition, applied perturbations can be propagated fully or approximated to any order in time dependent perturbation theory. Calculations are performed for various DFT functionals with a LANL2DZ ECP basis set. 8:48AM U26.00003 Local electron heating in nanoscopic conductors1 , ROBERTO D’AGOSTA, NA SAI, MASSIMILIANO DI VENTRA, University of California - San Diego — The electron current density in nanoscale junctions is typically several orders of magnitude larger than the corresponding one in bulk electrodes. Consequently, the electron-electron scattering rate increases substantially in the junction. This leads to local electron heating of the underlying Fermi sea [1] in analogy to the local ionic heating that is due to the increased electron-phonon scattering rates [2]. By using a novel hydrodynamic formulation of transport [3], we predict the bias dependence of local electron heating in quasi-ballistic nanoscale conductors [1], its effect on ionic heating [1], and the consequent observable changes in the inelastic conductance [4]. [1] R. D’Agosta, N. Sai and M. Di Ventra, accepted in Nano Letters (2006). [2] Y.-C. Chen, M. Zwolak, and M. Di Ventra, Nano Lett. 3, 1961 (2003); Nano Lett. 4, 1709 (2004); Nano Lett. 5, 621 (2005). M. J. Montgomery, T. N. Todorov, and A. P. Sutton, J. Phys. Cond. Matt. 14, 5377 (2002). [3] R. D’Agosta and M. Di Ventra, J. Phys. Cond. Matt. in press. [4] R. D’Agosta and M. Di Ventra, in preparation.

1Work supported in part by NSF and DOE.

9:00AM U26.00004 Theoretical study on transport properties of photo-reactive molecules , NORIHISA OYAMA, HISASHI KONDO, University of Tokyo, JUN NARA, TAKAHISA OHNO, NIMS — Azobenzene and stilbene molecules are powerful candidates for ultra-fast optical switches because of their ultra-fast photo-isomerization (trans-> cis and cis-> trans). These molecules have similar molecular structures. However, the isomerization mechanisms are completely diﬀerent. In this work, we investigate the transport properties of both azobenzene and stilbene molecules based on the non-equilibrium green function (NEGF) method, and compare the results. This study was supported by RSS21 project and Grant-in-Aid for Scientiﬁc Research (No.17064017) of MEXT of the Japanese government. The calculations in this work were carried out partly using the Numerical Materials Simulator in National Institute for Materials Science (NIMS), and partly using the NEC-SX5 at Cybermedia Center, Osaka University.

9:12AM U26.00005 Electroluminescence from individual CdS/CdSe nanowires contacted by poly(3-hexylthiophene) , KRISTIN MAHER, LIAN OUYANG, DONG YU, YONG-JOO DOH, CHUN YU, Department of Chemistry, Harvard University, HONGKUN PARK, Department of Chemistry and Department of Physics, Harvard University — Nanocrystal-polymer composites have been shown to exhibit interesting optoelectronic properties. However, only bulk properties of these materials have been measured, and the single nanocrystal-polymer interface is poorly understood. We report the fabrication and characterization of light-emitting transistors incorporating individual CdS/CdSe heterostructure nanowires and a thin ﬁlm of poly(3-hexylthiophene) (P3HT). The nanowire is contacted at one end by a metal electrode and at the other by a thin ﬁlm of P3HT, a p-type conducting polymer. The devices show rectifying current-voltage behavior and light emission can be observed at forward bias. The peak wavelength and the full width at half-maximum of the electroluminescence were 1.68 eV and 0.08 eV, respectively. The mechanism for light emission will be discussed.

9:24AM U26.00006 Photoconductivity and multiple exciton generation in arrays of coupled semiconductor nanoparticles , MATTHEW BEARD, JOSEPH LUTHER, KELLY KNUTSEN, QING SONG, RANDY ELLINGSON, ARTHUR NOZIK, NREL — Three dimensional arrays of semiconductor nanocrystals (NCs) in p-i-n structures are a novel approach to solar energy conversion that offers the potential to control the microscopic charge generation, separation, and transport so as to maximize solar energy conversion efficiencies. A necessary characteristic of the NC arrays is that they exhibit very high conductivity for electrons and holes; this requires strong inter-NC electronic coupling and the subsequent formation of extended electronic states. Many factors, such as inter-NC spacing, site energy dispersion, NC size and shape, cross linking, and Coulomb charging determine the inter-NC coupling. In addition, efficient carrier transport in NC solids requires minimization of carrier loss processes such as surface trapping. All of these factors are highly interdependent. Time-resolved THz spectroscopy (TRTS) is a powerful experimental tool that measures both photoconductivity, in a non-contact fashion, and carrier dynamics simultaneously, with sub-picosecond temporal resolution. We report TRTS for a series of chemically treated PbSe NCs where the inter-NC separation has been varied in a systematic manner. We also report multiple exciton generation (MEG) QYs within the coupled arrays.

9:36AM U26.00007 Photoconductivity of Nanotapes Self-assembled from meso-Tri(4- sulfonatophenyl)monophenylporphine , A. L. YEATS, B. MASSARE, W. F. SMITH, Haverford College, A. D. SCHWAB, Applachian State U., J. C. DE PAULA, Lewis and Clark College, D. E. JOHNSTON, A. T. JOHNSON, U. of Pennsylvania — We have shown1 that meso-Tetra(4- sulfonatophenyl)porphine (TPPS4) forms well-deﬁned nanorods in acidic solution. Experiments on related molecules provide insight into the mechanisms for self-assembly and photoconduction. Meso-Tri(4-sulfonatophenyl)monophenylporphine (TPPS3) has one fewer sulfonate group than TPPS4, but is otherwise identical. Previous work2 has shown that, when deposited onto substrates by rotary evaporation, it forms folded nano-ribbons. We have found that, when deposited via immersion and spin-drying, it forms tape-like aggregates of two distinct heights. The larger width of these nanotapes (compared to TPPS4 nanorods) is expected from the smaller in-solution charge of the monomer. The TPPS3 aggregates exhibit photoconductive properties very similar to those of 1 2 TPPS4. The aggregates ordinarily form in solution, but can also be surface-catalyzed. A.D. Schwab et al., Nano Letters 4, 1261 (2004). J. Crusats et al., Chem Commun. 1588 (2003).

9:48AM U26.00008 Inelastic electron tunneling -induced light emission from a metal - quantum dot - metal double barrier tunnel junction , ANTTI MAKINEN, ALAN WAN, JAMES LONG, Naval Research Laboratory, Washington, DC 20375 — A double barrier tunnel junction formed by a scanning tunneling microscope (STM) tip together with the substrate-tethered quantum dots provides a ﬂexible architecture to explore the characteristics of envisaged nanoparticle-based optoelectronic devices. STM-induced light emission (STM-LE) measurements of ligand-capped CdSe/ZnS quantum dots, tethered to a gold substrate, reveal a light generation mechanism, which is driven by inelastic electron tunneling (IET) at a threshold voltage. The threshold voltage for STM-LE is found to depend on the optical gap of the quantum dots, stipulating a simple energy conservation rule for light emission through IET.

10:00AM U26.00009 Break-down of the density-of-states description of scanning tunneling spectroscopy in supported metal clusters , MARTIN GARCIA, Physics Department, UniversitätKassel, MARIO DE MENECH, Physics Department, Universität Kassel and Max-Plank-Institute fürPhysik komplexer Systeme, ULF SAALMANN, Max-Plank-Institute fürPhysik komplexer Systeme — Low-temperature scanning tunneling spectroscopy allows to probe the electronic properties of clusters at surfaces with unprecedented accuracy. By means of quantum transport theory, using realistic tunneling tips, we obtain differential conductance curves which considerably deviate from the cluster’s density of states. Our study explains the remarkably small number of peaks in the conductance spectra observed in recent experiments. We demonstrate that the unambiguous characterization of the states on the supported clusters can be achieved with energy-resolved images, which we are able to construct with a complete simulation of the experimental imaging procedure. 10:12AM U26.00010 Measurement of the Conductance of Single Conjugated Molecules , AMIR YACOBY, Harvard University — Electrical conduction through molecules depends critically on the delocalization of the molecular orbitals, and their weight on the metallic contacts. Thiolated conjugated organic molecules are therefore often considered as good candidates for molecular conductors. In such molecules the orbitals are delocalized throughout the molecular backbone, with substantial weight on the sulfur-metal bonds. However, their relatively small size, typically 1 nm, calls for innovative approaches to realize a functioning single molecule device. In this paper we report a new approach for contacting a single molecule and use it to study the effect of localizing groups within a conjugated molecule on the electrical conduction. Our method is based on synthesizing a dimer structure, consisting of two gold colloids connected by a di-thiolated short organic molecule, and electrostatically trapping it between two metal electrodes. We study the electrical conduction through three short organic molecules: A fully conjugated molecule, 4,4’-biphenyldithiol (BPD), 4,4’-biphenyletherdithiol (BPED) in which the conjugation is broken at the center by an oxygen atom, and 1,4-benzenedimethanethiol (BDMT), where the conjugation is broken near the contacts by a methylene group. We find that the oxygen in the BPED and the methylene groups in the BDMT suppress the electrical conduction relative to the BPD.

Thursday, March 8, 2007 11:15AM - 2:15PM — Session V18 DCP: Chemical Dynamics & Molecular Spectroscopy Colorado Convention Center 103

11:15AM V18.00001 Ultrafast 2D IR vibrational echo chemical exchange spectroscopy1 , JUNRONG ZHENG, MICHAEL FAYER, Stanford University, Chemistry Department — Ultrafast 2D IR vibrational echo chemical exchange spectroscopy, akin the 2D NMR methods, is applied to the study of dynamics of weakly hydrogen bonded solute-solvent complexes in liquid solutions. The strengths of the solute-solvent hydrogen bonds are adjusted by modifying the chemical structures of the solutes and solvents. For the eight samples studied, the formation enthalpies vary from -0.6 kcal/mol to -2.5 kcal/mol, and the dissociation time constants vary from 3 ps to 32 ps. The dissociation rates of the hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. As another example of chemical exchange spectroscopy, the rate of carbon-carbon single bond rotational isomerization of an ethane derivative in room temperature liquid solution is measured. Based on the experimental results and density functional theory calculations, the time constant for the ethane internal rotational isomerization under the same conditions is about 12 ps.

1This work was supported by grants from AFOSR (F49620-01-1-0018) and NSF DMR (DMR-0332692).

11:27AM V18.00002 Dynamic Nuclear Polarization (DNP) Using Nitroxide Radicals , BRANDON ARMSTRONG, Dept. of Physics, University of California, Santa Barbara, EVAN MCCARNEY, SONGI HAN, Dept. of Chemistry, University of California, Santa Barbara — The theory of the Overhauser Effect in liquids is well established, but measured DNP enhancements from nitroxide radicals depart significantly from prediction. To achieve large signal enhancements, milli-molar concentrations of radicals are needed, a regime where Heisenberg exchange of the unpaired electron is significant. Therefore, the three electron transitions resulting from hyperfine interactions with the 14N nucleus cannot be treated as independent in a DNP experiment. Furthermore, the relaxation rate of 14N can be easily on the same order of magnitude or even greater than the relaxation rate of the unpaired electron, contributing to the mixing of the hyperfine states, even in the absence of Heisenberg exchange. We present a quantitative study and a new model of 1H DNP enhancement of water by varying radical concentrations and solvent viscosities of natural abundance 14N versus 15N isotope enriched 4-Oxo-TEMPO free radical at 0.35 Tesla.

11:39AM V18.00003 Comparison of Electronically Excited Photodissociation between Nitramine Energetic Materials and Model Systems , YUANQING GUO, MARGO GREENFIELD, ATANU BHATTACHARYA, ELLIOT BERNSTEIN, Department of Chemistry, Colorado State University — Nitramine energetic materials (RDX, HMX and CL20) have broad applications as explosives and fuels. Model systems (1,4-dinitropiperazine, nitropiperidine, nitropyrrolidine and DMNA) have similar molecular structures, but they are unable to be used as fuels and explosives. To elucidate the diﬀerence between them, both nanosecond and femtosecond mass resolved excitation spectroscopy have been employed to investigate the mechanisms and dynamics of the electronically excited photodissociation of these materials. NO is a dominant dissociation product. Based upon the experimental observation and calculations of potential energy surfaces for these systems, we suggest that energetic materials dissociate from their ground electronic states after relaxing from the ﬁrst excited states, and that the model systems dissociate from their excited state. In both cases a nitro-nitrite isomerization is part of the reaction mechanism. Parent ions of DMNA and nitropyrrolidine are observed in fs experiments. All the other molecules generate NO as a product even in fs time regime.

11:51AM V18.00004 UV excited electronic state decomposition of energetic materials and model systems using fs laser spectroscopy , MARGO GREENFIELD, YUANQING GUO, ATANU BHATTACHARYA, ELLIOT BERN- STEIN, Colorado State University, Chemistry Department — Time resolved (fs) photodissociation experiments have been performed in eﬀorts to elucidate the dynamics controlling the excited electronic state decomposition of the energetic materials RDX and HMX and their associated model systems (dimethyl- nitramine, nitropyrrolidine, nitropiperidine, and dinitropiperazine). The initial decomposition product of the energetic materials and model systems is the NO molecule. Femtosecond pump-probe techniques have been employed to measure the photodissociation dynamics of these systems via the initial NO product at three wavelengths (226 nm, 228 nm, 230 nm). The NO molecule has a non-resonant two-photon absorption at 228 nm and 230 nm and single photon resonant absorption for the A2Σ ←X2Π(0,0) transition. Both pump-probe transients at non-resonant absorption and resonant absorption wavelengths indicate the dynamics of the energetic material’s decomposition from the excited electronic state is faster than the time duration of our laser pulse (180 fs) and notably diﬀerent from some of the model systems.

12:03PM V18.00005 Photoinduced ring-opening mechanism in several model diarylethenes1 , PETRA SAUER, ROLAND E. ALLEN, Texas A&M University — Recent experimental results suggest that derivatives of diarylethenes may be viable candidates for switches in molecular devices. In these molecules, the ring-opening and ring-closing reactions are induced with laser pulses of diﬀerent frequencies. We have shown that the ring-opening mechanism in the simplest of all diarylethenes, stilbene, occurs via a HOMO-LUMO avoided crossing and subsequent depopulation of the excited state with minimal involvement of other orbitals. We now show that the same photoinduced ring-opening process for both oxygen (C10H8O2) and sulfur (C10H8S2) containing diaryethenes involves higher order excited states. We will show simulation results in which the initial laser pulse excitation induces a transition from HOMO to LUMO. Due to both nuclear motion and symmetry changes, this laser pulse also excites some percentage of the electronic population out of orbitals lower in energy than the HOMO and into orbitals higher in energy than the LUMO. In order for the ring-opening event to occur, the electronic population in the higher excited states is ﬁrst transferred, via a series of avoided crossings, into the LUMO. A subsequent avoided crossing between the HOMO and LUMO then allows ring-opening.

1This work was supported by the Robert A. Welch Foundation (Grant A-0929). 12:15PM V18.00006 Cooling and Trapping of NH radicals , L. PAUL PARAZZOLI, CARLOS ROMERO, DANIEL LOBSER, HEATHER LEWANDOWSKI, University of Colorado — In the past decade, cooling and trapping of atoms has allowed physicists to probe the nature of quantum mechanics on a macroscopic scale. Molecules, having a more complex structure, are considerably more diﬃcult to cool. However, it is their complex structure, including rovibrational states and permanent dipole moments, which make them so interesting. We cool metastable NH (1∆) radicals using supersonic expansion coupled with Stark deceleration. The NH radicals are created by photolysis of HN3 during supersonic expansion. The supersonic expansion produces a cold beam of radicals, which is loaded into a Stark decelerator. The Stark decelerator uses time varying inhomogeneous electric ﬁelds to decelerate the NH molecules. The resulting molecular sample has a temperature of 10 -100 mK. Further cooling will be explored using interactions with ultracold Rubidium atoms.

12:27PM V18.00007 First Principles Simulations of THz Spectra of Acephate: Insight Into the Phonon Signatures. , YIMING ZHANG, XIHONG PENG, YUNQING CHEN, SAROJ NAYAK, X.-C. ZHANG, Rensselaer Polytechnic Institute, RENSSELAER POLYTECHNIC INSTITUTE TEAM — Acephate is an insecticide that kills insects by disrupting nervous system functions. THz spectroscopy oﬀers a unique tool for detecting trace amount of these materials. Using a combination of solid state ﬁrst principles simulations and gas phase quantum mechanical modeling we have studied phonon spectra of acephate compound. This talk will present a detailed vibrational spectra analysis over a wide range of frequency and our computational data will be compared with available experimental results.

12:39PM V18.00008 Hydrophobic dependence of molecules at the liquid/solid interface as studied with infrared-visible sum frequency generation spectroscopy , BRYAN HSU, VERONIQUE LACHAT, GA- BOR SOMORJAI, MOHSEN YEGANEH, DEPARTMENT OF CHEMISTRY, UNIVERSITY OF CALIFORNIA, BERKELEY COLLABORATION, CORPORATE STRATEGIC RESEARCH, EXXONMOBIL RESEARCH AND ENGINEERING COMPANY COLLABORATION — We report IR-vis SFG spectra obtained at the interface of liquids with hydrophobic and hydrophilic solid surfaces. The hydrophilic and hydrophobic surfaces used were sapphire and a dense methyl-terminated sapphire surface from chemically bonded octadecyltrichlorosilane (OTS), respectively. Orientation calculations of SSP (IR, vis, and SF polarizations) and SPS polarizations of acetonitrile on the OTS and sapphire showed tilt angles of approximately 90 and 40 degrees, respectively. The CD3 symmetric stretch of methanol (d4) at OTS and sapphire showed a blue-shift for the latter but no shift for the former when compared to FTIR of the bulk liquid. This may be due to changing H-bonding characteristics with methanol orienting its hydroxyl end towards sapphire and away from OTS. PPP spectra of n-heptane (d16) and n-hexadecane (d34) showed weaker intensity CD3 antisymmetric stretches on sapphire compared to OTS, with a larger decrease for n-hexadecane. This can be interpreted as the hydrocarbons curling away from sapphire more so than OTS, especially with n-hexadecane.

12:51PM V18.00009 Observation of the Ae − Xf Electronic Transition of the Jet-Cooled Methyl Peroxy Radical by High Resolution CRDS , PATRICK DUPRE´1, The Ohio State University, Columbus, SHENGHAI WU, PATRICK RUPPER, TERRY MILLER, The Ohio State University — Reactive intermediates are of crucial importance both for combustion and atmospheric chemistry. By using our new home made Fourier Transform limited (10–30 MHz) Ti:Sa laser source we have probed the vibrationless level of the first electronic state (in the near-IR range) of both CH3OO and CD3OO radical species. The radicals are formed inside a Ne/He/O2/CH3I plasma created by a DC or a RF electrical 2 discharge. The supersonic jet expansion necessary for the rotational cooling (∼ 20 K) is obtained by a pulsed slit nozzle (∼ 50 × 0.5 mm ). The√ near-IR radiation, obtained by Stimulated Raman Scattering (SRS) is injected inside a high finesse cavity. A sensitivity of the order of ∼ 20 × 10−9 /pass/ Hz is currently obtained. Spectrum with a resolution ∼ 350 MHz for CD3OO clearly shows rotational and spin-rotation structure with effects of the internal methyl group rotation possibly evolved.

1Department of Chemistry

1:03PM V18.00010 Modeling the transient vibrational dynamics of photofragments , STEVE YOUNG, SARA MASON, The Makineni Theoretical Laboratories, Department of Chemistry, University of Pennsylvania, HAI-LUNG DAI, Department of Chemistry, University of Pennsylvania, ANDREW RAPPE, The Makineni Theoretical Laboratories, Department of Chemistry, University of Pennsylvania — Knowledge of radical spectroscopy and the structure of radicals is important in many scientific areas, such as atmospheric systems, combustion reactions, biological processes, and more. Because many radicals are transient, unstable, and generally produced in small quantities, they are often difficult to characterize spectroscopically. In this talk, we will present our synthesis of theoretical and experimental data to understand the behavior of radical photofragments. The first part of the talk outlines our approach to understanding vibrationally hot but electronically cold radical dynamics, with direct molecular dynamics and performing electronic structure calculations using DFT within the GAMESS package. We will then summarize our recent development and application of time-resolved FTIR emission spectroscopy for the study of photofragments. Finally, we will present a joint theoretical and experimental investigation of the dynamics of the vinyl radical, including characterization of the complex interaction of rotation, alpha-proton motion, and anharmonic effects, and discuss their influence on the IR spectrum.

1:15PM V18.00011 Raman spectra of benzene derivatives adsorbed on metal substrates , D.A. ALEXSON, S.C. BADESCU, O.J. GLEMBOCKI, S.M. PROKES, R.W. RENDELL, U.S. Naval Research Laboratory — We study the molecular orientations of several benzene derivatives on large Ag and Au clusters via first-principles calculations. We find the lowest-energy structures, several local minima and the diffusion barriers for benzene, nitrobenzene, 2,4-dinitrotoluene (DNT) and 1,4-benzenedimethanethiol (BDMT). The theoretical calculations are compared to experimental measurements of SERS for 2,4-DNT and 1,4-BDMT on Ag and Au coated dielectric nanowires.

1:27PM V18.00012 ABSTRACT WITHDRAWN — 1:39PM V18.00013 Single photon ionization of hydrogen bonded clusters with a desk-top size soft x-ray laser: (HCOOH)n and (HCOOH)m(H2O)n , SCOTT HEINBUCH, FENG DONG, JORGE ROCCA, ELLIOT BERN- STEIN, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University — Pure neutral (HCOOH)n clusters and mixed (HCOOH)m(H2O)n clusters are investigated employing time of ﬂight mass spectroscopy and single photon ionization at 26.5 eV (from a soft x-ray laser). The distribution of pure (HCOOH)nclusters is dependant on experimental conditions. At certain conditions a magic number is found at n = 5. During the ionization process, neutral clusters suﬀer little fragmentation because almost all excess energy above the vertical ionization energy is taken away by the photoelectron. Metastable disso- + 4 −1 ciation rate constants of (HCOOH)n are measured in the range of (0.1–0.8)x10 s for cluster sizes of 4

2:03PM V18.00015 UV Single Photon Dissociation of Furazan Based Energetic Materials: DAAF , ATANU BHATTACHARYA, YUANQING GUO, MARGO GREENFIELD, ELLIOT BERNSTEIN, Colorado State University — The new series of furazan-based energetic materials is characterized by low sensitivity to impact and friction. They have broad application as fuels and propellants; however, extra nitro functional groups attached to the furazan ring (e.g. 4,40-dinitro-3,30-azoxyfurazan) adversely impact the thermal stability of these energetic materials. In order to evaluate the effect of nitro functional groups on furazan-based energetic materials the decomposition of 4,40-diamino-3,30-azoxyfurazan (DAAF), from excited electronic states, has been investigated by UV excitation (8 ns duration) and time of flight mass spectroscopy. The NO molecule is observed as an initial product. Three vibronic transitions of NO are characterized. Simulation of the NO [A 2Σ (v0=0)←X 2Π (v0=1)] transition and fitting to the intensity ratios among NO vibronic transition yields rotational and vibrational temperatures of 30 K and 1265 K, respectively. Compared with NO gas spectra, under comparable condition, the NO from decomposition of DAAF is vibrationally hot and rotationally cold.

Thursday, March 8, 2007 11:15AM - 2:15PM — Session V19 DCP: Focus Session: Ultrafast Dynamics using X-rays and Electrons II Colorado Convention Center 104 11:15AM V19.00001 Picosecond X-ray absorption spectroscopy of light-induced processes in liquids , MAJED CHERGUI, Ecole Polytechnique Fédérale de Lausanne — The importance of capturing the dynamics of molecular motion in real-time is crucial for our understanding of physical, chemical and biological phenomena. In addition, structural changes in molecular systems stem from ultrafast electronic structure changes, which change the field of forces within a molecule, and between a molecule and its environment. Therefore, observing both electronic and structural changes in a given system provides deeper insight into its dynamics. Ultrafast optical spectroscopy does not deliver molecular structure. Ideal structural tools in this respect are X-rays, via methods such as diffraction or spectroscopy. Here, we will present our recent results on the probing of structural changes in electronically excited solvated species, using picosecond X-ray absorption spectroscopy, in a laser pump/X-ray probe configuration. We will demonstrate the power of this new approach on three different types of processes: intramolecular electron transfer, ultrafast molecular magnetism and solvation dynamics around an atomic ion, and discuss future extensions to biological systems. We will also discuss future experiments with femtosecond time resolution at synchrotrons and 4th generation light sources.

11:51AM V19.00002 Ultrafast Structural Dynamics of Photoactive Metal Complexes in Solar Energy Conversion.1 , LIN CHEN, Argonne National Laboratory — The photoexcited states of metal complexes are precursors for many important photochemical processes in solution phase. Using laser-initiated time-resolved x-ray absorption spectroscopy (LITR-XAS), transient metal oxidation states, coordination geometry, and atomic rearrangements that closely reflect photochemical processes can be probed, which complements with ultrafast optical laser spectroscopic studies for kinetics and coherence among different excited states as well as intra- and intermolecular energy/charge transfer processes associated with solar energy conversion. We have studied by LITR-XAS combined with transient absorption spectroscopy excited state structures, such as metalloporphyrins and platinum(II) complexes, in solution. Direct evidence of photoinduced redox reactions and coordination geometry changes have been observed. These experimental studies are combined with time-dependent density functional theory (TDDFT) calculations to rationalize the excited state structural nuclear changes with electronic configuration changes that may be responsible for the reactivity of the molecules. These studies will have a great impact in fundamental understanding of solar fuel production.

1The work is supported by the U. S. Department of Energy, Oﬃce of Science, Oﬃce of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357.

12:27PM V19.00003 Watching proteins function with 150-ps time-resolved X-ray crystallography1 , PHILIP ANFINRUD, National Institutes of Health/NIDDK/LCP — We have used time-resolved Laue crystallography to characterize ligand migration pathways and dynamics in wild-type and several mutant forms of myoglobin (Mb), a ligand-binding heme protein found in muscle tissue. In these pump-probe experiments, which were conducted on the ID09B time-resolved beamline at the European Synchrotron and Radiation Facility, a laser pulse photodissociates CO from an MbCO crystal and a suitably delayed X-ray pulse probes its structure via Laue diﬀraction. Single-site mutations in the vicinity of the heme pocket docking site were found to have a dramatic eﬀect on ligand migration. To visualize this process, time-resolved electron density maps were stitched together into movies that unveil with <2-A˚ spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration. These studies help to illustrate at an atomic level relationships between protein structure, dynamics, and function.

1This research was supported by the Intramural Research Program of the NIH, NIDDK.

1:03PM V19.00004 The Laser-Assisted Photoelectric Effect on Surfaces , LUIS MIAJA-AVILA, GUIDO SAATHOFF, CHIFONG LEI, MARGARET MURNANE, HENRY KAPTEYN, JILA, Univ. of Colorado, MARTIN AESCHLIMANN, Univ. of Kaiserslautern, Germany, JOHN GLAND, Univ. of Michigan — The laser-assisted photoelectric effect (LAPE) in atoms is widely used for the characterization of ultrashort EUV pulses and for femtosecond-to-attosecond spectroscopy. We recently observed the equivalent process in the original manifestation of the photoelectric effect i.e. photoemission from surfaces [PRL 97, 113604 (2006)]. In our experiment, ultrafast 800nm pulses are split into probe and pump beams. The probe beam is upconverted into the EUV at 30nm using high harmonic frequency conversion. The 800nm pump beam is spatially and temporally overlapped with the EUV beam on a Pt(111) sample. A time-of-flight detector measures the kinetic energy of the photoemitted electrons. In the presence of the pump beam, these electrons can either absorb or emit an IR photon, leading to sidebands in the EUV photoelectron spectrum. These sidebands are visible as modulations near the Fermi edge. Surface LAPE will extend EUV pulse measurements to higher photon energies. It also has the potential to study ultrafast, femtosecond-to-attosecond time-scale processes in solids and in surface-adsorbate systems, where complex, correlated, electron dynamics are expected. 1:15PM V19.00005 Dynamics of small polaron formation in epitaxial pentacene films , MATTHIAS MUNTWILER, WILLIAM TISDALE, EHUA FAN, CHAD LINDSTROM, XIAOYANG ZHU, University of Minnesota, Minneapolis — Using time-resolved two- photon photoemission (TR-2PPE) we observe the formation of a small polaron from electrons injected into the LUMO band of thin epitaxial pentacene films. Such observation is made directly in the energy and time domains by analysing the photoelectron after excitation by pump and delayed probe pulses from a femtosecond laser system. The LUMO level of pentacene is observed in a charge transfer process that originates from an initial state of the substrate and as such does not involve exciton formation. Due to interaction with the nuclear lattice, the energy level of the LUMO-derived polaron state relaxes by about 200 meV towards lower energy over a time interval of several hundred femtoseconds. Small polarons account for one possible mechanism of charge trapping in organic semiconductors. In our experiments, pentacene films are grown in a bulk-like structure (standing phase) on a thin film Bi(111) substrate.

1:27PM V19.00006 Dynamics on nanointerfaces investigated by ultrafast electron nano- crystallography , CHONG-YU RUAN, YOSHIE MUROOKA, RAMANI KALYAN RAMAN, RYAN MURDICK, Michigan State University — The correlation between the material structures and the size-dependent properties is a fundamental problem in nanoscience. Through the development of ultrafast electron nano-crystallography and spectroscopy techniques, we have looked at some important mechanisms pertaining to the nanometer scales. To accentuate the structurally correlated transformations from bulk to the molecular length scale, we size-select and deposit nanoparticles (Au, Ag) on well characterized interfaces. Using femtosecond optical pulse as the pump and femtosecond electron pulse as the probe, the electronic and temperature driven transformations of nanostructures and phases are examined at calibrated levels on the energy landscape with atomistic spatialtemporal resolutions (≤ 10−12 sec, ≤ 0.01 A).˚ We observed the ultrafast nonthermal phase transformations of nanoparticles with transient full-scale radial distribution function accurately determined. The coherent motions of atoms driven by nonthermal energy transfer persist into the liquid phase. But the recrystallization process is more thermal-like with interesting reconstruction of lattices from the melt, nonreciprocal to that of melting. We also examined the ultrafast molecular structural responses to charge transfer that exhibits a dynamical phase transition going from conducting to insulating phases.

1:39PM V19.00007 Multiple Reference Soft X-ray Fourier Transform Holography1 , W. SCHLOTTER, K. CHEN, R. RICK, A. SCHERZ, J. STOHR, J. LUNING, Stanford Synchrotron Radiation Laboratory — We demonstrate multiple reference Fourier transform holography with soft x-rays. This technique results in enhanced image quality without increased exposure to the sample. There are two categories of experiments where this is particularly relevant: imaging with limited intensity sources and imaging radiation sensitive samples. In Fourier transform holography a unique image of the sample object is reconstructed for each reference source that is used to record the hologram. Thus with multiple reference sources, multiple images are reconstructed with the same radiation exposure to the sample necessary for a single image. When the multiple images are formed by effectively identical reference sources the images can be averaged to enhance image quality. X-ray free electron lasers are an example of sources where single shot images must be captured with one ultrafast x-ray pulse. Since the number of photons in each pulse, incident on a nanoscale sample, is finite, high efficiency imaging is essential. To mimic a finite illumination scenario we have successfully imaged a nanoscale test object by detecting fewer than 2500 soft x-ray photons.

1This presentation is supported by the Melvin P. Klein Scientiﬁc Development Award for work carried out at the Stanford Synchrotron Radiation Laboratory, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy.

1:51PM V19.00008 X-ray Resonant Photoemission in organic thin films. , ALBERTO MORGANTE, DEAN CVETKO, ALBANO COSSARO, LUCA FLOREANO, GREGOR BAVDEK, Laboratorio TASC-INFM-CNR Trieste — Resonant photoemission (RESPES) allows to investigate the charge transfer processes in thin films at the femtosecond time scale and it has been recently applied to thin organic films on inorganic substrates in order to obtain information related to the carrier injection at the interface, a process of great importance for organic electronic applications. High resolution RESPES on monolayer and multilayer organic films on semiconductor and metal substrates at C K-edge will be presented. It will be shown that in the monolayer range RESPES makes possible to clearly identify very weak molecular valence band structures which can’t be distinguished from substrate ones in normal photoemission. Moreover the charge transfer time information will be deduced from the spectroscopic data by the comparison of monolayer and multilayer RESPES spectra. It will be also demonstrated that, due to the localized nature of the resonant process, RESPES gives a clear spatial correlation between filled and empty states and that this effect should be carefully taken into account in the analysis of the resonant spectra for the charge transfer time determination.

2:03PM V19.00009 Atomic Scale Force Spectroscopy Suggests Low Reorganization Entropy For Electron Transfer , J.T. SAGE, A. BARABANSCHIKOV, B. BARBIELLINI, Northeastern Univ., E.D. COULTER, D.M. KURTZ, Univ. Georgia, E.E. ALP, W. STURHAHN, Argonne Natl. Lab — Molecular mechanics simulations of the electron transfer protein rubredoxin suggest significant delocalization of active site vibrations, but experimental vibrational data have been successfully modelled using empirical models that exclude distant atoms. We address this question using nuclear resonance vibrational spectroscopy (NRVS), an emerging synchrotron-based technique that yields the complete vibrational spectrum of 57Fe in rubredoxin, coupled with quantum chemical vibrational predictions. The measured vibrational density of states reveals that oxidation strengthens the Fe-S bonds linking iron to the polypeptide, as expected from the reported decrease in Fe-S bond lengths. Moreover, comparison with Raman isotope shift measurements provides direct experimental evidence that the Fe-S vibrations remain localized at the active site. Vibrational predictions based on DFT calculations reproduce the observed vibrational data and confirm the localized nature of the Fe-S vibrations, although lower frequency vibrations mix significantly with the polypeptide. The Fe-S vibrations are an important component of the electron transfer reaction coordinate, and we suggest that vibrational localization may facilitate electron transfer by minimizing the reorganization entropy of the reaction.

Thursday, March 8, 2007 11:15AM - 2:03PM — Session V26 DCP: Focus Session: Charge Transport in Nanostructures II Colorado Convention Center 205 11:15AM V26.00001 Electronic transport in semiconductor nanowires: physics studies and possible device applications1 , LARS SAMUELSON, Lund University, Solid State Physics / the Nanometer Structure Consortium, Box 118, S-221 00 Lund, Sweden — Semiconductor nanowires are attractive for physics as well as for applications due to the highly ideal character of their electronic and structural properties. We grow our III-V nanowires by what can be described as guided self-assembly, by which we can accurately control location as well as dimensions of epitaxially nucleated nanowires. The level of control of growth allows controlled formation of axial as well as radial heterostructures. I will describe studies of charge transport via single, double and multiple quantum dots positioned inside InAs/InP nanowires. Such studies have allowed detailed studies of the addition of electrons one-by-one, from the very first electron into an empty quantum dot to the addition of up to 50 electrons. By replacing the one-dimensional emitter by a small quantum dot in a double-dot configuration, the discrete character of the injecting state allows ever more detailed spectroscopic studies of the charge additions to the second dot. Comparisons will be made with transport through quantum dots defined by tunnel barriers induced via gating techniques. Finally, a recently developed technique for the formation vertical wrap-gate field-effect transistors around InAs nanowires will be described, suggesting interesting opportunities for the realization of high-speed and low-power transistors and circuits. The geometrical design of such nanowire wrap-gate field-effect transistors, offers exciting ways of formation of ultra-short transistor gate-lengths as well as the use of heterostructures to further enhance the performance of such devices.

1This work is supported by grants from the Swedish Research Council (VR), the Swedish Foundation for Strategic Research (SSF), the Knut and Alice Wallenberg Foundation (KAW), the Office of Naval Research (ONR) and from the EU-program NODE 015783. 11:51AM V26.00002 Charge Transport in Semiconductor Nanocrystal Solids , DMITRI TALAPIN, ELENA SHEVCHENKO, JONG SOO LEE, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, JEFFREY URBAN, DAVID MITZI, CHRISTOPHER MURRAY, IBM T. J. Watson Research Center, Yorktown Heights, NY — Self-assembly of chemically-synthesized nanocrystals can yield complex long-range ordered structures which can be used as model systems for studying transport phenomena in low-dimensional materials [1]. Treatment of close-packed PbSe nanocrystal arrays with hydrazine enhanced exchange coupling between the nanocrystals and improved conductance by more than ten orders of magnitude compared to native nanocrystal films [2]. The conductivity of PbSe nanocrystal solids can be switched between n- and p-type transports by controlling the saturation of electronic states at nanocrystal surfaces. Nanocrystal arrays form the n- and p-channels of field-effect transistors with electron 2 −1 −1 2 −1 −1 3 4 and hole mobilities of 2.5 cm V s and 0.3 cm V s , respectively, and current modulation Ion/Ioff ∼10 -10 . The field-effect mobility in PbSe nanocrystal arrays is higher than the mobility of organic transistors while the easy switch between n- and p-transport allows realization of complimentary circuits and p-n junctions for nanocrystal-based solar cells and thermoelectric devices. [1] E. V. Shevchenko, D. V. Talapin, N. A. Kotov, S. O’Brien, C. B. Murray. Nature 439, 55 (2006). [2] D. V. Talapin, C. B. Murray. Science 310, 86 (2005).

12:03PM V26.00003 Tuning the Height of the Tunnel Barrier in Colloidal Semiconductor Nanoparticle Films , VENDA PORTER, SCOTT GEYER, JONATHAN HALPERT, MOUNGI BAWENDI, Department of Chemistry, Massachusetts Institute of Technology, TAMAR MENTZEL, MARC KASTNER, Department of Physics, Massachusetts Institute of Technology — Much of the work in the field of charge transport through arrays of semiconductor nanoparticles has focused on improving the conductivity by tuning the organic ligand spacer between particles. We present a study in which we enhance the conductivity in nanoparticles films by instead tuning the energetic height of the tunnel barrier by removing the organic ligand spacer and tuning the inorganic shell around each particle. Experimentally, we modify the height of the tunnel barrier by depositing an array of core/shell nanoparticles and burning away all of the organic ligands. The height of the tunnel barrier is now the energy difference between the conduction band of the core and the conduction band of the shell, rather than the much larger energy difference between the conduction band of the nanoparticle and the LUMO of the organic ligand. In addition, this method may reduce the impact of surface states on conductivity as the shell may provide better passivation than organic ligands that may leave surface trap sites unbound. These unpassivated sites can trap charge carriers, lowering the mobility in nanoparticles films. The reduction of charge trapping is also critical to raising the efficiency of nanoparticle solar devices.

12:15PM V26.00004 Transport measurements of semiconductor nanocrystals and nanorods using nanoscale devices. , CLAUDIA QUERNER, MICHAEL D. FISCHBEIN, MARIJA DRNDIC, University of Pennsylvania — Efficient charge transport through nanocrystal arrays is important for many applications in electronics or optoelectronics. Various parameters can influence the transport in nanocrystals. Beside the material itself, other parameters such as shape (spherical, rod-shaped or branched structures), surface capping (insulating or electroactive surface-ligands), as well as the nanocrystal assembly may affect the observed transport phenomena. We carry out transport measurements of semiconductor nanoparticles using devices made on silicon nitride membranes. This approach enables both transport measurements and device imaging using high-resolution transmission electron microscopy, allowing a direct correlation of the measured transport phenomena with the local structure of the nanomaterial on the device surface. We will discuss the effects that we observe by varying parameters such as shape, size and surface capping of the nanoparticles, in particular CdSe, as well as temperature and photo-excitation. This work was supported by ONR Young Investigator Award (N000140410489), NSF Career Grant (DMR-0449553), NSF NSEC Grant (DMR-0425780), and NSF-IGERT (DGE 022166).

12:27PM V26.00005 Electron Transport in Arrays of Lead Selenide Nanocrystals1 , TAMAR MENTZEL, VENDA PORTER, SCOTT GEYER, Massachusetts Institute of Technology, SOPHIE CHARPENTIER, Universite de Sherbrooke, MOUNGI BAWENDI, MARC KASTNER, Massachusetts Institute of Technology — We report on measurements of electron transport in self-assembled arrays of PbSe nanocrystals (NCs). NCs ∼8 nm in diameter are colloidally synthesized and drop cast onto an inverted field effect structure. The NCs self assemble into hexagonal close-packed arrays with ∼1.5 nm interdot spacing after annealing. The field-effect device enables us to measure the dependence of current on gate voltage (Vg) as well as source-drain voltage (Vds). At high temperature we find that the conductance is exponentially dependent on both Vds and temperature. At low temperature the conductance is still exponentially dependent on Vds, but is independent of temperature indicating a tunneling mechanism. While the conductance is independent of Vg at high temperatures, it decreases with Vg at low temperature suggesting that holes are the dominant carriers.

1This work was supported by the MRSEC program of the NSF (DMR 02-13282). T. M. acknowledges support from NDSEG.

12:39PM V26.00006 Charge Transport in Magnetite Nanoparticle Arrays , SEONGJIN JANG, HAO ZENG, University at Buﬀalo, the State University of New York — Charge transport properties of magnetite (Fe3O4) nanoparticle arrays were studied as a function of annealing conditions. These arrays were prepared by self-assembling chemically synthesized nanoparticles with micro-gaps between lateral electrodes. Annealing removed surfactant molecules and varied the interparticle spacing systematically. Arrays annealed under 200 oC are insulating. Arrays annealed between 200 oC to 500 oC show thermally assisted tunneling behavior, with the tunneling barrier decreasing with increasing annealing temperatures. Above 500 oC, a transition from tunneling to hopping mechanism is observed. Magnetoresistance decreases with increasing annealing temperature. For the hopping samples, Verway transition is observed from both the resistivity and magnetoresistance measurements. Work supported by NSF DMR 0547036

12:51PM V26.00007 Single Step Growth and Low Resistance Interconnecting of Metallic Nanowires , BRET FLANDERS, BIROL OZTURK, Oklahoma State University — We present an innovative approach to nanowire growth and interconnecting with external circuitry. Depositing salt-solution over a pair of on-chip electrodes and applying an alternating voltage induces the growth of metallic nanowires between the electrode tips. The voltage-signal provides sensitive control over the metal deposition process. For example, precise speciﬁcation of the nanowire-diameter is attained through the frequency ω of the alternating voltage that induces the wire-growth process. For indium wires, increasing ω from 0.5 to 3.5 MHz increases the growth velocity of the wires from 11 to 78 µm/s and reduces their diameter from 770 to 114 nm. Gold wires exhibit diameter-tunability that extends below 100 nm. By the feedback-controlled application of the alternating voltage, it becomes possible to produce electrode- nanowire-electrode assemblies with contact-resistances of less than 25 Ω, which would not be possible were the voltage terminated manually. This combination of capabilities enables study of the intrinsic transport properties of metallic nanowires. An area of particular interest is the contribution of electron-surface scattering to the total resistivity, an eﬀect that is expected to increase with decreasing diameter.

1:03PM V26.00008 ABSTRACT WITHDRAWN — 1:15PM V26.00009 Electronic-structure and quantum conductance of pristine and defective graphene layers and ribbons , GIOVANNI CANTELE, Coherentia CNR-INFM and Universitàdi Napoli “Federico II”, YOUNG-SU LEE, MIT, DOMENICO NINNO, Coherentia CNR-INFM and Universitàdi Napoli “Federico II”, NICOLA MARZARI, MIT — Graphene has recently emerged as a fascinating alternative to carbon nanotubes as a subject both of fundamental research and of promising technological applications. In this work, we study the electronic structure and the transport properties of graphene layers and of graphene ribbons in the presence of several defects - from vacancies to topological defects to substitutional impurities. Very large systems with random distributions of defects are treated fully from first-principles and with chemical accuracy thanks to a formulation that combines density-functional theory and maximally-localized Wannier functions 1. Our results are also compared with previous tight-binding calculations, when available.

1Young-Su Lee et al, Phys. Rev. Lett. 95, 076804 (2005)

1:27PM V26.00010 Theory of transport through molecular magnets , HERBERT SCHOELLER, Institut für Theoretische Physik A, RWTH Aachen, Germany — Quantum transport through single molecular magnets (SMM) is starting to become a new exciting field in molecular spin electronics. Recent experiments [1,2] have shown that magnetic excitations can be identified in transport measurements and that NDC effects and complete current suppression can be explained by charge dependent anisotropies. Recent theoretical investigations [3,4,5] are presented which demonstrate fingerprints of quantum tunneling of magnetization (QTM). For weak tunneling, the violation of spin-selection rules leads to the occurence of fake resonances with temperature-dependent position [3]. For strongtunneling, it is show that a pseudo spin-1/2 Kondo effect is induced by QTM. If the Kondo temperature TK is smaller than the distance to excited magnetic states, selection rules depending on spin and symmetry of the SMM are derived for the Kondo effect to occur [4]. If TK exceeds the anisotropy barrier, it is shown that a reentrant Kondo effect can be induced by application of a longitudinal magnetic field for SMM with half-integer or integer spin [5]. This effect can be used for transport spectroscopy of the various anisotropies characterizing a SMM. [1] H.B. Heersche et al., Phys. Rev. Lett. 96, 206801 (2006). [2] Moon-Ho Jo et al., Nano Lett. 6, 2014 (2006). [3] C. Romeike, M.R. Wegewijs, H. Schoeller, Phys. Rev. Lett. 96, 196805 (2006). [4] C. Romeike, M.R. Wegewijs, W. Hofstetter, H. Schoeller, Phys. Rev. Lett. 96, 196601 (2006). [5] C. Romeike, M.R. Wegewijs, W. Hofstetter, H. Schoeller, to be published in Phys. Rev. Lett., cond-mat/0605514.

Thursday, March 8, 2007 2:30PM - 5:18PM — Session W18 DCP: Theoretical Methods and Algorithms Colorado Convention Center 103

2:30PM W18.00001 Quantum Entanglement and Electron Correlation in Molecular Systems1 , HEFENG WANG, SABRE KAIS, Department of Chemistry, Purdue University, West Lafayette, IN, 47906 — We study the relation between quantum entanglement and electron correlation in quantum chemistry calculations. We prove that the Hartree-Fock (HF) wave function does not violate Bell’s inequality, thus is not entangled while the conﬁguration interaction (CI) wave function is entangled since it violates Bell’s inequality. Entanglement is related to electron correlation and might be used as an alternative measure of the electron correlation in quantum chemistry calculations. As an example we show the calculations of entanglement for the H2 molecule and how it correlates with the traditional electron correlation, which is the diﬀerence between the exact and the HF energies.

1US-Israel Binational Science Foundation

2:42PM W18.00002 Infinite, periodic systems in external fields – an efficient, theoretical method , MICHAEL SPRINGBORG, University of Saarland, Germany — The response of periodic systems to external electric fields is a challenging theoretical problem. We show how the vector potential approach yields a numerically efficient treatment of the combined electronic and nuclear response to a finite static field. Our method is based on a self-consistent reformulation of the charge flow term in the single particle Hamiltonian. Careful numerical implementation yields a treatment whose computational needs are only marginally larger than those of a conventional field-free calculation. To prove the method we have performed model calculations for a qusi-one-dimensional (polymeric) system. The model contains all essential elements of an ab initio Kohn-Sham or Hartree-Fock Hamiltonian but allows for extensive testing.

2:54PM W18.00003 Quantum master equation in phase space: Application to the Brownian motion in a periodic potential1 , WILLIAM COFFEY, Dept. Electronic and Electrical Engineering, Trinity College, Dublin 2, Ireland, YURI KALMYKOV, MEPS, Universitéde Perpignan, 52 Av. Paul Alduy, 66860 Perpignan Cedex, France, SERGEY TITOV, Inst. Radio Engineering and Electronics of the Russian Academy of Sciences, Vvedenskii Square 1, Fryazino, Moscow Region, 141190, Russia, BERNARD MULLIGAN, Dept. Electronic and Electrical Engineering, Trinity College, Dublin 2, Ireland — The quantum Brownian motion of a particle in a periodic potential V (x) = −V0 cos(x/x0) is treated using the master equation for the time evolution of the Wigner distribution function W (x, p, t) in phase space (x, p). Explicit equations for the diffusion coefficients of the master equation for this dissipative quantum system are derived. The dynamic structure factor and longest relaxation time are evaluated by using matrix continued fractions. The longest relaxation time so obtained is compared with the quantum-mechanical escape rate formula. The matrix continued fraction solution agrees well with the analytical solution of the corresponding Kramers turnover problem.

1We thank the ﬁnancial support of Science Foundation Ireland (Project 05/RFP/PHY/0070).

3:06PM W18.00004 Scrutinizing concepts in chemical kinetics: Sensitivity analysis and mean- field approximation , HAKIM MESKINE, KARSTEN REUTER, MATTHIAS SCHEFFLER, Fritz-Haber-Institut, Faradayweg 4-6, D-14195 Berlin, HORIA METIU, University of California at Santa Barbara, Santa Barbara CA 93106 — We present kinetic Monte Carlo (kMC) simulations for the CO oxidation reaction at RuO2(110), based on rate constants determined by density-functional theory and transition-state theory. The composition and structure of the catalyst surface are computed in reactive environments ranging from ultra-high vacuum (UHV) to technologically relevant conditions (pressures of several atmospheres and elevated temperatures). This setup enables us to scrutinize frequently employed concepts in the modeling of chemical kinetics: Sensitivity analyses are performed to identify the rate determining steps under the different environmental conditions. While helpful under UHV conditions, this analysis proves to be of little use for catalytically relevant environments, since then a larger number of elementary processes contributes equally to the total rate of product formation. We also check on the mean-field approximation employed in phenomenological microkinetics by comparing rate equations based on the same first-principles rate constants to the kMC simulations, where the spatial distribution of the chemicals at the catalyst surface is explicitly considered. The rate equation activities are found to be in serious error, even failing to identify the correct dominant reaction mechanism. 3:18PM W18.00005 A new mixed quantum/semiclassical propagation methodology , STEVEN SCHWARTZ, Albert Einstein College of Medicine — We present a new propagation algorithm for the evolution of a highly quantum subsystem coupled to a more classical like bath. The quantum system is treated exactly, while the bath is evolved with a frozen Gaussian evolution. An evolution operator correction scheme we recently developed is then applied to compute the coupling between the quantum systems and the semiclassical bath. The scheme is applied to test problems and found to be accurate and not significantly more difficult to implement than standard classical molecular dynamics. The approach also admits the possibility of higher order correction to obtain exact quantum results.

3:30PM W18.00006 Improved Polarizabilities and Dissociation in DFT: Vignale-Kohn Revis- ited , NEEPA MAITRA, Hunter College and the City University of New York, New York, META VAN FAASSEN, Rutgers University, Piscataway, NJ — We develop a novel approach to the problem of polarizabilities and dissociation in electric fields from the static limit of the Vignale-Kohn (VK) functional. The VK response potential, extracted from the longitudinal component of the VK vector potential has ground-state properties that notably improve over VK response and over usual (semi-)local functionals. The VK density response is not the ground-state response in the corresponding field. Cases where VK density response yields poor polarizabilities, eg the H2 chain, work well in our approach. This is the first density functional method that correctly dissociates open-shell fragments in a field.

3:42PM W18.00007 What decides if a smarter army can win a battle? , LINDA SHANAHAN, State Univ of New York at Buffalo, SURAJIT SEN1, State University of New York at Buffalo — We study the kinetics associated with a “war” in which an attacking army attempts to win over a spatially dispersed defender on a 2D lattice. The levels of engagement are comparable in our study. The conflicting parties can annihilate, win or lose at any given site depending upon certain preselected rules of engagement. The attacker possesses higher intelligence, which is manifested through the moves of the attackers. We show that an “intelligent” attacker with subcritical number of attackers cannot win in the engagement.

1Supported by UB2020 Scholar’s Fund at SUNY-Buﬀalo

3:54PM W18.00008 Foundations for Cooperating with Control Noise in the Manipulation of Quantum Dynamics1 , FENG SHUANG, HERSCHEL RABITZ, Department of Chemistry, Princeton University, MARK DYKMAN, Department of Physics and Astronomy, Michigan State University — This work develops the theoretical foundations for the ability of a control field to cooperate with noise in the manipulation of quantum dynamics. The noise enters as run-to-run variations in the control amplitudes, phases and frequencies with the observation being an ensemble average over many runs as is commonly done in the laboratory. Weak field perturbation theory is developed to show that noise in the amplitude and frequency components of the control field can enhance the process of population transfer in a multilevel ladder system. The analytical results in this paper support the point that under suitable conditions an optimal field can cooperate with noise to improve the control outcome.

1The authors acknowledge support from the Department of Energy and NSF-PHY 0555346

4:06PM W18.00009 Enthalpy of molecular solids beyond the harmonic approximation: application to hydrogen storage1 , NIKOLAI ZARKEVICH, D.D. JOHNSON, Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W. Green St. Urbana, IL 68101. — With low potential energy barriers, the harmonic approximation for phonon modes can be invalid [1]. Molecular solids are composed of strongly-bonded molecules held together by relatively weak intermolecular forces. As intermolecular interactions are usually not harmonic, a new theoretical approach is needed to obtain enthalpies of molecular solids at finite temperature. We develop such a theory for molecular solids and liquids, and apply it to obtain enthalpy differences between various phases from the first principles. We also calculate Gibbs free energy, and show that a phase diagram (e.g., a van’t Hoff plot) can be constructed as a graphical solution of the Gibbs equation. To exemplify important applications, we consider materials and reactions for the high-capacity hydrogen storage. [1] Phys.Rev.Lett.97, 119601 (2006).

1We acknowledge support by the DOE Sandia Metal-Hydride Center of Excellence (DEFC36-05GO15064) and BES (DEFG02-03ER46026), and by the NSF through NCSA (DMR060017N).

4:18PM W18.00010 Realistic simulations of low temperature Cu(100) growth: extending time and length scales by parallel temperature-accelerated dynamics1 , Y. SHIM, J.G. AMAR, University of Toledo, A.F. VOTER, B.P. UBERUAGA, Los Alamos National Laboratory — The temperature-accelerated dynamics (TAD) method is a powerful tool for carrying out non-equilibrium simulations of systems with infrequent events over extended time-scales. However, due to the serial nature of the method the computation time scales as N 2 − N 3, where N is the number of atoms. As a result, TAD simulations have been limited to relatively small system sizes. By combining temperature-accelerated dynamics with a recently proposed parallel synchronous sublattice algorithm, we are able to simulate the dynamic evolution of systems over much larger length as well as longer time scales. In particular, we find that the computational time using our parallel accelerated dynamics method scales as log(N) or better. Preliminary results for the growing film morphology in low-temperature Cu(100) growth will also be presented. These include the observation of a wide variety of defect configurations.

1Supported by NSF-DMR.

4:30PM W18.00011 Electrostatics in Periodic-boundary Conditions and Real-space Correc- tions , ISMAILA DABO, NICOLA MARZARI, Massachusetts Institute of Technology — We address periodic-image errors arising from the use of periodic- boundary conditions to describe systems that do not exhibit full three-dimensional periodicity. We show that the diﬀerence between the Coulomb potential calculated by Fourier transforms and the exact potential can be characterized analytically. Based on this observation, we present an eﬃcient real-space method to correct periodic-image errors in plane-wave calculations. Comparing the method with existing schemes, we show that it is particularly advantageous for studying systems exhibiting one- or two-dimensional periodicity. As an application, we consider the vibrational properties of CO adsorbed on charged platinum surfaces.

4:42PM W18.00012 Quantum instanton evaluation of the kinetic isotope effects , JIRI VANICEK, Institute for Advanced Study, Princeton, WILLIAM H. MILLER, Department of Chemistry, University of California, Berkeley — The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in enzymatic reactions. The calculation is carried out using thermodynamic integration with respect to the mass of the isotopes and a path integral Monte Carlo evaluation of relevant thermodynamic quantities. Efficient “virial” estimators are derived for the logarithmic derivatives of the partition function and the delta-delta correlation functions. These estimators require significantly fewer Monte Carlo samples since their statistical error does not increase with the number of discrete time slices in the path integral. The calculation treats all 39 degrees of freedom quantum-mechanically and uses an empirical valence bond potential based on a modified general AMBER force field. The importance of quantum effects due to the skeleton motion is demonstrated by comparison with a mixed quantum-classical calculation. 4:54PM W18.00013 Derivative Interpolating Polynomial Multi-wavelets: An Efficient Algo- rithm for the Computation of the Exchange-Correlation Functional , C. J. TYMCZAK, Texas Southern University and Los Alamos National Lab, MATT CHALLACOMBE, Los Alamos National Lab — We report on the development of a novel multi-wavelet basis optimized for large scale electronic structured calculations. This novel multi-wavelet basis has several important properties which are ideally suited for electronic structure calculations: i) These multi-wavelets are maximally compact. ii) These multi-wavelets are highly interpolating. iii) These multi-wavelets, as opposed to most wavelets derived from the signal processing community, are analytic. These three properties lead to a very efficient and compact multi scale representation. We then demonstrate the utility of this novel multi-wavelet basis for the computation the exchange correlation functional of density functional theory, where a highly accurate and compact representation is essential in order for the electronic structure calculation to be computationally stable.

5:06PM W18.00014 Novel mechanism of dissipation in synthetic rotary motors , CORINA BARBU, VINCENT CRESPI, The Pennsylvania State University — We study novel mechanisms of dissipation in nanoscale and molecular-scale motors. In traditional treatments of such systems, the background degrees of freedom are integrated out into a thermal bath, and the rotator is coupled directly to this bath via phenomenological terms such as viscous damping or Langevin forces. We have investigated a situation in which one degree of freedom is pulled out from the thermal bath and into the explicit equations of motion, interposed between the bath and the motor. We describe a regime in which the deceleration of an unpowered rotor follows a universal power law, rather than a standard exponential decay.

Thursday, March 8, 2007 2:30PM - 5:30PM — Session W19 DCP: Ultrafast Dynamics using X-rays and Electrons Colorado Convention Center 104

2:30PM W19.00001 Rydberg electrons spy conformational dynamics of hot molecules , PETER M. WEBER, Department of Chemistry, Brown University — The observation of structural dynamics of flexible molecules at high temperatures is arguably one of the most challenging problems of molecular dynamics. We succeeded in observing conformational dynamics by using electrons in Rydberg orbits as spies of the molecular structure. The time-resolved photoionization from the Rydberg states, providing a purely electronic spectrum that serves to characterize the molecular structure, allows us to follow the molecular motions in real time. The internal rotation about carbon-carbon bonds affords the unsaturated hydrocarbon chain molecules N,N-dimethyl-2-butanamine (DM2BA) and N,N-dimethyl-3-hexanamine (DM3HA) an opportunity to assume multiple conformeric structures. We explore the equilibrium compositions and the dynamics of transitions between such structures. An ultrashort laser pulse rapidly increases the molecule’s internal energy and changes the potential energy landscape. The molecules respond by adjusting their shape, i.e. by converting between conformeric molecular structures. For DM2BA at a total internal energy of 1.79 eV, the time constants for interconversion between conformers are 19 ps and 66 ps, respectively. In DM3HA, the respective time constants are 23 and 41 ps. Comparison with a calculated conformational energy landscape reveals the conformeric forms of DM2BA involved in the molecular shape transformation. Thus, for the first time a time-resolved and quantitative view of the conformational dynamics of a flexible hydrocarbon chain at high temperature is revealed.

3:06PM W19.00002 Attosecond Electron Interferometry1 , P.B. CORKUM, Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ont. K1A 0R6 — Attosecond optical pulse generation is electron interferometry. Quantum mechanical tunnelling in an intense laser field splits the electron. After tunnelling, one component of the electron wave function is accelerated away from the ion by the laser field, but returns once the field reverses its sign. The other component remains bound to the ion. These two paths form the two arms of the interferometer. When the two components of the electron wave function overlap, they interfere. The interference leads to an oscillating dipole that produces attosecond optical pulses and simultaneously images molecular orbitals. Interferometry allows sub-wavelength changes in the length of one arm to be measured relative to another. Using rotational wave packets, we show that the high harmonics are very sensitivity to very small molecular motion and local fields. We adapt transient grating spectroscopy with two or more grating elements to observe phase changes to the high harmonics as we rotate a molecule.

1In collaboration with Y. Mairesse, N. Dudovich, and D. M. Villeneuve.

3:42PM W19.00003 Ultrafast Transient Absorption and Photoelectron Spectroscopy with High Order Harmonics1 , STEPHEN LEONE, University of California, Berkeley — Laser-produced high order harmonics are used to probe chemical dynamics of atoms and molecules on femtosecond timescales. Two basic methods are developed, ultrafast transient absorption and photoelectron spectroscopy. The high order harmonics are produced with an 800 nm Ti:sapphire laser focused into a capillary or rare gas jet. Both inner shell core levels and outer shell valence states are investigated. The transient absorption of xenon ions produced by high ﬁeld ionization of neutral xenon atoms is probed by core level spectroscopy. The alignment of the vacancy created in forming the ion is measured as a function of pump-probe delay by promotion of an inner d electron to the vacancy in the outer shell. Small molecules are excited to repulsive dissociative states and individual harmonics are used to obtain time-resolved photoelectron spectra. A wave packet on the dissociative state of bromine molecules is detected, as well as the production of atoms at longer time delays. By the use of velocity map imaging, the angular distributions of outgoing photoelectrons are analyzed. In a new experimental system, carrier-envelope phase-stabilized few-cycle pulses will be used to create attosecond pulses of the high order harmonics, to study electronic-time-scale processes in atoms and molecules.

1supported by NSF, AFOSR, and DOE

4:18PM W19.00004 Observation of Intra-molecular Dynamics using High-Harmonic Genera- tion as a Probe , NICK WAGNER, XIBIN ZHOU, WEN LI, ROBYNNE HOOPER, MARGARET MURNANE, HENRY KAPTEYN, JILA/University of Colorado — We report two observations of intramolecular dynamics using electrons rescattered during the process of high-order harmonic generation. In the ﬁrst experiment, we excite coherent vibrations in SF6 using impulsive Raman scattering. A second, more-intense pulse generates high-order harmonics from the excited molecules, at wavelengths of 20-50nm. The harmonic yield is observed to oscillate, at frequencies corresponding to all the Raman-active modes of SF6, with an asymmetric breathing mode most visible. This is in contrast to conventional Raman spectroscopy where only the symmetric breathing mode of the molecule is easily observed. The data also show evidence of relaxation dynamics following impulsive excitation of the molecule. Our results indicate that harmonic generation is a very sensitive probe of vibrational dynamics, yielding more information simultaneously than conventional ultrafast spectroscopies. In our second experiment, we dissociate CF3I with a 266nm pulse, and monitor the dissociation by probing high harmonic emission from the intact and dissociated molecule. Since the de Broglie wavelength of the recolliding electron is on the order of interatomic distances (∼1.5A),˚ small changes in the shape of the molecule lead to large changes in the high harmonic yield. 4:30PM W19.00005 Ultrafast x-ray pulses emitted from a liquid mercury laser target , CHRISTO- PHER LAPERLE, CHRISTIAN REICH, BRIAN AHR, XIAODI LI, FRANK BENESCH-LEE, CHRISTOPH ROSE-PETRUCK, Brown University — We report the generation of ultrashort, hard x-ray pulses from a liquid mercury target irradiated by 5-kHz laser pulses. The new x-ray source is designed for time-resolved x-ray absorption spectroscopy as well as imaging applications. This marks the ﬁrst laser-driven plasma x-ray source that continuously recycles the target material, facilitating maintenance-free operation. Theoretical calculations show mercury targets emit shorter x-ray pulses than targets of lighter elements under identical illumination and x-ray detection conditions. The plasma-physical properties of mercury are very well suited for sub-50-fs hard x-ray pulse generation. The x-ray emission properties of this source have been simulated by a combination of particle-in-cell (PIC) and Monte-Carlo (MC) calculations of the laser target interaction and the resulting electron dynamics. All calculations were performed for p-polarized, 100-fs, 800-nm laser pulses with an incidence angle of 45 degrees. The calculated x-ray yields are in good agreement with the measured emission spectra. The simulated x-ray pulses have a width of 60 fs (fwhm), as short as the driving laser pulse width. Applications of laser-pump x-ray probe measurements are presented.

4:42PM W19.00006 Control and interrogation of electronic dynamics by above-threshold ionization , MARK ABEL, THOMAS PFEIFER, PHIL NAGEL, DANIEL NEUMARK, STEPHEN LEONE, Department of Chemistry, UC Berkeley — While direct interrogation of coherent nuclear dynamics has been possible for some time, only recently have the motions of valence- and core-level electrons become experimentally accessible. This access is provided by strong-ﬁeld physics, through the application of high harmonic generation to ultrafast x-ray pulse synthesis. We show that another phenomenon from strong-ﬁeld physics, above-threshold ionization (ATI), can yield information about electronic states and electronic dynamics without using subfemtosecond x-ray pulses. In particular, quantum beating in Xe atoms and in a 1-dimensional argon atom model show that electronic motion can be excited and interrogated in a pump-probe ATI experiment. Measurements in molecular gases show that this technique is also applicable to ro-vibrational dynamics.

1 4:54PM W19.00007 Vibrational Modulation of High Harmonic Generation in SF6 , ZACHARY WALTERS, Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309-0440, USA, STEFANO TONZANI, Northwestern University Chemistry Dept. 2145 Sheridan Rd. Evanston,IL 60208-3113, CHRIS H. GREENE, Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309-0440, USA — In a recent experiment performed at JILA (N. Wagner et al, PNAS 103 13279, 2006), a molecule is hit by two pulses: the ﬁrst stimulates Raman-active vibrations while the second generates high-order harmonics. The harmonic intensity oscillates as a function of delay time between the two pulses, with oscillation frequencies equal to those of the Raman-active modes. We interpret this oscillation as a form of quantum interference between neighboring vibrational states of the molecule. Nonzero derivatives of the ionization and recombination amplitudes with respect to nuclear coordinates give the molecule some amplitude to change vibrational states during the high harmonic process. We present a theoretical description of vibrational high harmonic modulation and compare with the experimental results of Wagner et al.

1This work was supported in part by the Department of Energy, Oﬃce of Science, and in part by the NSF EUV Engineering Research Center.

5:06PM W19.00008 Strong-field ionization of Xe probed by femtosecond high-order harmonic absorption spectroscopy1 , ZHI-HENG LOH, MUNIRA KHALIL, RAOUL E. CORREA, Department of Chemistry, University of California, Berkeley, CA 94720, ROBIN SANTRA, Argonne National Laboratory, Argonne, IL 60439, STEPHEN R. LEONE, Departments of Chemistry and Physics, University of California, Berkeley, CA 94720 — Recent experiments on strong-field ionization of atoms and ions have led to conflicting conclusions regarding the existence of orbital alignment in the ionized species. Using table-top, femtosecond high-order harmonic absorption spectroscopy, we have measured the alignment of Xe+ formed via strong-field ionization. High-order harmonics generated by focusing an intense 800 nm pulse into a Ne-filled capillary are spatially overlapped with an optical pump pulse in a sample gas cell before they are spectrally dispersed in an extreme ultraviolet spectrometer. Probing the transition 2 + from the 4d core level to the P3/2 state of Xe at 55.4 eV yields a polarization anisotropy of 0.12 ± 0.01, in good agreement with the theoretical value of + 2 0.1. This result suggests that strong-field ionization exclusively populates the mJ = ±1/2 sub-levels in the Xe P3/2 state.

1Supported by the NSF EUV ERC (0310717) and the LBNL LDRD program. R.S. was supported by DOE (DE-AC02-06CH11357).

5:18PM W19.00009 Using high-order harmonics with momentum imaging techniques to study atomic and molecular dynamics , ARVINDER SANDHU, ETIENNE GAGNON, ARIEL PAUL, MARGARET MURNANE, HENRY KAPTEYN, JILA, University of Colorado and NIST, Boulder, Colorado 80309-0440 — Laser-generated high-order harmonics provide a source of extreme- ultraviolet radiation with unique capabilities for probing atomic and molecular dynamics. Here we present the first studies that employ high harmonics in conjunction with coincidence momentum imaging (COLTRIMS) techniques for studies of molecular dynamics. We generate pulse at ∼ 43 eV photon energy 14 −2 by upconverting intense (> 10 Wcm ) 25 fs laser pulses in an argon filled waveguide. These photons illuminate a cold molecular beam of CO, CO2 or N2, with the ion and electron products from ionization/dissociation detected using time-and-position resolved detectors. We obtain count rates as high as 0.25 per harmonic pulse, sufficient for a variety of studies. By employing pump-probe techniques, we can launch molecules into highly excited states near the molecular double-ionization threshold, from where the dynamics unfold along different channels. We also employ field-free impulsive molecular alignment to demonstrate for the first time the use of single photon excitation to obtain ion and electron angular distributions in the lab frame.

Thursday, March 8, 2007 2:30PM - 5:30PM — Session W26 DCP: Focus Session: Charge Transport in Nanostructures III Colorado Convention Center 205

2:30PM W26.00001 Magneto-Resistance of Nanoscale Molecular Devices1 , ERAN RABANI, Tel Aviv University — Affecting the current through a molecular or a nano-scale junction is usually done by a combination of bias and gate voltages. Magnetic fields are less studied because nano-devices can capture only low values of the magnetic flux. Here, I review our recent theoretical work on the use of magnetic fields as gates for such junctions. Several plausible model systems of such devices will be presented, such as the quantum corral, carbon nanotubes and polycyclic aromatic hydrocarbon molecules. Despite the similarly between gating properties of the magnetic and electric fields, we find that there are also striking differences. This will be illustrated for a multi-terminal device, where the polarity of the magnetic field plays a key role, and with respect to inelastic effects, where the conductance as a function of the gate voltage broadens upon coupling to phonons while it actually narrows considerably in response to a magnetic field.

1In collaboration with Oded Hod, Rice University and Roi Baer, The Hebrew University. 3:06PM W26.00002 Shot Noise in Single-Molecule Transistors , ZACHARY KEANE, DOUGLAS NATELSON, Rice University — While single-molecule electronic devices have been studied extensively, both experimentally and theoretically, a detailed understanding of the physics of charge transport through molecules is still lacking. Recent experiments have shown that it is feasible to measure shot noise in mechanically fabricated single-molecule transistors. Shot noise is a particularly interesting measurement in that it has the potential to reveal details about the correlations between electrons as they cross a molecule. In devices known to exhibit strong correlated-electron eﬀects (e.g. in the Kondo regime), shot noise measurements could provide useful guidance to theorists as they attempt to develop working models for electron transport. We present preliminary results of noise measurements in three-terminal single-molecule devices fabricated by electromigration.

3:18PM W26.00003 Magnetoconductance of molecularly linked Au nanoparticle arrays near the metal-insulator transition , AL-AMIN DHIRANI, JEFF DUNFORD, Chemistry, University of Toronto, BRIAN STATT, Physics, University of Toronto — Magnetoconductance of 1,4-butanedithiol-linked Au nanoparticle films reveal features consistent with “weak localization” (coherent backscattering). Elastic, inelastic, and spin-orbit-scattering time scales extracted using a theoretical model are consistent with those found in other studies on granular Au films, and in particular, reveal that elastic-scattering time scales are comparable to those required for an electron to traverse a nanoparticle. The latter result is consistent with non-Arrhenius conductance vs temperature data. Together, the data suggest that scattering within clusters of molecularly linked nanoparticles plays a critical role in hopping-electron transport in films near a percolationdriven metal-insulator transition.

3:30PM W26.00004 Metal to Insulator Transition in Films of Molecularly Linked Gold Nanoparticles , AMIR ZABET-KHOSOUSI, AL-AMIN DHIRANI, Department of Chemistry, University of Toronto — Self-assembled structures comprising nanoparticles (NPs) and molecular linkers exhibit remarkable electronic behaviours ranging from insulating to metallic. These behaviours can be controlled via chemical synthesis and choice of linker molecules. However, charge transport through these structures is not well understood. Here, we report a metal-insulator transition (MIT) in films of alkanedithiol (CnS2)-linked gold NPs, as the length of linkers (n) is systematically varied. Our results provide strong evidence for a MIT occurring at n = 5. We describe these results in a context of a Mott-Hubbard model. We find that all insulating samples (n ≥ 5) exhibit a universal p scaling behaviour R ∼ exp[(T0/T ) ] (where R is resistance, T is temperature, T0 is a fitting parameter and p = 0.65), and all metallic samples (n ≤ 5) exhibit weaker R–T dependencies than bulk gold. We discuss these observations in terms of competitive thermally-activated processes and strong T -independent elastic scattering, respectively.

3:42PM W26.00005 Theoretical study of molecule mediated spin-polarized electron tunneling between magnetic materials , HAIYING HE, RAVINDRA PANDEY, Department of Physics and Multi-Scale Technology Institute, Michigan Technological University, Houghton, MI 49931, SHASHI KARNA, US Army Research Laboratory, Weapons and Materials Research Directorate, ATTN: AMSRD- ARL-WM; Aberdeen Proving Ground, MD 21005-5069 — There has been a recent interest in organic molecule-mediated spin-polarized electron transport with a potential application in molecular-scale spintronics. In this presentation, we present the results of a theoretical study on the spin-dependent electron tunneling via a self-assembled monolayer of σ-bonded bicyclo[2.2.2]octane-1,4-dithiol on Ni(111). Comparison with a similar study involving π-conjugated molecules, suggests that the magnitude of the tunnel current and the spin-dependent current are strongly inﬂuenced by the nature of chemical bonds in the molecular structure. It gives further understanding of the role of the organic molecules on the spin-polarization of electron transport and provides a basic guideline in choice of molecules in this respect.

3:54PM W26.00006 Inﬂuence of Correlated Hybridization on the Conductance of Molecular Transistors1 , JONG-CHIN LIN, University of California, Davis, FRITHJOF ANDERS, Universitat Bremen, DANIEL COX, University of California, Davis — We study the spin-1/2 single-channel Anderson impurity model with correlated (occupancy dependent) hybridization for molecular transistors using the numerical renormalization-group method. Correlated hybridization can induce nonuniversal deviations in the normalized zero-bias conductance and, for some parameters, modestly enhance the spin polarization of currents in applied magnetic ﬁeld. Correlated hybridization can also explain a gate-voltage dependence to the Kondo scale similar to what has been observed in recent experiments.

1This work was supported by the NSF International Institute for Complex Adaptive Matter (NSF Grant No. DMR-0645461), the U.S. Department of Energy oﬃce of Basic Energy Sciences, Division of Materials Research, and the NIC, Forschungszentrum J¨ulich.

4:06PM W26.00007 Path integral simulations of quantized conductance in nanowires1 , JOHN SHUMWAY, Department of Physics, Arizona State University, MATTHEW GILBERT, Microelectronics Research Center, University of Texas at Austin — Theoretical studies of spin and charge transport in nanostructure often include interactions perturbatively or at a mean-field level. In some cases it is desirable to have a fully quantum many-body method to describe the interacting system: such is the case when investigating spin ordering near the “0.7-structure” in quantum point contacts or for simulating systems with strong polaronic effects. We have developed a new path-integral quantum Monte Carlo (QMC) approach to transport. Previous QMC simulations have been valued for accurately treating electronic correlation in quantum dot spectroscopy—this work now opens up many new opportunities for simulating quantum transport. We show simulation data demonstrating how current-current correlation functions in the Kubo formalism lead to quantization of conductance in GaAs nanowires. This new, finite-temperature, many-body computation technique should have many uses in the study of quantum wires and molecular electronics.

1Work supported by SRC-NRI SouthWest Academy of Nanoelectronics (SWAN) and NSF Grant DMR-0239819.

4:18PM W26.00008 Ab-initio study of transport in the Coulomb-blockade regime , HAITAO WANG, OSAMU HINO, GARNET CHAN, Cornell University — Here we report a new ab-initio model for molecular conductance in the Coulomb blockade regime using unrestricted Hartree-Fock theory within the non-equilibrium Greens function (NEGF) formalism. We demonstrate calculations on recent experimentally studied transition metal complexes, studying the eﬀect of gating on current and the corresponding Coulomb blockade eﬀects.

4:30PM W26.00009 Non-Markovian Transport of Charges in Solid-State Quantum Dots e. , YING-TSAN TANG, Department of Electrophysics, National Chiao Tung University, Hsinchu 300, Taiwan, YUEH-NAN CHEN, National Center for Theoretical Sciences, National Cheng Kung University, Tainan, Taiwan, BRANDES TOBIAS, Institut fürTheoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin, Germany, DER-SAN CHUU, Department of Electro-physics, National Chiao Tung University, Hsinchu 300, Taiwan, TU, BERLIN COLLAB- ORATION — The population dynamics of an electron in a double-dot system coupled to reservoirs is theoretically investigated. Basically, as we put an extra single dot that is strongly coupled to the extended reservoir, it would be possible for experimentalists to realize their modification of coupling strength; therefore we could properly control the memorial effect between system and reservoir by extra coupling. Throughout this study, we effectively change the decay of the entire system. Moreover, the exact results for non-Markovian couplings to both phonon and electron reservoirs with structured tunneling density of states are obtained, which contains the coherent states created by the distance of double dot embedding in the same system as well as the energy shift caused by purely electron-phonon coupling. Eventually, the relaxation dynamics of the Zeno or Anti-Zeno effect reveals insight into the defined decay rate. 4:42PM W26.00010 Controlled production and electronic characterization of defects in carbon nanotubes , BRETT GOLDSMITH, VAIKUNTH KHALAP, ALEXANDER KANE, PHILIP COLLINS, Univ. of California, Irvine — Electrochemical functionalization of nanotubes allows fine control of the number of functionalized sites on a nanotube down to the limit of single, point functionalizations in otherwise pristine devices. This presentation will describe the local and 2-terminal electronic properties of the resulting devices. Point-functionalized devices exhibit spatially-localized resistance as mapped by scanning Kelvin probe microscopy and local gate sensitivity associated with the chemical disorder. The findings are reinforced by further attachment of specific chemical markers visible to electron microscopy.

4:54PM W26.00011 Electrons, holes, and electron-hole junctions in carbon nanotubes , PAUL MCEUEN, LASSP, Cornell University — Carbon nanotubes possess an unusual band structure consisting of symmetric electron and hole subbands separated by a gap determined by the nanotube’s chirality, diameter and any external perturbations. Here, we study the properties of both electrons and holes in these one-dimensional subbands. Capacitance measurements are used to directly probe the van Have singularities in the density of states and the energies of the electron and hole subbbands[1]. Electrical[2] and photocurrent measurements are employed to investigate the properties of nanotube p-n junctions. These measurements directly yield the nanotube bandgap and show fascinating step-like behavior in the reverse-bias region. Finally, measurements of p-n-p nanotube quantum dots are presented where the bandgap is tuned to zero by an external magnetic ﬁeld. These experiments illustrate just a few of the exciting opportunities available in electron-hole nanotube devices. [1] S. Ilani, L.A. Donev, M. Kinderman, and P.L. McEuen, Nature Physics 2, 687 (2006). [2] K. Bosnick, N. Gabor, and P. L. McEuen; Appl. Phys. Lett. 89, 163121 (2006)

Friday, March 9, 2007 8:00AM - 11:00AM — Session X19 DCP: Surfaces, Interfaces, and Colloids II Colorado Convention Center 104

8:00AM X19.00001 Low Energy Inelastic Helium Atom Scattering from a Monolayer Solid. , L.W. BRUCH, Department of Physics, University of Wisconsin-Madison, F.Y. HANSEN, Department of Chemistry, Technical University of Denmark — A time-dependent wave packet calculation for inelastic low energy atomic scattering by a physisorbed monolayer1 has demonstrated that 4He atoms incident on an incommensurate monolayer solid of Xe/Pt(111) readily excite shear horizontal monolayer phonons. Adding an absorbing potential has enabled the calculation to be extended to such long times that transient trapping has decayed and the scattering event is nearly complete. Extending the spatial grids has enabled the use of more nearly monochromatic, spatially broad, wave packets and the inelastic intensities are found to be sensitive to variations of scattering energy by 0.3 meV at incident energies of 4 to 9 meV. Trends for the inelastic intensities at low incident energies, near thresholds, are determined and correlations between the inelastic scattering results and the time development of the elastic scattering are discussed. These calculations were stimulated by the systematic body of experimental data available for 4He scattering by a Xe/Pt(111) monolayer2.

1L. W. Bruch and F. Y. Hansen, J. Chem. Phys. 122, 114714 (2005) 2L. W. Bruch, A. P. Graham, and J. P. Toennies, J. Chem. Phys. 112,314 (2000)

8:12AM X19.00002 Study of Oxidation of Silicon by X-ray Photoelectron Spectroscopy1 , A.R. CHOURASIA, WILLIAM JOHNSTON, R.L. MILLER, RYAN JACOB, Department of Physics, Texas A&M University-Commerce — The oxidation of silicon has been investigated using the technique of x-ray photoelectron spectroscopy. The silicon substrates have been exposed to oxygen at a partial pressure of 5 × 10−6Torr. The exposure was done at substrate temperatures of 100˚C, 200˚C, 300˚C, 400˚C, 500˚C, and 600˚C, The substrates have been analyzed by angle resolved XPS. The magnesium anode (energy = 1253.6 eV) have been used for this purpose. The silicon 2p and oxygen 1s core level regions have been investigated. The spectral data have been recorded at 10˚, 20˚, 40˚, 60˚,80˚, and 90˚ take-oﬀ angles. The QUASES software has been used to determine the thickness of the oxide layer formed on the substrates. The experimental data on the thickness of the oxide layer has been correlated with that obtained from the QUASES model.

1Work supported by Research Corporation and Faculty Enhancement Research Grant, TAMU-C.

8:24AM X19.00003 Ab Initio Calculations for Br and Cl adsorption on the Ag(100) surface , TJIPTO JUWONO, Florida State University, IBRAHIM ABOU HAMAD, Mississippi State University, PER ARNE RIKVOLD, Florida State University — Ab-initio density-functional methods have been used to find the ground-state configurations of Br and Cl adsorbates on Ag(100) surfaces with coverages of 1/9, 2/9, 1/4, 1/3, and 1/2 monolayers. The supercell slab method was used to calculate the electron-density distributions for each configuration. The charge- transfer function, surface dipole moments, adsorbate resident charge, and adsorption energies were calculated and compared with results from electrochemical adsorption exeperiments and Monte Carlo simulations. The lateral adsorbate-adsorbate interactions and the binding energies were extracted from the adsorption energies using a lattice-gas model. The calculated quantities are weakly dependent on the coverage, and the overall shape of the charge-transfer function is nearly coverage independent.

8:36AM X19.00004 Cracks, Meltdowns and Crossover Sizes: An abrupt change in sublimation kinetics associated with the thermally-activated introduction of disclination charge in crystallites. , ALEX J. LEVINE, MOUMITA DAS, Department of Chemistry and Biochemistry, University of California, Los Angeles., DON BLAIR, Department of Physics, University of Massachusetts, Amherst. — Recent experiments and numerical studies of the sublimation kinetics of 2d colloidal crystals show an abrupt increase in the sublimation rate at a particular crystallite size [J. R. Savage et. al. Science 314, 795(2006)]. Motivated by this observation, we propose that the abrupt change in the sublimation kinetics is due to the thermally activated introduction of a disclination charge leading to large internal stresses. These stresses are then relaxed by a fission event precipitating the break-up of the remaining crystallite. We use our numerical simulations to show that the average disclination charge indeed increases to one at the ‘crossover size’ corresponding to the observed change in sublimation rate. Using the Griffith criterion for the spontaneous propagation of microscopic cracks, we see that the effect should depend sensitively upon the range of the attractive interparticle potential. We test this prediction using numerical simulations of the sublimating system. Where that potential is short-ranged, the crystal is brittle allowing for the proposed mechanism. For longer-ranged potentials, however, the material is more ductile preventing this abrupt fission event. 1 8:48AM X19.00005 The structure of a C60 monolayer on Ag(111) , RENEE DIEHL, HSIN LI, KELLY HANNA, Penn State University, WOLFGANG MORITZ, University of Munich — The structure of a monolayer√ √ of C60 on Ag(111) was studied using dynamical LEED, the first such study for C60 molecules. The C60 monolayer adopts a commensurate hexagonal (2 3x2 3)R30˚ structure with a nearest-neighbor separation of 10.0 A.˚ LEED intensities were measured at a sample temperature of 32 K using incident beam energies up to 600 eV. The LEED analysis was performed using conventional methods adapted for large molecular adsorbates, with up to 15 phase shifts to describe the scattering potential. The structure of the monolayer consists of C60 molecules occupying the top sites with their hexagonal faces down, at a distance of 2.27 A˚ above the Ag(111) surface. There is an accompanying deformation of the Ag surface that involves the downward displacement of the Ag atoms nearest to the C60 molecules, consistent with a charge transfer between the surface and the molecule. The C60 molecules have a significant librational motion about their vertical axes, even at 32 K.

1This material is based upon work supported by the National Science Foundation under Grant No. 0505160

9:00AM X19.00006 Accelerated Molecular Dynamics Simulation of Thermal Desorption1 , KELLY BECKER, KRISTEN FICHTHORN, Pennsylvania State University — Thermal desorption has been the focus of much surface science research recently. Alkane desorption experiments on graphite [1] show a prefactor that is constant with chain length, while experiments on magnesium oxide [2] show a prefactor that increases with chain length. We utilize an all-atom model to study alkane desorption from graphite. Transition state theory is used to obtain rate constants from the simulation. Accelerated molecular dynamics techniques are used to extend the simulations to experimentally relevant temperatures. Our results provide an explanation [3] for this seemingly contradictory functionality of the prefactor. We also examine the effect that film structure has on the rate of desorption and the shape of the desorption profile through varying coverage. [1] K.R. Paserba and A.J. Gellman, J. Chem. Phys. 115, 6737 (2001). [2] S.L. Tait et al., J. Chem. Phys. 122, 164707 (2005). [3] K.E. Becker and K.A. Fichthorn, J. Chem. Phys. 125, 184706 (2006).

1Supported by NSF DGE 9987589 and NSF DMR 0514336

9:12AM X19.00007 Irreversible nanoparticle adsorption on patterned substrates , A. CADILHE, N. A. M. ARAUJO, GCEP - Centro de Fisica - Universidade do Minho, V. PRIVMAN, Center for Quantum Device Technology - Clarkson University - Potsdam - NY 13699-5820 - USA — The adsorption of nanoparticles on a surface has interest in fields like heterogeneous catalysts and quantum dots. We simulate the monolayer adsorption of nanoparticles on patterned substrate. We adopted a pattern consisting of equal squares of size α and a distance β apart from each other, and characterize the system, by reckoning the mean value and variance of the distance between the nanoparticles and the radial distribution function of their distances. Proper control of α and β parameters leads to morphologies range from lattice to homogeneous, with interesting non-trivial behaviors in between. Our study shows the relevance of geometrical constraints to obtain different morphologies of colloidal monolayer films with potential for practical applications.

9:24AM X19.00008 Subsurface oxygen stabilization by a third species: Carbonates on Ag(210) , PUSHPA RAGHANI, SISSA, Trieste, Italy, LETIZIA SAVIO, ANDREA GERBI, LUCA VATTUONE, CNISM and Dipartimento di Fisica, Genova, Italy, MARIO ROCCA, IMEM-CNR and Dipartimento di Fisica, Genova, Italy, NICOLA BONINI, Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, STEFANO DE GIRONCOLI, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy, THEORY GROUP COLLABORATION, EXPERIMENTAL GROUP TEAM — Subsurface species have often been invoked to explain the activation of catalytic surfaces for speciﬁc reactions. In particular, subsurface oxygen is thought to be important for the chemistry of Ag catalysts. Here we show by high resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS) combined with density functional theory (DFT) and density functional perturbation theory (DFPT) that on Ag(210) surface, the subsurface oxygen is stabilised more eﬃciently by carbonates than by oxygen adatoms or when there is no supersurface oxygen present. Experimentally a maximum of six subsurface oxygens are found to be stabilised by each carbonate. These results could have an importance in catalytic reactions where subsurface oxygen is known to play a crucial role.

9:36AM X19.00009 Computer simulations of the Adsorption of Xenon onto a C60 monolayer on Ag (111)1 , SILVINA GATICA, Howard University, MILTON COLE, RENEE DIEHL, Pennsylania State University — We performed Grand Canonical Monte Carlo simulations to study the adsorption of Xenon on a substrate composed of C60molecules placed on top of a Ag(111) surface. The C60 molecules form a commensurate structure at a distance of 0.227 nm above the Ag surface. The interaction potential between the Xe atoms and the substrate has two contributions: from the C60 molecules and from the Ag atoms. In the simulations, the interaction with the Ag surface was computed using an ab initio van 3 der Waals potential, varying as 1/d . The interaction between the Xe atoms and each C60 molecule was computed using a potential previously developed by Hernandez et.al. (E. S. Hernandez, M. W. Cole and M. Boninsegni, “Wetting of spherical surfaces by quantum ﬂuids”, J. Low Temp. Phys. 134, 309-314 (2004)), who integrated the Lennard Jones interaction over the surface of a spherical buckyball. The total potential has especially attractive 3-fold sites, positioned 0.4 nm above the point between each three buckyballs. The low coverage uptake populates those sites, and then continues forming a monolayer. The adsorption isotherms show several steps, typical of substrates that have distinct adsorption sites. We compare the results with the experimental data.

1Support: National Science Foundation

9:48AM X19.00010 First-principles study of polar molecule adsorption on hydrogenated diamond (001)1 , YONG-HYUN KIM, S. B. ZHANG, National Renewable Energy Laboratory, YANG YU, L. F. XU, C. Z. GU, Chinese Academy of Sciences — Density functional theory calculations reveal that adsorption of small polar molecules such as H2O, HF, and HCl on hydrogenated diamond (001) surfaces can result in unexpected dihydrogen bonding. This implies that in a C-H bond, H may be more electronegative than C, thus deviating from the widely-accepted Pauling’s electronegativity scale, C(2.55) vs H (2.20). Detailed analysis of the self-consistent charge densities conﬁrms that electrons are indeed accumulated more at the H site than at the C site with respect to the free atoms. It further explains why dihydrogen bond can form for H2O and HF on the surfaces, but not for NH3. The true physical origin for the well-known reduction of the work function due to surface hydrogenation is now attributed to the replacement of loosely bonded surface C π electrons by more tightly bonded C-H σ electrons. We also propose that the favorable formation of the dihydrogen bonds may contribute to the observed p-type conductivity of diamond surfaces in acidic conditions.

1Supported by the US DOE/BES and EERE under contract No. DE-AC36-99GO10337. 10:00AM X19.00011 STM/S study of polycyclic aromatic hydrocarbons on Co (0001) , DAEJIN EOM, MICHAEL LEFENFELD, KWANG TAEG RIM, LI LIU, SHENGXIONG XIAO, COLIN NUCKOLLS, TONY HEINZ, GEORGE FLYNN, NANOSCALE SCIENCE AND ENGINEERING CENTER, COLUMBIA UNIVERSITY COLLABORATION — The fascinating physical properties of carbon nanotubes (CNT) have attracted attention for more than a decade. Both practical and scientiﬁc uses of CNTs have, however, been hindered by the incomplete synthetic control of nanotube structure (diameter and chiral angle). Understanding of growth at the microscopic level may advance our ability to control nanotube chirality. We have consequently explored the interaction of a cobalt substrate, a common catalyst for the growth of CNTs, with polycyclic aromatic hydrocarbon molecules, such as hexabenzocoronene (HBC). Using ultra-high vacuum, low-temperature scanning tunneling microscopy (STM), we have examined the changes in HBC topographic features and vibrational spectra that are induced by thermal annealing of the adsorbed molecules. The potential of hydrocarbon molecules like HBC as end caps for seeded growth of CNT of speciﬁc chirality will be discussed.

10:12AM X19.00012 Electrocatalytic property of PtBi and PtPb line compounds via DFT1 , LIN-LIN WANG, D. D. JOHNSON, Department of Materials Science and Engineering and the Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign — A major obstacle to practical, mass market fuel cell (e.g. hydrogen and direct methanol) technology is CO poisoning of Pt anode. Pt alloys, such as disordered PtxRu(1−x), are known to have an increased CO-tolerance. There has been significant effort to understand the mechanism for increased CO- tolerance and to design better catalyst via alloyed nanoparticles and surface alloys. Alternatively, Pt intermetallic compounds, such as with Bi and Pb, have been observed to improve dramatically the CO-tolerance. [E. Casado- Rivera et al. ChemPhysChem 4, 193 (2003) and J. Am. Chem. Soc. 126, 4043 (2004)] Here we use density functional theory to study the adsorptions of CO, H and OH on these materials. We find that (100) and (110) surfaces of PtBi and PtPb line compounds have lower cleavage energy than (001) surface. Adsorption energies and electronic structure are examined to explain the increased CO-tolerance.

1Supported by DOE Catalysis (DE-FG02-03ER15476) and Materials (DEFG02-91ER45439, through the Frederick Seitz Materials Research Laboratory at UIUC), and for critical computing support from the Materials Computation Center (NSF DMR-0325939)

10:24AM X19.00013 Surface adsorbates and mechanical dissipation in micromechanical resonators1 , THOMAS METCALF, BRADFORD PATE, JEFFREY BALDWIN, BRIAN HOUSTON, Naval Research Laboratory, MAXIM ZALALUT- DINOV, SFA, Inc. — Temperature dependence measurements of the mechanical quality factor of a silicon micromechanical resonator found a pronounced dissipation peak in the neighborhood of 160 K, the magnitude of which reduced dramatically upon in-situ annealing2. Present in all of the resonator’s normal modes, the peak is suﬃciently broad so that the mechanical dissipation was observed to decrease with increasing temperature near room temperature, indicating that this loss mechanism contributes signiﬁcantly to the room-temperature dissipation value. The leading candidates for the origin of the dissipation are surface adsorbates (e.g. water). We report an investigation of the dissipation of micromechanical resonators (between ∼ 100 K and room temperature) with carefully prepared and characterized surfaces as a function of adsorbate and of adsorbate coverage.

1Work supported by the Oﬃce of Naval Research 2Haucke, et al., Appl. Phys. Lett. 86, 181903 (2005)

10:36AM X19.00014 An STM Study of the Interaction of hexabenzocorone on a Ru(0001) Surface , KWANG TAEG RIM, Columbia University, Department of Chemistry and Columbia Center for Integrated Science and Engineering, DAEJIN EOM, LI LIU, SHENGXIONG XIAO, MICHAEL STEIGERWALD1, MARK HYBERTSEN, Columbia University, Department of Applied Physics and Applied Mathematics and Columbia Center for Integrated Science and Engineering, COLIN NUCKOLLS, GEORGE FLYNN — The interaction of hexabenzocorone (hbc) with Ruthenium surface has been investigated using Scanning Tunneling Microscopy in ultrahigh vacuum. The images obtained at 77K and 4.5K, after hbc molecules were vacuum deposited at 325oC onto a pristine Ru(0001) surface, exhibit surface bound molecules with oﬀ-centered bonding sites. After o annealing the hbc-Ru complex at 600 C for 15min, hbc molecules appear to be dehydrogenated to form the bowl-shaped C48. The nature of the interaction and the dehydrogenation of the hbc on Ru(0001) surface will be discussed with DFT calculation, the supplemental IR absorption, and Temperature Programmed Desorption studies. The possibility of growing carbon nanotubes on C48 end-cap upon dosing with C2H2 will also be discussed.

1Mark

10:48AM X19.00015 Commensurate ground states of monolayers on surfaces , ALEXANDRE TKATCHENKO, Universidad Autonoma Metropolitana — We present a procedure for generation of all commensurate monolayer-surface structures of a given symmetry, up to a certain number of adsorbate particles (atoms or molecules), Nads, in the unit cell. It is shown that each cell is related to a well-defined sequence of Fourier terms of the single particle-surface potential. Most importantly, the knowledge of Fourier amplitudes alone is sufficient to exactly predict the ground states of commensurate structures in multi-adsorbate unit cells. The impact of the developed theory for theoretical (i.e. DFT simulations) and experimental (LEED studies) determination of commensurate monolayer ground states is briefly discussed. Furthermore, the experimental results for epitaxy of alkali atoms on the Ag(111) surface and iodine on the Pt(111) surface can be described by this approach, in contrast to previous epitaxy theories.

Friday, March 9, 2007 8:00AM - 10:36AM — Session X26 DCP: Focus Session: Charge Transport in Nanostructures IV Colorado Convention Center 205

8:00AM X26.00001 Molecular Junction Transport - Some Vibronic Effects , MARK RATNER, Northwestern University — The behavior of molecular transport junctions in the coherent tunneling (Landauer-Imry) regime is rapidly becoming understood. But vibronic effects characterize molecules, and understanding how they act in such junctions is a significant issue. This talk will deal with the role of both weak and strong vibronic interactions in molecular junctions. The weak mixing appears in IETS spectra, and can be handled by perturbation theory in the coherent tunneling limit. It provides some quantitative comparisons between calculation and experiment, And can clarify pathways for transport. But strong vibronic interaction requires a more elaborate analysis, and changes the mechanisms for transport. Hysteresis and switching behaviors will be discussed. 8:36AM X26.00002 Vibrationally induced two-level systems in single molecule junctions , ROBERT THIJSSEN, Leiden University, DARKO DJUKIC, SANDER OTTE, ROLF BREMMER, JAN VAN RUITENBEEK, KAMERLINGH ONNES LABORATORY TEAM — It is found that differential conductance spectra of small single molecules contacted by metal electrodes display positive or negative peaks. The positions in energy of these peaks correspond with the energies of local vibration modes of the molecule in the junction. A model of vibrationally induced two-level systems is made in order to explain the physics responsible for the observed features. A molecule in an atomic junction can be contacted in two geometrically different configurations, each of which results into a different junction conductance. These two energy minima are separated by a large energy barrier. Only by vibrationally exciting the molecule above the barrier, a transition between the configurations is possible. This results in a sudden jump in conductance and a peak in differential conductance. The vibrationally induced two-level switching is expected to be quite general, since we have observed dI/dV peaks in many different single molecule-metal junctions. It acts as an intrinsic amplification mechanism for local vibration mode features, even when large conductance fluctuations are present. Therefore it could be exploited as a new spectroscopic tool for identifying local vibration mode energies.

8:48AM X26.00003 Electronic and Vibronic Spectroscopy of Molecular Junctions , JAMES KUSH- MERICK, National Institute of Standards and Technology — Transition voltage spectroscopy and inelastic electron tunneling spectroscopy are used to explore charge transport in molecular junctions. Our recent work has shown that a mechanistic transition occurs from direct tunneling to ﬁeld emission in molecular junctions. The magnitude of the voltage required to enact this transition is molecule-speciﬁc, and thus constitutes a form of spectroscopy. We demonstrate that the transition voltage of a conjugated molecule depends directly on the manner in which the conjugation path is extended. Furthermore using inelastic electron tunneling spectroscopy to measure the vibronic structure of non-equilibrium molecular transport, aided by a quantitative interpretation scheme based on non-equilibrium Greens function/density functional theory methods, we are able to characterize the actual pathways that the electrons traverse when moving through a molecule in a molecular transport junction.

9:00AM X26.00004 Charge Modification of Vibrational Features in Inelastic Electron Tun- neling Spectroscopy , LAM YU, JAMES KUSHMERICK, NIST — Inelastic electron tunneling (IET) spectroscopy of Au-decandithiol-Ni atoms- benzenethiol-Au, Au-decandithiol-Au colloids-benzenethiol-Au and Au-decandithiol-benzenethiol-Au junctions are investigated by cross-wire tunnel junctions. Both the IET spectroscopic features’ intensities and line shapes are observed to be significantly modified by the presence of a metal-sandwich layer. We attribute the vibronic features modification to the interaction between the metallic electronic levels and molecularly coupled phonons in the molecular junctions. Our results provide experimental insights into understanding the origin of some of the differences observed in two previous molecular IET spectroscopy experiments by Kushmerick et al. (Nano lett. 2004, 4, 639) and Wang et al. (Nano lett. 2004, 4, 643).

9:12AM X26.00005 Dynamic Molecular Nanostructures Assembled with Atomic Manipulation1 , BRIAN K. FOSTER2, HARI C. MANOHARAN3, Stanford University, Stanford, CA 94305 — Molecular nanostructures of CO were engineered on a Cu(111) surface by single molecule manipulation in a custom-built low-temperature scanning tunneling microscope (STM). The structures were designed to allow for well-deﬁned motion of either a single molecule or linked sets of molecules on the surface, for the purpose of studying the system’s dynamic translational behavior. Dynamics such as meta-stability, bi-stability and molecular vibration were observed; STM measurements were used to decipher dynamic behavior though coupling to electronic charge via elastic and inelastic tunneling. We also explore the coupling of vibrational modes of individual molecules (at THz frequencies) to the molecular translation rates (at kHz frequencies or below). The dynamic behavior of such structures oﬀers the potential to control and transmit information across surfaces.

1Performed in collaboration with R. G. Harris, L. S. Mattos, C. R. Moon and G. Zeltzer. This work was supported by ONR, NSF, DOE and the NDSEG fellowship program. 2Department of Electrical Engineering 3Department of Physics

9:24AM X26.00006 Classical Nuclear Motion in Quantum Transport1 , CLAUDIO VERDOZZI, GIANLUCA STEFANUCCI2, CARL-OLOF ALMBLADH, Department of Physics, Lund University, Lund, Sweden — A quantum-classical scheme is presented to study nuclear motion in time-dependent quantum transport. The nuclei are treated in the Ehrenfest approximation. We illustrate the method in terms of model systems results. We show how electron-lattice interactions may induce dynamical Peierls distortions in short wires, and change their conducting behavior. We also show time-resolved results for current-induced molecular desorption and suggest that AC biases could provide a way to tailor electromigration. The results illustrate the importance of non-adiabatic eﬀects for transient phenomena in nanodevices.

1Work supported by the European Community 6th framework Network of Excellence NANOQUANTA (NMP4-CT-2004-500198) 2Present Address: Department of Physics, FU Berlin, Berlin, Germany

9:36AM X26.00007 Inelastic effects in noise properties of molecular junctions , MICHAEL GALPERIN, Northwestern University, U.S.A., ABRAHAM NITZAN, Tel Aviv University, Israel, MARK A. RATNER, Northwestern University, U.S.A. — The effect of electron-phonon coupling on the current noise in a molecular junction is investigated within a simple model. The model comprises a one-level bridge representing a molecular level that connects between two free electron reservoirs and is coupled to a vibrational degree of freedom representing a molecular vibrational mode. The latter in turn is coupled to a phonon bath that represents the thermal environment. We focus on the zero frequency noise spectrum and study the changes in its behavior under weak and strong electron-phonon interactions. In the weak coupling regime we find that the noise amplitude can increase or decrease as a result of opening of an inelastic channel. In particular the relative Fano factor decreases with increasing off resonance distance and junction asymmetry. For resonant inelastic tunneling with strong electron-phonon coupling the differential noise spectrum can show phonon sidebands in addition to a central feature. A striking crossover of the central feature from double to single peak is found for increasing asymmetry in the molecule-leads coupling or increasing electron-phonon interaction. A possible use of noise data from scanning tunneling microscopy experiments for estimating the magnitude of the electron-phonon interaction on the bridge is proposed.

9:48AM X26.00008 In-situ Inelastic Electron Tunneling Spectroscopy of Oligoaniline Molecu- lar Junctions , HEAYOUNG YOON, MASATO MAITANI, LINTAO CAI, DAVID ALLARA, THERESA MAYER, The Pennsylvania State University — Recently, several studies have reported that self assembled monolayers of oligoaniline dimmers showed room temperature bistable switching behavior. In this talk, we will discuss the electrical and spectroscopic properties of thiol-substituted oligoaniline (OA) molecular junctions at the interface of lithographically-deﬁned bottom metal nanowire contacts and metal nanowire top contacts. The junctions showed reproducible room temperature bistable switching with the threshold voltages of approximately ± 1.5 V and I-V(T) showed the dominant transport mechanism is coherent tunneling. Inelastic electron tunneling (IET) spectra in low and high current states were obtained at 5 K using a standard AC modulation technique to collect the second harmonic signal directly. The observed IET peaks in a plot of d2I/dV2 versus V were compared to infrared and Raman spectra for the OA self-assembled monolayers. The measurement conﬁrms that the measured transport properties of molecular junctions are due to the intended molecule rather than process induced artifacts. In addition, the intensity change of vibrational modes of the benzene ring (185mV) and the quinon (197mV) of the OA in the low to the high current state suggest that the switching behavior is attributed to an inherent molecular feature of the OA molecules that form the junction. 10:00AM X26.00009 Shot noise measurements on a single molecule , JAN M. VAN RUITENBEEK, OREN TAL1, Kamerlingh Onnes Laboratorium, Leiden University, Leiden, Netherlands, MICHAEL KRIEGER TEAM, DARKO DJUKIC TEAM, BAS LEERINK TEAM — Fabrication of molecular junctions with diverse and controlled functionality requires a fundamental understanding of the relation between the structure and conductance properties of these junctions. We address this issue using simple organic molecules (e.g., hydrogen, carbon monoxide, and benzene) as a molecular bridge between two Pt electrodes formed by the mechanical break junction technique. Shot noise is used to reveal the number of conductance channels through the molecular junction, and their probabilities, while point contact spectroscopy yielded its characteristic vibration modes. This diverse information combined with theoretical calculations allows us to present a detailed picture of the relation between the conductance and the junction structure.

1The speaker

10:12AM X26.00010 Quantum-state-resolved probing of molecular inner-sphere reorganization using a single-molecule transistor , NATHALIE DE LEON, WENJIE LIANG, QIAN GU, HONGKUN PARK, Harvard University — The coupling of electron transport through a single molecule to various degrees of freedom, such as spin, charge, and vibrations, can be probed using a single molecule transistor. The addition or subtraction of electrons usually accompanies a change in molecular geometry, a phenomenon known as inner-sphere reorganization. n+ We have studied the eﬀects of inner-sphere reorganization on electron transport using two complexes, ferrocene and Fe(bpy)3 (n = 1, 2, 3), as model systems. n+ The reported energies of vibrational excitations in Fe(bpy)3 are in agreement with existing IR and Raman spectroscopic data.

10:24AM X26.00011 Quantum Channels and Conductance Oscillations in Metal/Molecule/Metal Switches , FENG MIAO, Department of Physics and Astronomy, University of California, Riverside, CA 92521, DOUGLAS OHLBERG, R. STANLEY WILLIAMS, HP Labs, 1501 Page Mill Rd., Palo Alto, CA 94304 , C. N. LAU, Department of Physics and Astronomy, University of California, Riverside, CA 92521 — We investigate conductance switching in Pt/stearic acid monolayer/Ti devices by pressure-modulated conductance microscopy. For devices with conductance G>>GQ and G<< GQ, where GQ is the conductance quantum, localized pressure-induced conductance peaks are observed, indicating formation of nanoscale conductance pathways on the electrodes. For devices with G∼ 1- 2 GQ, in addition of conductance peaks, we also observed conductance dips and oscillations in response to localized pressure. These results suggest formation of quantum conductance channels in our devices, and can be satisfactorily modeled by considering interfering electron waves between two partially transmitting electrodes. Moreover, the force dependence of such conductance modulations is fully consistent with this model. Our ﬁndings underscore the possible use of these devices as atomic switches.

Friday, March 9, 2007 11:15AM - 1:51PM — Session Y19 DCP: Surfaces, Interfaces, and Colloids III Colorado Convention Center 104

11:15AM Y19.00001 Surfactant Adsorption at the Air-Liquid and Hydrophobic Solid-Liquid Interfaces: Unraveling the Mechanism for Superspreading , MAKONNEN PAYNE, The Graduate School - University Center of CUNY & The City College of New York, CHARLES MALDARELLI, ALEXANDER COUZIS, The City College of New York — In this paper we report our findings with regard to the synergistic interactions between polyethylene oxide surfactants of the general structure CiEj and compare the behavior to a known super wetting surfactant. Pendant drop tensiometry experiments and sessile drop contact angle measurements on hydrophobic surfaces were conducted on combinations of CiEj surfactants with 1-dodecanol. We found that a number of combinations were capable of reducing significantly the air-liquid tension, however only systems that exhibited the propensity to form extended liquid crystalline phases, as shown by the combination of cross-polarized microscopy, cryo-TEM, and light scattering experiments, were able to improve on the wetting performance of the these systems. We have also conducted the parallel experiment focused on the surfactant adsorption at the hydrophobic solid-liquid interface. Using in-situ infrared internal reflection spectroscopy and complimentary sum-frequency generation spectroscopy, we are able to dynamically interrogate the surfactant adsorption kinetics and interfacial water structure evolution at the hydrophobic solid-liquid interface. We will relate these findings to gain insight into the molecular requirements for superspreading.

11:27AM Y19.00002 Interrogating the strength of the bond between salt and water: a combined DFT and MP2 study , BO LI, ANGELOS MICHAELIDES, MATTHIAS SCHEFFLER, Fritz-Harber-Institut der Max-Plank-Gesellschaft — The interaction of water with salt (NaCl) is of widespread importance and of considerable general interest. Although numerous theoretical studies have been reported [1], none has provided a convincingly reliable estimate of the strength of the bond between water and a ﬂat NaCl surface, such as NaCl(001). Moreover, the computed adsorption energies predicted by DFT vary from 0.2-0.7 eV/H2O depending on the choice of exchange-correlation functional [2]. Here, we address this issue through an extensive series of periodic Hartree-Fock and post-Hartree Fock [Møller-Plesset perturbation (MP2) and coupled cluster (CCSD(T))] calculations. Periodic Hartree-Fock calculations have been performed for H2O molecules adsorbed on NaCl slabs, and by evaluating the local dependence of the correlation contribution to the adsorption energy with respect to cluster size, we obtain accurate MP2 and CCSD(T) estimates of the H2O adsorption energy on NaCl(001). Our computed adsorption energy, which is around 0.6 eV/H2O, comes close to the experimental value [3] and is at the upper end of the range predicted by DFT. [1] A. Verdaguer, G. M. Sacha, H. Bluhm, and M. Salmeron, Chem. Rev. 106, 1478 (2006). [2] B. Li, A. Michaelides, and M. Scheﬄer, in preparation. [3] L. W. Bruch, A. Glebov, J. P. Toennies, and H. Weiss, J. Chem. Phys. 103, 5109 (1995).

11:39AM Y19.00003 Cluster Morphology and Aggregation Kinetics in Dense Aerosols , RAJAN DHAUBHADEL, AMITABHA CHAKRABARTI, CHRISTOPHER SORENSEN, Kansas State University — We studied the cluster morphology and kinetics of an aggregating aerosol system using the small angle light scattering technique. Exploding a mixture of a hydrocarbon gas and oxygen in closed chamber generated a system of aggregating soot particles. The soot particles started as individual monomers, ca. 38 nm radius, grew to bigger clusters with time and ﬁnally stopped evolving after spanning a network across the whole system volume. The gelled clusters showed a hybrid morphology with a lower fractal dimension at length scales of a micron or smaller and a higher fractal dimension at length scales greater than a micron. The study of the kinetics of the aggregating system showed that the system gelled when the homogeneity λ attained a value 0.4 or higher. The aggregation kernel K appearing in SE was also determined using the light scattering data.. The observed data indicated a slight increase in K value when the system was denser.

11:51AM Y19.00004 Adsorption of Water, Methanol and Toluene on the Surface of Soot Particulate Matter , MOHSEN YEGANEH, SHAWN DOUGAL, BERNARD SILBERNAGEL, EL-MEKKI EL-MALKI, ExxonMobil — Soot particles are byproducts of incomplete hydrocarbon combustion. The adsorption of water and organic molecules on the soot surfaces is of technological and environmental importance. We have applied a newly developed technique of SFG spectroscopy for high surface area materials [1] to investigate the adsorption of water, methanol, and toluene on the surface of standard soot particles from the National Institute of Standards and Technology (NIST). Adaptations of standard SFG procedures are required to compensate for the high refractive index of these carbonaceous materials. We find that adsorption of water, methanol, and toluene on the soot surface is reversible at room temperature. We also find that UV radiation modifies the surface composition of these soot particles. The effect of UV radiation on the adsorption, as well as the kinetics and thermodynamics of methanol adsorption/desorption will also be discussed. [1] Mohsen S. Yeganeh, Shawn M. Dougal, and Bernard G. Silbernagel, Langmuir 22, 637 (2006) 12:03PM Y19.00005 Drops Bouncing on a Superhydrophobic Surface1 , FRANK VAN SWOL, Sandia National Laboratories — Low solid interfacial energy and fractally rough surface topography confer to Lotus plants superhydrophobic (SH) properties like high contact angles, rolling and bouncing of liquid droplets, and self-cleaning of particle contaminants. By exploiting the porous fractal structure of a novel, synthetic SH surface it is possible to produce a synthetic lotus effect. This is relevant to realizing self-cleaning properties for particle concentration, and the slippery nature of the coating can be used to enhance the performance of fluidic devices. Here we report on molecular dynamics (MD) and some classical density functional theory calculations that provide valuable insight into the conditions needed to cause liquid droplets to form and bounce on a surface. The MD results report on the details of the droplets impacting surfaces of varying wettability, ranging from complete wetting to complete drying. For the SH surfaces we present results for the contact time, between droplet and surface, as a function of impact velocity, droplet size and surface friction.

1Supported by Basic Energy Sciences, and the DOE Oﬃce of Science’s ASCR program. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the US DOE under Contract No. DE-AC04-94AL85000.

12:15PM Y19.00006 Pair Interaction of microparticles at oil-water interfaces , CHUAN ZENG, ANTHONY DINSMORE, University of Massachusetts — We confined microparticles at fluid-fluid interfaces and measured the interaction between them. Aggregates of colloidal particles were observed, suggesting an attractive capillary force at long range, which cannot be explained by gravity. We report measurements of the interaction between carboxylate-modified polystyrene spheres (radius ∼ 1 micron) at the oil-water interface using image analysis and particle tracking. The interaction between two isolated spheres was measured from particle trajectories and analyzed through the Markovian Dynamics Extrapolation method developed by J.C. Crocker and D.G. Grier. Different choices of oil (1,1,1-trifluoroheptan, silicone oil, decahydronapthalene, etc.) and various sample geometries were explored. The role of surfactants will be discussed. We acknowledge support from NASA through the Fluid Physics program (NRA 02-OBPR-03-C).

12:27PM Y19.00007 Selective crystal nucleation at a soft organic template. , SUMIT KEWALRAMANI, KYUNGIL KIM, GUENNADI EVMENENKO, PULAK DUTTA, Northwestern University, PULAK DUTTA GROUP AT NORTHWESTERN UNIVERSITY TEAM — Langmuir monolayers floating on supersaturated aqueous solutions can guide the growth of oriented inorganic crystals.1 Although, oriented crystal growth under such monolayers has been observed for a variety of inorganic species, barium fluoride and strontium fluoride are the only systems where an epitaxial match between the organic and inorganic lattices is directly observed.2 We have studied different growth stages of this model system by varying the subphase conditions. We find that, in the earliest nucleation stages, strained epitaxial thin films of barium fluoride and barium fluoride chloride can be grown under the same organic structures. We will also discuss late crystal growth stages, specifically orientation/misorientation effects in thick films, which are governed by reorganization of preformed crystals. 1. S. Mann, Biomineralization Principles and Concepts in Bioinorganic Materials Chemistry, Oxford University Press, Oxford, 2001. 2. J. Kmetko et al. Phys. Rev. Lett. 89, 186102-1 (2002).

12:39PM Y19.00008 A Light Scattering Study of Solvent Solidification in Colloidal Suspensions , MELISSA SPANNUTH, Dept of Geology and Geophysics, Yale Univ, SIMON MOCHRIE, Dept of Physics, Yale Univ, JOHN WETTLAUFER, Dept of Geology and Geophysics and Dept of Physics, Yale Univ — Intermolecular forces between a solid and a foreign substrate can lead to the formation of a thin film of liquid between the two surfaces at temperatures below the solid’s bulk melting temperature. These forces also result in fluid flow towards colder regions of the interface when a temperature gradient is present. When the fluid component of a colloidal suspension solidifies, the particles become encased within the ice both individually and in clusters. Near the melting temperature, a premelted layer bathes the particles, providing a restricted, but finite volume of liquid that facilitates Brownian motion through the background solid. We will present the results of our X-ray Photon Correlation Spectroscopy experiments by which we can characterize the dynamics of the particles in a solidifying colloidal suspension and thereby extract information about the amount of premelted liquid.

12:51PM Y19.00009 Ion-size effect at the surface of silica hydrosol , ALEKSEY TIKHONOV, Center for Advanced Radiation Sources at the University of Chicago, and Brookhaven National Laboratory, NSLS, Beamline X19C — The forces of electrical imaging strongly polarize the surface of colloidal silica. I used X-ray scattering to study the ion-size effect in the adsorbed 2-nm-thick compact layer of alkali ions at the surface of concentrated solutions of 5-nm, 7-nm, and 22-nm particles, stabilized either by NaOH or a mixture of NaOH and CsOH, with the total bulk concentration of alkali ions ranging from 0.1- to 0.7-mol/L. The observed structure of the compact layer is almost independent of the size of the particles and concentration of alkali base in the sol; it can be described by a two-layer model, i.e., a ∼ 6 - 8-Angstrom-thick layer of directly adsorbed hydrated alkali ions with a surface concentration ∼ 3 × 1018 m−2, and a ∼ 13-Angstrom-thick layer with a surface concentration of sodium ions ∼ 8 × 1018 m−2. In cesium-enriched sols, Cs+ ions preferentially adsorb in the first layer replacing Na+; their density in the second layer does not depend on the presence of cesium in the sol. The difference in the adsorption of Cs+ and Na+ ions can be explained by the ion-size-dependent term in the electrostatic Gibbs energy equation derived earlier by others. Brookhaven National Laboratory is supported by U.S.D.O.E., Contract No. DEAC0298CH10886. X19C is partially supported through funding from the ChemMatCARS National Synchrotron Resource and the University of Chicago.

1:03PM Y19.00010 Steric effects on the dynamics of electrolytes , MUSTAFA SABRI KILIC, MARTIN BAZANT, Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139,USA., ARMAND AJDARI, Labortoire de Physico-Chimie Theorique, UMR ESPCI-CNRS 7083, 10 rue Vauquelin, F-75005 Paris, France. — The classical Poisson-Boltzmann (PB) theory of electrolytes assumes a dilute solution of point charges with mean-field electrostatics. Even for very dilute solutions, however, it predicts absurdly large ion concentrations (exceeding close packing) for surface potentials of only a few tenths of a volt. In this talk, we adopt a simple model for steric effects with only one parameter (the effective ion size), and we analyze the charging of a thin double layer, which must form a condensed layer of close-packed ions near the surface at high voltage. A surprising prediction is that the differential capacitance varies non-monotonically with the applied voltage, and thus so does the response time of an electrolytic system. This effect is able to predict the reversal of AC electro-osmotic flow at high voltage and high frequency, as well as the increase of capacitance with temperature in molten salts.

1:15PM Y19.00011 Transport of colloids in porous medium. , HSIANG-KU LIN, ROYA ZANDI, LEONID P. PRYADKO, University of California, Riverside — Pathogenic microorganisms such as bacteria and viruses in groundwater cause over one million illnesses per year in the United States. Despite the considerable research, the transport of microorganisms (colloids) in porous media is not well understood. In the reported work, we present a phenomenological ﬁltration model that describes transport of colloids and the dynamics of colloid deposition and release at the attachment sites. The model has a soliton-like solution for the ﬁltering front separating “clean” anterior and “dirty” posterior regions. The computed breakthrough curves and time-dependent deposition curves are in good agreement with experimental measurements.

1:27PM Y19.00012 Charge Inversion by Electrostatic Complexation: Molecular Dynamics Simulations , JORDI FARAUDO, Universitat Autonoma de Barcelona, ALEX TRAVESSET, Iowa State University — Ions near interfaces play an important role in many biological and physico-chemical processes and exhibit a fascinating diverse range of phenomena. A relevant example is charge inversion, where interfacial charges attract counterions in excess of their own nominal charge, thus leading to an inversion of the sign of the interfacial charge. In this work, we argue that in the case of amphiphilic interfaces, charge inversion can be generated by complexation, that is, electrostatic complexes containing several counterions bound to amphiphilic molecules. The formation of these complexes require the presence at the interface of groups with conformational degrees of freedom with many electronegative atoms. We illustrate this mechanism by analyzing all atomic molecular dynamics simulations of a DMPA (Dimirystoil- Phosphatidic acid) phospholipid monolayer in contact with divalent counterions. The results are found to be in agreement with recent experimental results on Langmuir monolayers. We also discuss the implications for biological systems, as Phosphatidic acid is emerging as a key signaling phospholipid. 1:39PM Y19.00013 Microscale Curveballs: Translational and Rotational Coupling of Colloids , STEPHEN ANTHONY, Department of Chemistry, University of Illinois, MINSU KIM, Department of Physics, University of Illinois, STEVE GRANICK, Department of Materials Science and Engineering, University of Illinois — Optically anisotropic MOON particles (modulated optical nanoparticles) allow the simultaneous measurement of translation and rotation for individual particles. Through chemical modification, these particles can be made hydrophilic, amphiphilic, or hydrophobic. Among those three, the boundary condition exhibits varying amounts of slip, which registers in the value of the rotational diffusion constant. Additionally, for the amphiphilic case, the translational and rotational motions are no longer independent of each other, exhibiting coupling due to the asymmetric hydrodynamic drag. Understanding these processes is fundamental to particle dynamics, with implications to kinetically limited processes such as the self-assembly of multi-unit proteins. Addressing the influence of these varied boundary conditions, this study presents single-particle tracking of micron-sized spherical colloids suspended in deionized water, tracked and quantified using home-written algorithms.

Friday, March 9, 2007 11:15AM - 1:51PM — Session Y26 DCP: Focus Session: Charge Transport in Nanostructures V Colorado Convention Center 205

11:15AM Y26.00001 What are ‘molecular wires’ and how might we use them?1 , STUART LINDSAY, Arizona State University — Through-bond tunneling is generally greatly enhanced over through-space tunneling, so organic ‘wires’ can connect electrodes over distances with >nS conductance over distances of several nm. Very small decay lengths (or even non-exponential decay) suggest that mechanisms other than tunneling can contribute to transport. Wires made with electroactive (reducible/oxidizable) molecules can be gated electrochemically, and can be switched without any gate at all if the ﬁeld owing to the applied bias is large enough, giving rise to switching and NDR. Wires that reconcile the competing requirements of ﬂexibility (so they can be properly bonded) with high conductance will be useful elements in nanoscale devices and sensors.

1Work supported by the NSF

11:51AM Y26.00002 Molecular conductance from density functional theory calculations , DANIEL KOSOV, ZHENYU LI, University of Maryland — We will present a plane-wave/pseudopotential implementation of a method to calculate the electron transport properties of nanostructures. We performed density functional theory based electron transport calculations of amine, dithiocarboxylate and dithiiocarbamate anchored junctions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The conductance enhancement factor is as large as 25 is predicted for dithiocarbame anchored junctions. A microscopic origin of the experimentally observed current ampliﬁcation by dithiocarboxylate anchoring groups is established. We calculated the conductance traces for amine and thiol anchored junctions as the molecules are pulled by the STM tip from the Au electrode. Our calculations show that the stretching of the thiol anchored junction during its formation is accompanied by signiﬁcant electrode geometry distortion. Oppositely, the electrode for the amine terminated junction remains intact when the junction is stretched by the STM tip. Z. Li and D. Kosov, J.Phys.:Cond.Matt. 18 (2006) p.1347; J.Phys.Chem B 110 (2006) p.19116, ibid p.9893

12:03PM Y26.00003 Exploring conductance switching properties of molecular scale devices - a computational approach.1 , BARRY D. DUNIETZ, ALEXANDER PROCIUK, MOUSUMI DAS, TRILISA PERRINE, University of Michigan, DUNIETZ TEAM — A computational approach is used and developed to study electron transport through molecular scale devices. The study identiﬁes and provides insight into mechanisms underlying transport switching properties. These systems include: 1. Spin-dependent electronic transport through a Porphyrin ring Ligating an Fe(II) atom, 2. Contact geometry and orientation eﬀects of conjugated molecular transistors and 3. Chemical sensors with focus on metal recognition properties recently exhibited only for certain short peptide chains. The research also involves developing new models and methods to describe electron conductance through single molecular systems.

1University of Michigan

12:15PM Y26.00004 Measurement of Single Molecule Conductance , JOSHUA HIHATH, XIULAN LI, FANG CHEN, NONGJIAN TAO, Arizona State University, DEPTARTMENT OF ELECTRICAL ENGINEERING; CENTER FOR SOLID STATE ELECTRONICS RESEARCH TEAM — Understanding the electron transport properties of single molecules is a basic requirement for achieving molecular-scale electronic devices reliable enough for everyday use. To help elucidate the transport mechanisms involved in various single metal-molecule-metal junctions we have performed measurements while applying an electrochemical gate, changing the environmental temperature, the chemical binding at the contacts, the bias, and the molecular length in an STM break junction system. Using this system and these handles to help elucidate conduction mechanisms we have explored several molecular systems, including simple alkane chains, conjugated redox molecules, and biologically relevant molecules such as DNA and proteins, in all cases we have gained some insight into the transport capabilities of each metal-molecule system.

12:27PM Y26.00005 Statistical Analysis of Electronic Transport in Alkanethiol Molecular Devices with Nanowell Structures. , HYUNWOOK SONG, TAKHEE LEE, Department of Materials Science and Engineering, Gwangju Institute of Science and Technology, NAK-JIN CHOI, HYOYOUNG LEE, Center for Smart Molecular Memory, IT Convergence Components Laboratory, Electronics and Telecommunication Research Institute — We study charge transport through nanoscale molecular monolayers. For example, alkanethiol [CH3(CH2)n−1SH] self-assembled monolayer (SAM) is one of the most standard molecular systems that has been extensively investigated, and is very useful as a control in molecular devices because their structure and configuration have been sufficiently well-characterized. Reported here is a statistical analysis of electronic transport in alkanethiol SAM using different length alkanethiols. Particularly, we fabricated more than 6,000 molecular devices with nanowell structure, a vertical type of metal-molecule-metal junctions with nanometer scale junction diameter. We investigated transport properties such as temperature-variable current-voltage I(V,T) characteristics from these mass-fabricated devices. Based on the extensive I(V,T) data, a statistical analysis of transport characteristics in alkanethiol SAM will be presented.

12:39PM Y26.00006 Electronic transport of low concentrations of P3HT molecules across nanogap source-drain electrodes. , JEFF WORNE, Electrical and Computer Engineering, Rice University, BEHRANG HAMADANI, NIST, Washington DC, DOUGLAS NATELSON, Physics and Astronomy, Rice University — Poly 3-hexothiophene (P3HT) is a widely studied, versatile material used in organic electronics. Little is known, however, about the electronic transport properties of individual or small groups of P3HT molecules. Initial experiments suggest that the behavior of low concentrations of molecules differ significantly from bulk P3HT. We have fabricated nanoscale P3HT transistors using electromigrated nanogap structures as source-drain electrodes and the underlying silicon/SiO2 substrate as a gate. We present preliminary transport data on these devices as a function of temperature and electrode material. 12:51PM Y26.00007 Adsorption and conductance of BDT on the Au(111) surface , A. FAZZIO, RENATO B. PONTES, FREDERICO D. NOVAES, ANTONIO J.R. DA SILVA, Instituto de Fisica - Universidade de Sao Paulo — Molecular electronics is a new trend in the science and technology at the nanometer-scale. A prototypical system where transport properties have been widely studied both experimentally and theoretically is benzene-1,4-dithiolate (BDT) on Au(111). We present, using Total Energy Density Functional Theory calculations, a detailed study of such a system for different surface coverages and sites, and we find that except at high enough coverages, the BDT lowest energy configuration has the molecule almost lying down on the Au surface. We also find that when the BDT is bridging two Au(111) leads, this lying down configuration still has the lowest energy when compared to the standing up configuration (by approximately 0.4 eV). We have also calculated, using a DFT-based non-equilibrium Green’s Function formalism, the conductance for a variety of BDT configurations, including how they vary as a function of the separation between the leads. We find that due to resonant features in the conductance, it can vary significantly depending on the distance between the leads. We also calculate the total energy, forces and conductance for a variety of BDT configurations for different separation between leads. We thank the Brazilian agencies FAPESP and CNPq, and CENAPAD-SP for computer time.

1:03PM Y26.00008 Ab-Initio calculations of electron transport properties of Si-Porphyrin-Si devices , FILIPE J. RIBEIRO, WENCHANG LU, JERRY BERNHOLC, North Carolina State University, Raleigh NC 27695-7518 — We present results of numerical calculations of the electronic transport properties of devices consisting of porphyrin molecules connected to Si(100) leads. Our calculations are based on ab-initio ultrasoft pseudopotentials and the generalized gradient approximation (GGA) to the exchange and correlation energy functional. Transport properties were calculated using a non-equilibrium Green’s function method in a basis of optimally localized orbitals. We studied three different molecules: H2-, Zn-, and Ni-porphyrins. The somewhat different alignments of the HOMO and LUMO levels of the molecules with the top of the valence and bottom of the conduction bands of the Si leads has strong implications on the I-V characteristics of the devices. In particular, the turn-on voltages are different for the different molecules. In addition, if the Si leads are heavily doped n-type, regions of negative differential resistance exist in all three systems.

1:15PM Y26.00009 Role of dephasing and surface states in Si based molecular electronics1 , HASSAN RAZA, NSF Network for Computational Nanotechnology and School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN — We study the effect of an unpaired dangling bond (DB) on occupied molecular orbital conduction through a styrene molecule bonded to a n++ H:Si(100)-(2×1) surface. For molecules relatively far from the DB, we find good agreement with the reported experiment using a model that accounts for the electrostatic contribution of the DB, provided we include some dephasing due to low energy phonon modes. However, for molecules within 10A˚ to the DB, we have to include electronic contribution as well along with higher dephasing to explain the transport features. Apart from this, we study the electronic band structure of unpaired and paired DBs, DB wires and clusters on H:Si(100)-(2×1) surface using Extended Hückel Theory (EHT) and report their effect on the Si band gap. An unpaired DB introduces a near-midgap state, whereas a paired DB leads to π and π* states. The unpaired and paired DB wires introduce states in similar fashion however with larger dispersion. Furthermore, different DB clusters exhibit states that can be interpreted as superposition of states due to unpaired and paired DBs. (cond-mat/0607226,0611417)

1This work was supported by the NASA Institute for Nanoelectronics and Computing and ARO-DURINT.

1:27PM Y26.00010 Time-Resolved, Single Molecule Spectroelectrochemistry of Conjugated Polymers in Contact with ITO1 , JOHN GREY, RODRIGO PALACIOS, WEI-SHUN CHANG, WILLIAM MILLER, ALLEN BARD, PAUL BARBARA, University of Texas at Austin — Time-resolved, single molecule spectroelectrochemistry was used to study excited-state interfacial electron transfer between single conjugated polymer (MEH-PPV) molecules (possessing about 200 redox sites) and an indium tin oxide (ITO) electrode. Decay kinetics and emission yields were obtained while cycling the electrode potential in the range of -.5V to +.5V (Silver wire), which lies between the reduction (-1.5 eV) and oxidation potentials (0.8 eV) of the ground state. At +0.5 V, the emission intensities and average lifetimes were observed to increase about 20% whereas at -0.5 V both values decrease by the same amount. Several possible origins of the potential-induced intensity modulation are proposed.

1We acknowledge support from the NSF and Welch foundation for this work

1:39PM Y26.00011 Renormalized Couplings and the Insulator and Metallic Behavior of Double-Stranded DNA1 , EFTA YUDIARSAH, SERGIO E. ULLOA, Ohio University — Electronic transport in double-stranded DNA is studied using a ladder model in a tight-binding Hamiltonian, withRealistic on- site energies [1] and hopping constants [2]. The effect of DNA molecules coupling to leads is studied on periodic poly (dG)-poly(dC) sequences with an embedded TGGGGT defect group. The differential conductance features diminish gradually and vanish at small coupling. The influence of counter-ions, local fields, and interaction with phonons can renormalize the hopping constants; we study the role of increasing intra-strand hopping on λ-phage DNA sequences. Increasing coupling results in the electronic transport of λ-sequences to change from insulator to metallic. Differential conductance dI/dV at low bias is vanishingly small for bare hopping constants found in the literature [2], and increases rapidly if they are enhanced by more than 5 times. Even at large uniform intra-chain coupling (1 eV), dI/dV drops drastically at low bias for sequences longer than 300 base pairs. Electron-phonon interactions are also considered. The diagonal (local) interaction results in polaronic effects while the non-diagonal terms yield phonon- assisted hopping. [1] S. Roche, Phys. Rev. Lett. 91, 108101 (2003). [2] A. A. Voityuk et al., J. Chem. Phys. 114, 5614 (2001).

1Supported by OU-BNNT.