Organizing Committee
Delbert Bagwell U.S. Army ERDC Jaroslav Burda Charles University in Prague Cary F. Chabalowski U.S. Army Research Laboratory Colleen Cummings U.S. Army ERDC Glake Hill Jackson State University William A. Lester, Jr. University of California at Berkeley Jerzy Leszczynski (Chairman) Jackson State University David Magers Mississippi College W. Andrzej Sokalski Wroclaw University of Technology
Staff
Shonda Allen-Hill Jackson State University Al’ona Furmanchuk Jackson State University Olexandr Isayev Jackson State University Biswarup Pathak Jackson State University
Support
National Science Foundation (CREST Program) National Science Foundation (EPSCoR Program) Department of Defense (Chemical Materials and Computational Modeling (CMCM) Project) through ERDC US Department of Commerce (Atmospheric Dispersion Project) National Institutes of Health (RCMI Program) Department of Defense (Computational Design of Novel Materials Project) Office of Vice President for Research and Strategic Initiatives, JSU Springer Parallel Quantum Solutions
Conference on Current Trends in Computational Chemistry 2008 October 31 – November 1, 2008 Jackson, Miss.
Schedule of Events
Conference on Current Trends in Computational Chemistry 2008
Schedule of Events Conference on Current Trends in Computational Chemistry 2008 5
Friday, October 31
7:30 – 9:00 Continental Breakfast 8:00 – 12:00 Registration 9:00 – 9:30 Opening Ceremony 9:30 – 10:30 1st Session (S1) Lester Lecture 10:30 – 10:40 Group photo 10:40 – 11:10 Coffee Break 11:10 – 12:40 2nd Session (S2) 2 Talks 12:40 – 2:15 Lunch 2:15 – 4:30 3rd Session (S3) 3 Talks 4:30 – 5:00 Coffee Break 5:00 – 7:00 First Poster Session (P1) 7:00 – 10:00 Conference Dinner Nobel Lecture Speaker: After Dinner Nobel Lecture Dr. Walter Kohn, UCSB
Saturday, November 1
8:00 – 9:00 Continental Breakfast 8:30 – 11:00 Registration 9:00 – 10:30 4th Session (S4) 2 Talks 10:30 – 11:00 Coffee Break 11:00 – 1:00 Second Poster Session (P2) 1:00 – 2:00 Lunch 2:00 – 3:30 5th Session (S5) 2 Talks 3:30 – 4:00 Coffee Break 4:00 – 5:30 6th Session (S6) 2 Talks 5:30 – 7:30 Third Poster Session (P3) 7:30 – 10:30 Banquet Banquet Speaker: Best Student Poster Award Dr. Jeffrey A. Nichols, ORNL Presentation
Invited Talks Conference on Current Trends in Computational Chemistry 2008 7
Session Chairman: Glake Hill Lester Lecture Jackson State University
William A. Lester, Jr Quantum Monte Carlo for Molecular Systems University of California, Berkley
nd Session Chairman: Marek Urban 2 Session University of Southern Mississippi Jorge M. Seminario Graphene Structures for New Scenarios for Molecular and Nano Texas A&M University Electronics Priya Vashishta Multimillion to Billion Atom Simulations of Nanosystems Under University of Southern California Extreme Conditions
rd Session Chairman: Frances Hill 3 Session US Army ERDC Vincent Meunier Using Computational Approaches for the Understanding, Design, Oak Ridge National Laboratory and Predictions at the Nanoscale Ruth Pachter Molecular-to-Nano-Biomaterials: Understanding and Design by US Air Force Research Laboratory Computation Edward J. Perkins Hierarchical Feedback Control and Reverse Engineering of US Army Engineering Research Transcriptional Networks Involved in Sex Hormone Synthesis in and Development Center Ovaries
th Session Chairman: Peter Pulay 4 Session University of Arkansas Ernest R. Davidson Koopmans’ Theorem for Open Shell Systems University of Washington So Hirata Exact Solutions of the Polyatomic Schrödinger Equations University of Florida
th Session Chairman: Jane Murray 5 Session University of New Orleans Magdolna Hargittai Structural Effects in Inorganic Chemistry Budapest University of Technology and Economics G. Narahari Sastry A Theoretical Analysis of Non-Covalent Interactions in Isolated Indian Institute of Chemical and Associated Forms Technology
th Session Chairman: Andrzej Wierzbicki 6 Session University of South Alabama Maria Barysz Relativistic Effects in Chemistry – Experiment and Theory Nicolaus Copernicus University Tim Clark Molecular Dynamics and Signal Transduction University of Erlangen–Nuremberg
Table of Contents
Conference on Current Trends in Computational Chemistry 2008
Contents for Abstracts Conference on Current Trends in Computational Chemistry 2008 11
Session† Presentation Page
P1 Dynamics of Interaction in Isoelectronic Systems CsBr + Kr and CsBr + Br- 19 Vladimir M. Azriel and Lev Yu. Rusin
P1 TDDFT investigation of the Asorption Spectra of a Cyanine Dye 20 Anu Bamgbelu, Indu Shukla, Jing Wang, and Jerzy Leszczynski
S6 Relativistic Effects in Chemistry – Experiment and Theory 21 Maria Barysz
P1 Probing the Effects of Heterogeneity on Delocalized π•••π Interaction Energies 23 Desiree M. Bates and Gregory S. Tschumper
P1 Are Density Functional Theory Predictions of the Raman Spectra Accurate 24 Enough to Distinguish Conformational Transitions of Proteins? Workalemahu Berhanu, Ivan A. Mikhailov, Alfons Schulte, Artem E. Masunov
P1 A Comparison of Substituent Effects on Aromatic Compounds 28 Manikanthan Bhavaraju and Steven R. Gwaltney
P1 The Performance of the 6-31G## Basis Set for DFT Calculation of 13C Nuclear 29 Magnetic Shielding V. Bolshakov, V.V. Rossikhin, E.O. Voronkov, S.I. Okovytyy, and J.Leszczynski
P1 An Investigation of the 1H NMR Chemical Shifts for the Derivatives of Endic 31 Imide Using Magnetically Corrected Basis Sets V.Bolshakov, S.I. Okovytyy, V.V. Rossikhin, E.O. Voronkov, I.N.Tarabara, I.V.Tkachenko, and J.Leszczynski
P1 Study of Silver Clusters: Agn : for n=13 to 55 Spectroscopic Calculations with 32 ADF Program and Optimizations with Gaussian2003 Program with B3LYP Functional and LANL2DZECP Basis P.Bonifassi, P.Karamanis, Meng-Sheng Liao, J.D.Watts, M.J.Huang, P.C.Ray and J.Leszczynski
P1 Study of Cadmium Selenium Clusters: CdnSen for n=1 to 16 Spectroscopic and 36 dynamic hyperpolarizability calculations P.Bonifassi, Meng-Shen Liao, J.G.Watts, M.J.Huang, Y.Daoudi, P.C.Ray and J.Leszczynski
P1 (PCCP)2 Dimer: A New Prototype for Delocalized π-type Interactions 38 Bei Cao and Gregory S. Tschumper
P1 Enthalpies of Formation of TNT Derivatives by Homodesmotic Reactions 39 Erica Chong, Amika Sood and David H. Magers
S6 Molecular Dynamics and Signal Transduction 40 Tim Clark
S4 Koopmans’ theorem for open shell systems 41 E. R. Davidson
P1 Conformational Study of Oxacyclododecan-2-one by Dynamic NMR Spectroscopy 42 and Computational Methods Dalephine Davis, Gurvinder Gill, Diwakar M. Pawar, Sumona V. Smith, and Eric A. Noe
P1 A Theoretical Study on Structures, Binding Energies and Vibrational Spectra of 43 the Interactions of Alkali Metal Cations (Li+, Na+ and K+) with Mono- and Bi- cyclic Ring Fused Benzenes T. C. Dinadayalane and Jerzy Leszczynski 12 Conference on Current Trends in Computational Chemistry 2008 Contents for Abstracts
P1 Theoretical Calculation of Electronic Circular Dichroism of a 45 Hexahydroxydiphenoyl-Containing Flavanone Glycoside Yuanqing Ding, Xing-Cong Li, and Daneel Ferreira
P1 Theoretical Studies on Addition Reactions between Norbornene and 2- 46 Azoniaallene Cations Yuanqing Ding, Shu-Lin Li, De-Cai Fang, Xing-Cong Li, Daneel Ferreira, and Ruo-Zhuang Liu
P1 Classical Molecular Dynamics Simulations Toward the Understanding of 47 Nitroamine Binding within the NR1 S1S2 Domain J. Ford-Green, L. Gorb, M. Qasim, E. Perkins, J. Leszczynski
P1 Conformational studies of Organophosphorus pesticides towards the 48 discernment of their Esterase inhibition Jason Ford-Green, D. Majumdar, Jerzy Leszczynski
P1 Singlet-Triplet Gaps and Rearrangements of 1,2-Dihydro-3H-pyrazol-3-ylidenes 49 and 1,2,4,5-Tetrahydro-3H-pyrazol-3-ylidenes Fillmore Freeman and Damilola A. Adepegba
P1 Mechanisms of Insertion Reactions, 1,2-Rearrangements, and 1,2- 51 Cycloadditions of Aminocarbenes: Three Center Transition States Fillmore Freeman and Vickie Tamdoan Bui
P1 Improvement of Molecular Mechanics Force Fields forNucleic Acids. Ab Initio 52 Based Amino Group Description. A. Furmanchuk, V. I. Poltev, E. Gonzalez, A. Deriabina, A. Martinez, L. Gorb, and J. Leszczynski
P1 Density Functional Theory and Multiscale Simulations Combined With 53 Spectroscopic Study of Barium/Strontium Ferrate/Cobaltate (BSCF) as a Promising Material For Solid Oxide Fuel Cell (SOFC) Shruba Ganopadhyay, Talgat Inerbaev, Artëm E. Masunov, Deanna Altilio, Nina Orlovskaya, Jaruwan Mesit, Ratan Guha, Ahmed Sleiti, Jayanta Kapat
P1 Application of New Pairwise Spin-Contamination Correction Approach to Study 57 the Transition Metal Hydrides Satyender Goel and Artëm E. Masunov
P1 Gold Nanoparticle Based NSET Assay for Monitoring RNA Folding Kinetics 61 Jelani Griffin, Uma Shanker Rai and Paresh Chandra Ray
P1 The role of Metal Substrate Reconstruction in the Self-Assembly of Thiol 62 Adsorbates Frank Hagelberg, and Georgi Nenchev, Bogdan Diaconescu, Karsten Pohl
S5 Structural Effects in Inorganic Chemistry 64 Magdolna Hargittai
P1 High-Accuracy ab initio Studies of Sn (n=1-4) Electronic Structure 66 John A.W. Harkless
P1 Theoretical Study on the Cation-π interactions of the Ring Fused Benzene 67 Molecules Ayorinde Hassan, T. C. Dinadayalane, and Jerzy Leszczynski
S4 Exact Solutions of the Polyatomic Schrödinger Equations 69 So Hirata, Toru Shiozaki, Muneaki Kamiya, and Edward F. Valeev
P1 Predicted NMR Shift Changes in the Aromatic Ring Due to Cation-π Interactions 70 Estelle M. Huff, Peter Pulay, T.K.S. Kumar Contents for Abstracts Conference on Current Trends in Computational Chemistry 2008 13
P1 Relative Stability of Isomers of a Dipseudoacid 71 Peter J. Huwe, Dmitriy V. Liskin, Edward J. Valente, and David H. Magers
P1 Prediction of Thermal Cycloreversion and Fatigue-resistance in Photochromic 73 Compounds: A Density Functional Theory Study Pansy Iqbal, Ivan A. Mikhaylov, Kevin D. Belfield, Artëm E. Masunov
P2 Structure and Properties of Bacterial Nitroreductase 77 Olexandr Isayev, Leonid Gorb, Narimantas Cenas, Mo Qasim, and Jerzy Leszczynski
P2 DFT study on the Glycine-(H2O)n and Protonated Glycine-(H2O)n (n=1 and 2) 78 Jyothsna Kanipakam, T. C. Dinadayalane and Jerzy Leszczynski
P2 Electronic Structure and Optical Properties of Si(111)/SiO2 Plane Interface 80 Valentin V. Karasiev, Dmitri S. Kilin and Anatoli Korkin
P2 Prediction of Nitro Compounds Water Solubility by Modified COSMO-RS Method 82 Yana Kholod, Eugene Muratov, Leonid Gorb, Anatoly Artemenko, Mohammad Qasim, Victor Kuz’min, Francis Hill and Jerzy Leszczynski
P2 Self-consistent Computations of Molecular Vibrational Spectra on a Base of 83 Stable Numerical Methods I.V.Kochikov, G.M. Kuramshina, V.M.Senyavin
NL The Power of the Sun 86 Walter Kohn
P2 Stability of Single-Walled Carbon Nanotubes and Their Cut Ends 87 Wojciech Kołodziejczyk, Jakub Baran, Peter Larsso, Rajeev Ahuj, J. Andreas Larsso
P2 Probing the Role of P=O Stretching Mode Enhsncement in Nerve-agent Sensors: 88 Simulation of the Adsorption of Nerve-agents on the Model MgO and CaO Surfaces W. Kolodziejczyk, D. Majumdar, S. Roszak, J. Leszczynski
P2 First Principles Non-Adiabatic Molecular Dynamics Study of the DNA-SWCNT 89 System Dmytro Kosenkov, Oleg V. Prezhdo, Bradley F. Habenicht, Leonid Gorb, and Jerzy Leszczynski
P2 The Analysis of Textures of Mesophases of Liquid Crystals by Fractal Structural 90 Descriptors N.A. Kovdienko, L.N. Ognichenko, A.G. Artemenko, E.N. Muratov, N.S. Novikova, V.E. Kuz’min, and H.Novohatskaya
P2 A Tetra-pirrolic Iron Molecular Biosensor to Detect Gas Pollutants 93 Carlos Kubli-Garfias, Karim Salazar-Salinas, and Jorge M. Seminario
P2 Hydrogen Bonded Complexes of Pyridoxale-5'-phosphate Derivatives with Water 95 Molecules G.M. Kuramshina, S.A. Sharapova,D.A. Sharapov, Yu.A. Pentin
P2 Toxicity of Benzene and its Derivatives toward Mammals: Development and 99 Applications of QSAR Models Hrvoje Kušić, Bakhtiyor Rasulev, Danuta Lesczynska, Jerzy Leszczynski, Natalija Koprivanac
P2 Hydrogen Generation Mechanism from Lithium Hydride + Ammonia Borane: An 100 ab initio Study Tae Bum Lee and Michael L. McKee 14 Conference on Current Trends in Computational Chemistry 2008 Contents for Abstracts
S1 Quantum Monte Carlo for Molecular Systems 101 William A. Lester, Jr.
P2 Supramolecular Interactions of Fullerenes with (Cl)Fe− and Mn Porphyrins. A 102 Theoretical Study Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang
P2 Hydrogen Bonding in Complexes of Isocyanato orIsothiocyanato Compounds 103 with Alcohols or Thiols Nannan Lin and David H. Magers
P2 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of 104 Carbon and silicon C. Davis Lofton, Crystal B. Coghlan, and David H. Magers
P2 Are Conventional Strain Energies in Bicyclic Alkanes Additive? 105 Andrew K. Magers, D. Brandon Magers, and David H. Magers
P2 Are Conventional Strain Energies in Bicyclic Alkenes Additive? 106 D. Brandon Magers and David H. Magers
P2 Binding Energies in Dimers of N-methyl methyl carbamate,N-methyl S-methyl 107 thiocarbamate, andN-methyl methyl dithiocarbamate Harley R. McAlexander and David H. Magers
S3 Using computational Approaches for the Understanding, Design, and Predictions 108 at the Nanoscale Vincent Meunier
P2 Computational Predictions of Partitioning Coefficients Values 109 A. Michalkova, L. Gorb, F. Hill, Mo Qasim, and J. Leszczynski
P2 The Effects of Ionic Strength and pH on the Thermal Stabilities of DNA Aptamers 111 Brandon Mitchell, G. Reid Bishop, and David H. Magers
P2 Conventional Strain Energy in Boracycloproane, Diboracyclopropane, 112 Boracyclobutane and Diboracyclobutane Elizabeth Mobley, Brandon Magers, Harley McAlexander, and David H. Magers
P2 Hydration of Urea and Trimethylamine-N-oxide 113 Katherine Munroe, J. Chase Burns, and David H. Magers
P2 Reaction Force Analysis of the Effect of the Solvent Chloroform on the 114 Markovnikov and Anti-Markovnikov Addition Reactions of HCl + Propene Jane S. Murray, Jaroslav V. Burda, Alejandro Toro-Labbé, Soledad Gutiérrez-Oliva, and Peter Politzer
P2 Structure and Geometry of Isomers of Nano N20 Clusters 115 Jamshid Najafpour, Farrokh Roya Nikmaram, Maryam Kordi Peykani
P2 Shape Dependent Nonlinear Optical Properties of Nanomaterials 119 Adria Neely, Anant Kumar Singh, Jelani Griffin, Gopala Krishna Darbha, Uma Shanker Rai, and Paresh Chandra Ray
P2 Conformational Study of Oxacyclotridecan-2-one 120 Eric A. Noe, Gurvinder Gill, and Diwakar M. Pawar
P2 The Strange Case of the Cyclopropenyl Anion 121 Brandice Nowell, Willard Collier, Pornpun Rattananakin, and Charles U. Pittman Jr. Contents for Abstracts Conference on Current Trends in Computational Chemistry 2008 15
P3 The Quantum-Chemical Investigation of Diphenyl Chlorophosphate Aminolysis 122 by Cage Amines S.I. Okovytyy, A.V. Tokar, G.V. Gryn’ova, L.I. Kasyan, J. Leszczynski
P3 Determination of internuclear distances in binary ionic crystals 123 Valentin V. Oshchapovsky
S3 Molecular-to-nano-biomaterials: Understanding and Design by Computation 124 R. Pachter
P3 Enthalpies of Formation of Furan and Pyrrole Derivatives by Homodesmotic 125 Reactions Yunfeng Pan, Alison Cochran, and David H. Magers
P3 Theoretical Investigations of the Structure and Bonding of Several Transition 126 Metal Complexes to Probe their Carbon monoxide (CO) Releasing Properties Biswarup Pathak, D. Majumdar, Jerzy Leszczynski
P3 Quantitative Structure – Activity Relationship Study of Organophosphorus 127 Pesticides, Nerve Agents and their Derivatives Y. Paukku, E.N. Muratov, A.G. Artemenko, N.A. Kovdienko, V.E. Kuz’min, and J. Leszczynski
P3 Quantum-chemical Investigation of the Interaction of Organophosphorus 128 Compounds with Zinc Oxide Surfaces Y. Paukku, A. Michalkova, and J. Leszczynski
S3 Hierarchical Feedback Control and Reverse Engineering of Transcriptional 130 Networks involved in Sex Hormone Synthesis in Ovaries Edward J Perkins, Natàlia Garcia-Reyero, Sandy Brasfield, Daniel L Villeneuve, Xin Guan, Dalma Martinovic, Nancy Denslow, Youping Deng, Ying Li, Tanwir Habib, Jason Shoemaker, and Francis Doyle III
P3 Theoretical Study of RDX and TATP Interactions with MOF-5 131 T. Petrova, A. Michalkova and J. Leszczynski
P3 Mechanisms of the Aryl Azide Addition to Substituted Norbornene Imides. 132 Computational Study T. Petrova, S.Okovytyy, L. Gorb, I.Tarabara, J.Leszczynski
P3 Gas Phase and Solution Structures of 1-Methoxyallenyllithium 134 Lawrence M. Pratt, Darryl D. Dixon and Marcus A. Tius
P3 Dynamics on the Nanoscale: Time-Domain ab initio Studies of Quantum Dots 135 and Carbon Nanotubes Oleg Prezhdo
P3 Graphene Terahertz Generators for Molecular Circuits and Sensors 136 Norma L. Rangel and Jorge M. Seminario
P3 Excitation Energies of Small Planar Polycalicenes 140 Pornpun Rattananakin, Willard Collier, Steven R. Gwaltney, and Charles U. Pittman Jr.
P3 Modeling Polyamides and DNA Binding 141 Joshua M. Rodgers and Steven R. Gwaltney
P3 Molecular Hydrogen Storage in Spherophanes 142 A. Saal, O. Ouamerali, C.A. Daul, T. Jarrosson
P3 Odor Detection Based on DNA for Nitroaromatic Compounds 143 Karim Salazar-Salinas, Carlos Kubli-Garfias, and Jorge M. Seminario 16 Conference on Current Trends in Computational Chemistry 2008 Contents for Abstracts
P3 Hydrogen Storage in Boron/Carbon Systems 145 Julia Saloni, Wojciech Kolodziejczyk, Szczepan Roszak and Glake Hill
P3 Theoretical Study of Interactions of Thymine and Uracil and their Tautomers 146 with Tetrahedral Edge Clay Minerals Fragments B. Sanders, A. Michalkova, and J. Leszczynski
S5 A Theoretical Analysis of Non-Covalent Interactions in Isolated and Associated 148 Forms G. Narahari Sastry
S2 Graphene Structures for New Scenarios for Molecular and Nano Electronics 149 Jorge M. Seminario
P2 Size and Distance Dependence NSET Ruler for Selective Sensing of Hepatitis C 150 virus RNA Dulal Senapati, Jelani Griffin, Anant Kumar Singh, and Paresh Chandra Ray
P3 Interaction of Gold Clusters with Guanine and Watson-Crick Guanine-Cytosine 151 Base Pair: A Theoretical Investigation Manoj K. Shukla, Madan Dubey, Eugene Zakar and Jerzy Leszczynski
P3 A Theoretical Study of the Interactions of In+ and In+3 with Stone-Wales Defect 152 Single-Walled Carbon Nanotubes Tomekia Simeon, Krishnan Balasubramanian and Jerzy Leszczynski
P3 Hydrogenated Gallium-Oxide Clusters [Ga2O2H2]2+ as Models of Catalytic Sites 154 for the Ethane Dehydrogenation in Oxidized Ga/ZSM-5: a DFT Study Vitaly Solkan
P3 Protonated Molecular Oxygen and Sulfur Dioxide as Chemical Precursors in the 156 Conversion of SO2 to SO3 by Oxygen in super acid: A Theoretical Study on Mechanism of Acid-Catalyzed oxidation of SO2 with Molecular Oxygen Vitaly Solkan
P3 Post-Hartree-Fock Study on Decomposition of Nitrous Oxide on Ga–ZSM-5 158 Vitaly Solkan and Jerzy Leszczynski
P3 DFT Study on Interaction of Acylation Reagents with 4-phenyl-1,3-dihydro-1,5- 161 benzodiazepin-2-one L. Sviatenko, S. Okovytyy, A. Gaponov, L. Kasyan, I. Tarabara, J. Leszczynski
P3 Two-photon Absorption Predicted with Time-Dependent Density Functional 162 Theory: Sum over States vs. Coupled Electronic Oscillator formalisms Sergio Tafur, Ivan A. Mikhailov, Artëm E. Masunov
P3 Ab Initio Calculations of Guanine-Aspartic Acid Interactions 165 Patrina Thompson-Harris, Bridgit O. Crews, Mattanjah S. de Vries, Glake Hill
P3 The Time Dynamics of Spherical Nanoparticles Aggregation 166 Oleg G. Tovmachenko, Paresh C. Ray
P3 A Theoretical and Matrix-Isolation Infrared Spectroscopic Study of Mixed MDyX4 167 (M = Alkali Metals, X = Halogens) Vapor Complexes Zoltán Varga, Attila Kovács, Cornelis Petrus Groen, Magdolna Hargittai
S2 Multimillion to Billion Atom Simulations of NanoSystems Under Extreme 170 Conditions Priya Vashishta
P3 Stacking Influences on the Spectra of the Monomer of PFBT: A Theoretical Study 171 Jing Wang, Jiande Gu, and Jerzy Leszczynski Contents for Abstracts Conference on Current Trends in Computational Chemistry 2008 17
P3 Computational Study of Interfacial Reaction Dynamics and Basicity 172 Collin D. Wick
P3 Contribution of Nonpolar Interactions to Molecular Recognition and Binding of 173 Type I Antifreeze Proteins at the Ice-Water Interface Andrzej Wierzbicki and E. Alan Salter
P3 Theoretical Study on the Magnetism in Finite Size Single Wall Carbon Nanotube 174 Jianhua Wu and Frank Hagelberg
P3 Phospholipid Molecular Recognition at the Monomer Boundaries of Copolymer 176 Surfaces; Spectroscopic and Ab Initio Studies Min Yu, Marek W. Urban, Yinghong Sheng, and Jerzy Leszczynski
P3 TGA SAM: a Potential Switch 177 Jian-Ge Zhou and Quinton L. Williams
†S* – Oral presentation (* denotes session number); P* – Poster presentation (* denotes poster session number); NL – After Dinner Nobel Lecture
Conference on Current Trends in Computational Chemistry 2008 19
Dynamics of Interaction in Isoelectronic Systems CsBr + Kr and CsBr + Br-
Vladimir M. Azriel and Lev Yu. Rusin
Institute of Energy Problems of Chemical Physics RAS, Leninski prospect 38, Bldg.2, Moscow 119334, Russia E-mail: [email protected]
Trajectory calculations show that interaction in the systems CsBr + R, where R=Kr and R=Br-, includes two channels:
CsBr + R → Cs+ + Br- + R (1) → RCs+ + Br- (2)
It is necessary to note, that ion Br- and atom Kr are isoelectronic particles with similar masses. In the above presented scheme the channel (1) represents typical collision-induced dissociation, and excitation functions of this channel for both systems demonstrate qualitatively similar behaviour, but absolute values of cross sections for interaction in the system CsBr + Br- is a little bit higher (figure 1,a). The channel (2) for the system CsBr + Kr leads to formation weakly bounded ionic complex KrCs+, while in the system CsBr + Br- this channel corresponds to thermoneutral reaction of replacement of ion Br-, originally connected with caesium, by other similar ion of bromine. As is clear from figure 1,b the behaviour of excitation functions of this channel for two systems qualitatively differs in all calculated range of collision energies. And if for the system CsBr + Kr excitation function shows similarly to the channel (1) strongly pronounced threshold behaviour, reaches a maximum at energy near 5 eV and further decreases with growth of collision energy, then for the system CsBr + Br- the cross section of this channel has a maximum at collision energies near to zero and further monotonously decreases with growth of energy.
6 40 a b + - 35 5 CsBr + R -> Cs + Br + R CsBr + R -> RCs+ + Br- 30
4 25 - 3 R=Br- 20 R=Br 15 2 10 R=Kr (*1000)
1 R=Kr 5 Cross section,Cross units arb. Cross section, arb. units arb. section, Cross 0 0 0 5 10 15 20 25 0 5 10 15 20 25 Collision energy, eV Collision energy, eV
Fig. 1. Excitation functions of channels (1) (a) and (2) (b) for interaction in the systems CsBr + Kr and CsBr + Br-. 20 Conference on Current Trends in Computational Chemistry 2008
TDDFT investigation of the Asorption Spectra of a Cyanine Dye
Anu Bamgbelu, Indu Shukla, Jing Wang, and Jerzy Leszczynski*
Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217 U. S. A.
Cyanine dyes have attracted attention as active components for optoelectronic applications. Cyanines are a class of symmetrically, charged polymethine dyes. They generally show a very strong п- п* excited absorption, which can be tuned through visible and near infrared region by varying the length of the polymethine chain. As one member of the cyanine dyes, Cy5 has absorption edges around 649nm and it has been applied in labeling proteins and nucleic acids. In the present study, the geometries of the ground state of the studied models have been fully optimized by analytical gradient techniques and the local minimum energy structures are found by ascertaining that all of the harmonic frequencies are real. The density functional theory (DFT) with Becke’s three parameter (B3) exchange functional along with the Lee-Yang-Parr (LYP) nonlocal correlation functional (B3LYP) was applied and two basis sets (LanL2DZ and SDD) were used respectively for all the atoms in this study. Based upon the optimized structures of the ground state, the time-dependent density functional theory (TDDFT) was adopted to compute the vertical singlet excitation energies and the absorption spectrum of the anionic polymethine cyanine dye (Cy5) and various anionic halide substituted polymethine cyanine dyes (Cy5-X) (Fig. 1). The presence of the anionic halogen group was found to have different effects on optical properties of Cy5. The excitation energy is lowered when the heavier halogen group is involved, which indicates red shift effects for the absorption wavelengths. The polarizable continuum model (PCM) self-consistent reaction field of Tomasi and co-workers was employed for all gas- phase-optimized structures to evaluate the solvation effects on the excitation properties of the studied species.
Figure 1: Structure of Cy5-X (X=I, Cl, Br, F)
Conference on Current Trends in Computational Chemistry 2008 21
Relativistic Effects in Chemistry – Experiment and Theory
Maria Barysz
Department of Quantum Chemistry, Institute of Chemistry, Nicolaus Copernicus University, PL-87 100 Torun, Poland
The two basic theories of modern physics are the theory of relativity and quantum mechanics. While the theory of the latter in chemistry was instantly recognized, the full relevance of relativistic effects in chemistry is not even fully appreciated. The relativistic effects are always present in our life. This is the reality. They can be observed and calculated in the quantum chemical calculations only. The relativistic effects are important for both light and heavy-elements chemistry; for light elements when one searches the limits of accuracy of quantum mechanics and quantum electrodynamics, for heavy elements in calculations of atomic and molecular properties at the chemical accuarcy of about 0.1eV. The relativistic effects are important not only for the core properties but for the valence properties as well. They are important for intrinsic and response properties of molecules and for chemical reactions. The reaction energies can not be calculated properly without the relativistic theory. Similarly, the proper description of the hydrolisis reactions [1, 2] or the core dependent X-ray spectroscopy [3] is not possible without the inclusion of the relativistic quantum mechanics. The heavy-element chemistry needs to be based on the Dirac equation. The Dirac equation is based on the completely different philosophy than the nonrelativistic theory. However it can be transfered to the two-component form which enable one to follow all computational and conceptual experience gained in the nonrelativistic approach. Recently we have proposed [4, 5] a method for the generation of two–component solutions of arbitrarily high accuracy which are formally equivalent to solutions of the Dirac equation for the discrete electronic part on its eigenspectrum. The method is formally of infinite order in the fine structure constant and has been acronymed as the IOTC (infinite–order two–component) theory. Its equivalence to the four–component Dirac approach has been documented by calculations of spinorbital energies. However, this does not say too much about the accuracy of the corresponding wave functions [4, 5, 6]. In the present report the accuracy of the IOTC wave functions is probed by the evaluation of of different moments, < rk >, of the radial density distribution. The two–component hamiltonian of the IOTC theory is obtained by a unitary block–diagonalizing transformation of the Dirac hamiltonian. Once the IOTC spinorbitals are calculated, they can be back–transformed into four–component solutions. The transformed four component solutions are then used to evaluate different moments of the electron density distribution. As shown by the present study, with sufficiently large basis set of Gaussian functions, the Dirac values of these moments are fully recovered [8]. The evaluation of expectation values in the framework of any two–component method requires that the operators are brought into the form appropriate for the given two–component scheme. This is what is known as the change of picture [7] of operators. The importance of the change of picture effect is also studied and shows that for high enough (large k) moments this effect can be neglected without severely affecting the calculated moments. This explains why the common practice of neglecting the change of picture in calculations of dipole and quadrupole moments works so well. The two–component methods are frequently addressed as being quasirelativistic. In the case of the IOTC approach the Dirac solutions are completely recovered. Hence, the IOTC method for time–independent problems is as relativistic as the four–component Dirac approach. The equations of the two methods are related by the unitary transform of the energy operators. This 22 Conference on Current Trends in Computational Chemistry 2008
transform does not affect the energy eigenspectrum, though it reduced the four–component by spinors to spinor solutions. The four–component solutions, if needed, can be obtained by the inverse transformation.
References
[1] M. Barysz, J. Leszczynski, A. Bilewicz Phys. Chem. Chem. Phys., 6 (2004) 4553 - 4557. [2] M. Barysz, D. Kёedziera, J. Leszczyґnski, A. Bilewicz Int. J. Quant. Chem., 106 (2006) 2422-2427 [3] M. Barysz, J. Leszczynski, J. Chem. Phys. 126 (2007) 154106 [4] M. Barysz, A. J. Sadlej, J. Chem. Phys. 116 (2002) 2696–2704 [5] M. Barysz, ”Theoretical chemistry and physics of heavy and superheavy elements”, ”Progress in Theoretical Chemistry and Physics” by Kluwer Academic Publishers. (2003) 349–397, Review paper. [6] Dariusz Kёedziera, Maria Barysz, Journal of Chemical Physics, 121 (2004) 6719 - 6727 [7] M. Barysz, A. J. Sadlej, Theor. Chim. Acta, 97 (1997) 260-270. [8] M. Barysz, L. Mentel, J. Leszczynski, in preparation.
Conference on Current Trends in Computational Chemistry 2008 23
Probing the Effects of Heterogeneity on Delocalized π•••π Interaction Energies
Desiree M. Bates and Gregory S. Tschumper
Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677 1848 USA
Dimers composed of (Bz), 1,3,5-triazine (Tz), cyanogen (Cy) and Diacetylene (Di) are used to examine the effects of heterogeneity at the molecular level and at the cluster level on π•••π stacking energies. The MP2 complete basis set (CBS) limits for the interaction energies (Eint) of these model systems were determined with extrapolation techniques designed for correlation consistent basis sets. CCSD(T) calculations were used to correct for higher-order correlation effects which were as large as +2.81 kcal mol-1. The introduction of nitrogen atoms into the parallel-slipped dimers of the aforementioned molecules causes significant changes to Eint. The -1 CCSD(T)/CBS Eint for Di/Cy is -2.47 kcal mol which is substantially larger then either Cy/Cy (-1.69 kcal mol-1) or Di/Di (-1.42 kcal mol-1). Similarly, the heteroaromatic Bz/Tz dimer has an -1 -1 (Eint) of -3.75 kcal mol which is much larger then either Tz/Tz (-3.03 kcal mol ) or Bz/Bz (- 2.78 kcal mol -1). Symmetry-adapted perturbation theory calculations reveal a correlation between the electrostatic component of Eint and the large increase in the interaction energy for the mixed dimers. However, all components (exchange, inductions, dispersion) must be considered to rationalize the observed trend. Another significant conclusion of this work is that the basis set superposition error has a negligible impact on the difference between MP2 and CCSD(T) interaction energies. Consequently, counterpoise corrections are not necessary when computing higher-order correlation effects on Eint. Spin component scaled MP2 (SCS-MP2 and SCSN-MP2) calculations with a correlation consistent triple-ζ basis set reproduced the trends in the interaction energies despite overestimating the CCSD(T)/CBS Eint of Bz/Tz by 20-30%.
24 Conference on Current Trends in Computational Chemistry 2008
Are Density Functional Theory Predictions of the Raman Spectra Accurate Enough to Distinguish Conformational Transitions of Proteins?
Workalemahu Berhanu 1,2, Ivan A. Mikhailov2, Alfons Schulte3, Artem E. Masunov1,2,3
Department of Chemistry, Nanoscience Technology Center, Department of Physics, University of Central Florida, Orlando, FL 32826; E mail: [email protected]
Recent research efforts have produced mounting evidence that most neurodegenerative diseases, including Alzheimer's disease, are closely linked with accumulation of the amyloid beta-protein (Abeta) produced through endoproteolysis of the beta-amyloid precursor transmembrane protein. Formation of amyloid fibrils includes conformational transition from alpha-helix into beta-sheet structure. The analysis of the three different conformation of the lysine and glutamic acid hexapeptides (with six explicit solvent molecules) has been computed using the density functional theory (DFT) B3LYP/6-31G and B3LYP/6-31G*. We compared the previously reported experimental amide vibrational frequencies of polyglutamic acid and polylysine in their three different conformation (alpha, beta and random coil/PPII) with our theoretical prediction. We found that the predicted wave numbers of amide I, amide II and amide III frequencies of the three conformations of hexamers of lysine and glutamic acid are in good agreement with the experimental values of polyglutamic acid and polylysine (in non-deutrated water solvent). The agreement with experiment was found better when a polarization functional is included to the 6-31G* basis set. The results indicate that DFT is a viable tool for examining conformational changes in peptides.
Introduction
Recent research efforts have produced mounting evidence that most neurodegenerative diseases, are closely linked with accumulation of the amyloid β-protein (Aβ) produced through endoproteolysis of the β-amyloid precursor transmembrane protein. Formation of amyloid fibrils includes conformational transition from alpha-helix into beta-sheet structure. The detailed mechanism of oligomer formation and the influence of protein stability on the aggregation kinetics are still matters of debate. In order to study the dynamics of amyloid formation, different experimental techniques can be used. These include Infrared (IR) and Fluorescence spectroscopy, Circular Dichroism Raman Optical Activity, Raman, and UV Resonance Raman Spectroscopy (UVRR) [1]. The peptide bond itself has an absorption band in UV region around 190 nm, so excitation of proteins and peptides with ~200 nm selectively enhances peptide backbone amide vibrations. The resultant UV Raman spectral are dominated by amide vibrations, designated as Amide I, II, III and the spectrum carries easily recognizable features of different secondary structure elements [2]. All calculations used the Gaussian 2003 program. Geometry optimizations and frequency calculations were carried out at the hybrid density functional theory level in the gas phase, using the standard 6-31G basis set and B3LYP functional. The frequency calculations were also carried out with 6-31G* with a polarization function. In addition explicit water molecules were taken into account (one molecule per residue) for a total of six water molecules for hexamers of lysine and glutamic acid. Different hydrogen bonding patterns were tested. We studied three conformations of hexamers of glutamic acid and lysine: random coil (PPII confirmation) an Conference on Current Trends in Computational Chemistry 2008 25
alpha (α) helix and the third one is beta (β) sheets [3]. The initial geometry of α –helix and β- sheet conformations of polyglutamic acid were obtained by modification of the respective conformations of the polyalanine [4]. The random coil confirmation was obtained by modification of the polyproline II obtained from the Protein Data Bank (PDB, ref. code of 1AWI). End capping of the free amino and carboxylic groups were done using acetyl group for N-terminus and methylamine for the free C-terminus of the polypeptides.
Results and Discussion The structure and Raman spectra are investigated for different conformation of hexamer of glutamic acid and lysine using geometry optimizations and frequency calculations. The calculated amide frequencies are indicated in Tab. 1. The DFT prediction of the amide vibrational frequencies for hexamers of lysine are in good agreement with the experimental values. Calculation with 6-31 G basis set always over estimate the wave numbers for amide normal modes compared to experimentally observed values. Whereas in the calculation that have been done using the 6-31 G* the values were close to experimental values by not more than 25 cm-1 for amide I and II for all the three conformation. In the case of calculations done using the 6-31 G basis set for the same vibrational modes (amide I and II) the difference between calculated values and experimental observation is as high as 47 cm-1 in the case of beta sheet conformation. The calculated amide III vibration in both 6-31 G and 6-31 G* basis set is over estimated by about 100 cm-1 when compared to experimental values. On careful examination of the result in Tab. 1 we can concluded the DFT method is capable of reproducing the trend in the position of amide vibrtional frequencies. The experimental amide I vibration for beta sheet conformation has the highest wave number (1661) followed by PPII conformation (1655) and the smallest being for the alpha helix [3]. In our calculation using B3LPY (basis set:6-31G & 6- 31G*) DFT methods we found the same trend for amide I in the three conformations and amide I position is important in determining the type of conformation in the peptides. As shown in Tab. 1 the DFT prediction of the amide vibrational frequencies for hexamers of glutamic acid are also in good agreement with the experimental values. The calculation with 6-31 G basis set always over estimate the wave numbers for amide normal modes in comparison with experimentally observed values. Whereas in the calculation that have been done using the 6-31 G* basis set the frequency of amide I were under estimated for all the three conformations. The calculated amide III vibration frequency with both 6-31 G and 6-31 G* basis set is over estimated as in the case of hexamer of glutamic acid but the wave number difference between theoretical calculation and experimental values are not as big as in the case of lysine.
Table 1: Experimental and calculated vibrational frequencies of amid I, II and III for hexamers of lysine. Conformations Theory level Amide I Amide II Amides III B3LYP/6-31G//B3LYP/6-31G 1656 1556 1350 B3LYP/6-31G*//B3LYP/6-31G 1622 1546 1369 helix helix Alpha Experimental (non-deuterated water) 1644♦ 1548 1275 B3LYP/6-31G//B3LYP/6-31G 1681 1566 1349 B3LYP/6-31G*//B3LYP/6-31G 1650 1548 1342
PPII Experimental (non-deuterated water) 1655♦ 1559 1258 B3LYP/6-31G//B3LYP/6-31G 1708 1581 1351 B3LYP/6-31G*//B3LYP/6-31G 1674 1560 1340
Beta sheet Experimental (non-deuterated water) 1661♦ 1559 1244
♦ Experimental values taken from (Song and Asher 1989). 26 Conference on Current Trends in Computational Chemistry 2008
Table 2 Experimental and calculated vibrational frequencies of amid I, II and III for hexamers of glutamic acid.
Conformations Theory level Amide I Amide II Amides III B3LYP/6-31G//B3LYP/6-31G 1658 1576 1360 B3LYP/6-31G*//B3LYP/6-31G 1620 1570 1347 helix helix Alpha Experimental (non-deuterated water) 1651♦ 1552 1279 B3LYP/6-31G//B3LYP/6-31G 1683 1616 1352 B3LYP/6-31G*//B3LYP/6-31G 1656 1586 1337
PPII Experimental (non-deuterated water) 1664♦ 1564 1257 B3LYP/6-31G//B3LYP/6-31G 1649 1521 1341 B3LYP/6-31G*//B3LYP/6-31G 1644 1534 1305
Beta sheet Experimental (non-deuterated water) 1648♦ 1548 1248
♦ Experimental values taken from (Song and Asher 1989).
Conclusion
Overall as see in the results for PPII, beta sheet and alpha helix confirmations we have observed same similar trends between the experimental and calculated Raman frequencies with B3LYP density functional theory at both 6-31 G and 6-31G* basis sets for the wave numbers of amides normal mode vibrations. The B3LYP/6-31G*level of theory predicts functional with the 6-31 G* basis set predicts the theoretical Raman frequencies that are in good agreement with experiment for amides (I, II, and III) vibrational frequencies compared to the calculation with 6-31G basis set. We can conclude from the theoretical calculation of both hexamer glutamic acid and lysine conformations that the amide I and amide II calculations differ from experiment by relatively small wave numbers than in opposite to the case of amide III where there is a big difference between experimental values and theoretical calculations. The second observation is that the amide vibrational frequencies are over estimated for amide I, II and III in the theoretical calculation with 6-31G basis. In the case of 6-31 G* it over estimate the amide III but underestimate amide I and II. Based on these observations we can see that both DFT methods are capable of predicting the amide vibrational frequencies which is an indicator of the type of conformation that is there in peptides [5]. The results in both Tab. 1 and 2 indicates that the DFT method is capable of reproducing the trend in the position of amide vibrational frequencies. Our DFT calculations indicate that DFT method is useful in the study of transformation conformation of peptide and in detecting conformational change of peptides which is observed in amloyide forming peptides and in amyloide disease.
Reference
1 Schweitzer-Stenner, R. (2006). "Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure - A critical review." Vibrational Spectroscopy 42(1): 98-117. Conference on Current Trends in Computational Chemistry 2008 27
2 Chi, Z. H., X. G. Chen, et al. (1998). "UV resonance Raman-selective amide vibrational enhancement: Quantitative methodology for determining protein secondary structure." Biochemistry 37(9): 2854-2864 3 Song, S. H. And S. A. Asher (1989). "Uv Resonance Raman Studies Of Peptide Conformation In Poly(L-Lysine), Poly(L-Glutamic Acid), And Model Complexes - The Basis For Protein Secondary Structure Determinations." Journal Of The American Chemical Society 111(12): 4295-4305. 4 Wieczorek, R. and J. J. Dannenberg (2004). "Comparison of fully optimized alpha- and 3(10)-helices with extended beta-strands. An ONIOM density functional theory study." Journal of the American Chemical Society 126(43): 14198-14205. 5 Nielsen, O. F. (2005). Raman Spectoscopy. Methods for Structural Analysis of Protein Pharmaceuticals. W. C. D. J. A. Jiskoot. Arlington AAPS press: 167-199.
28 Conference on Current Trends in Computational Chemistry 2008
A Comparison of Substituent Effects on Aromatic Compounds
Manikanthan Bhavaraju and Steven R. Gwaltney
Department of Chemistry, Mississippi State University, Mississippi State, MS 39759
The energies and geometries of a series of substituted aromatic compounds were calculated. The aromatic molecules are aniline, benzaldehyde, nitrobenzene, and phenol. The substituents are -CH3, -F, -OCH3, -NO2, -CH2=CH2. Each substituent was placed at the ortho, meta, and para positions on all of the model aromatic molecules, for a total of 60 compounds. The resultant structures were optimized with AM1, HF, B3LYP, RI-MP2, and CCSD(T). The HF, DFT, RI-MP2, and CCSD(T) calculations used the cc-pVDZ and cc-pVTZ basis sets. All the HF calculations were performed with Spartan '06. For DFT and RI-MP2 Q-Chem 3.1 was used. We used ACES II for the CCSD(T) calculations. For each combination of model aromatic and substituent, the relative energies were calculated, and a population analysis was done. We present the results of these calculations and compare the performance of the methods versus each other and versus experiment where available.
Conference on Current Trends in Computational Chemistry 2008 29
The Performance of the 6-31G## Basis Set for DFT Calculation of 13C Nuclear Magnetic Shielding
V. Bolshakov,1 V.V. Rossikhin,1 E.O. Voronkov,2 S.I. Okovytyy,3 and J.Leszczynski4
1Pridneprovs’ka State Academy of Civil Engineering and Architecture, Dnepropetrovsk, Ukraine; 2State Technical University, 49010, Dnepropetrovsk, Ukraine; 3 Dnepropetrovsk National University, 49050, Dnepropetrovsk, Ukraine; 4 Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
Nuclear magnetic resonance (NMR) spectroscopy is one of the most often applied experimental techniques since it provides useful information about a wide variety of organic and inorganic species. Combining experimental and calculated parameters of NMR spectra is becoming increasingly popular procedure for identification of synthesized compounds. Recently we proposed magnetically corrected 6-31G## basis set constructed by augmentation of the standard 6-31G basis set by functions, obtained from solution of the nonhomogeneous Schrodinger equation for the model problem “one-electron atom in an external uniform magnetic field” using the closed representation of the Green’s function [1]. A performance of the approach where standard 6-31G basis set used for calculations of nuclei of interest magnetic shielding constants while magnetically corrected 6-31G## basis used for the rest of nuclei has been tested on the set of molecules collected in Table.
Table. Absolute magnetic shielding (ppm) of 13C nuclei calculated using 6-31G##//6-31G Basis Set and Parameters of the Linear Regression Equation σexpt = Aσcalc + B
B3LYP PBE1PBE Molecule Expt.2,3 CSGT GIAO CSGT GIAO
CH4 186.7 199.0 189.9 202.3 198.7 CH3F 113.7 125.3 118.4 130.4 116.8 CF4 54.1 56.0 61.5 64.2 64.5 HCN 83.7 93.8 83.3 94.3 82.1 180.6 192.8 184.3 196.7 187.7 CH CN 3 78.7 87.5 79.3 88.9 73.8 CH3NH2 154.1 165.7 158.8 170.6 158.3 C2H2 120.0 127.7 120.3 128.8 117.2 C2H4 63.3 74.45 65.3 77.0 64.5 C2H6 175.2 186.5 179.5 190.9 180.9 C6H6 60.0 70.4 63.4 74.3 57.2 H2CO -4.7 5.7 -3.7 7.4 -4.4 CO2 68.0 70.0 70.0 73.5 58.8 H2CN2 155.5 168.4 159.6 173.2 164.5 R 0.9964 0.9957 0.9977 0.9974 A 1.058 1.026 1.048 1.021 B -3.945 -10.329 -5.894 -13.383
Obtained results confirm good performance of proposed approach and shows superiority of CSGT approach over GIAO scheme. 30 Conference on Current Trends in Computational Chemistry 2008
References 1. Rossikhin, V. V.; Kuz'menko, V. V.; Voronkov, E. O.; Zaslavskaya, L. I. J. Phys. Chem., 1996, 100, 19801. 2. Ruiz-Morales, Y.; Ziegler, T. J. Phys. Chem. A 1998, 102, 3970-3976 3. Zhao, Y.; Truhlar D.G. J. Phys. Chem. A, 112, No. 30, 2008
Conference on Current Trends in Computational Chemistry 2008 31
An Investigation of the 1H NMR Chemical Shifts for the Derivatives of Endic Imide Using Magnetically Corrected Basis Sets
V.Bolshakov,1 S.I. Okovytyy,2 V.V. Rossikhin,1 E.O. Voronkov,3 I.N.Tarabara,2 I.V.Tkachenko,2 and J.Leszczynski4
1Pridneprovs’ka State Academy of Civil Engineering and Architecture, Dnepropetrovsk, Ukraine; 2 Dnepropetrovsk National University, 49050, Dnepropetrovsk, Ukraine; 3State Technical University, 49010, Dnepropetrovsk, Ukraine; 4Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
Nuclear magnetic resonance (NMR) is one of the most commanding methods in structural chemistry. An important part of the information contained in an NMR spectrum is represented by the chemical shift. Relations between chemical shifts and molecular structure have so far been mostly given by empirical rules. However, the augmentation of information from experimental NMR spectra by ab initio quantum mechanical predictions of chemical shifts is becoming vital. The goal of this investigation is an evaluation of 1H NMR chemical shifts for series derivatives of endic imide (1 –4).
HO HO
O O O O
N N N N O Ph O CH CH3 3 Et HO CH3 Ph Ph OH 1 2 3 4 Molecular geometries of all compounds were fully optimized at the MP2/6-311G(d) level. The calculations of magnetic shielding were based on the IGAIM and GIAO formulations at the DFT level using set of B3LYP, BP86, PBE functionals. Previously developed in our group magnetically corrected 6-31G## basis sets has been used for calculations in two ways: (1) applying 6-31G## for whole set of nuclei and (2) applying 6-31G## for “heavy” nuclei and original 6-31G basis set for all nuclei of interest – protons (6-31G##/6-31G). The second way is based on the property of first-order correction functions which in the case of
external magnetic field equals zero at the point of origin (Rx,y,z =0). Comparison of calculated at different levels values of 1H NMR chemical shifts with experimental data demonstrates the efficiency of cost-effective GIAO/PBE/6-31G##/6-31G approach. For accurate prediction of chemical shifts by CSGT calculations 6-31G## basis sets has used for all nuclei. The results of our calculations allowed solving a problem of the signal assignments in the NMR spectra of aforementioned compounds.
32 Conference on Current Trends in Computational Chemistry 2008
Study of Silver Clusters: Agn : for n=13 to 55 Spectroscopic Calculations with ADF Program and Optimizations with Gaussian2003 Program with B3LYP Functional and LANL2DZECP Basis
P.Bonifassi, P.Karamanis, Meng-Sheng Liao, J.D.Watts, M.J.Huang, P.C.Ray and J.Leszczynski
Chemistry Department, Jackson State University, Jackson, MS39217, Mississipi, USA
We study these clusters with two symetries d4h for Ag15,Ag26, Ag36 and Ag51 with a first geometry ad4h nd Ag24,Ag33 and Ag51 with a seconf geometry d4h. For the symetry d5h we were using the structures Ag13,Ag19, Ag25, Ag31,Ag37,Ag43 and Ag55. For the spectroscopic calculations we use 5 methods as shown in the table below .With all the metods and basis used with the program gaussian2003 if we compare with the results obtained with the ZORA method of the ADF program are too low.We have checked that on 2 pyramidal structures Ag10 and Ag20 of the work of Schatz(J.Phys.Chem 2008. So, we need to use ADF program for the spectroscopic calculations in collaboration with Dr Meng-Dheng Liao and also some static second order hyperpolarizability with the collaboration of Dr P.Karamanis.All the structures were optimized with the b3lyp DFT functional and the lanl2dzecp basis.
In the last column our result with ADF proragm on Ag15 and Ag13 optimized by gaussian with b3lyp method and lanl2dzecp basis
method 1 method 2 method 3 method 4 ADF gaussian200 gaussian200 method 5 b3lyp 3 b3lyp b3lyp b3pw91i2003 b3pw91 CIS 3 pbe pbe VWN Becke88 and Perdew86 structur lanl2dzecp ccpvdzpp sbkjc lanl2dzecp ccpvdzpp lanl2dzecp lanl2dzecp skjbc DZ.4p Ag25 0.6765 3.239 Ag15 1.76 1.732 1.769 1.752 3.57062
Ag13 1.82 1.923 1.9097 3.817
Ag10 2.318 2.3344 2.3155 2.3428 2.0948 2.2587 2.2532
Ag20 1.956
Calculations of Shatz with ZORA in ADF program on clusters of Ag10 and Ag20 with different basis and our calculation in the last column on the same clusters with ADF- ZORA and DZ.4p basis :
Conference on Current Trends in Computational Chemistry 2008 33
Schatz calculation : basis Our check test with ADF ZORA struct DZ.4p TZP.4P TZP QZ4P DZ.4p ur Ag10 3.81 3.823 Ag20 3.59 3.45 3.29 3.23 3.604
SPECTROSCOPIC RESULTS for Clusters of symmetry D5h
Correlations of the maximum peak location (λ max) with the length of the clusters
cluster lenght(nm) Absorption Peak cluster λ max(nm) Gap in eV 1/L L Maximum in eV size Ag13 324.58 1.36 1.5323 0.6526 3.81723 Ag19 328.98 1.1968 1.2366 0.8087 3.7662 Ag25 382.50 1.1424 0.9170 1.0905 3.2392 Ag31 398.55 0.7616 0.7243 1.3806 3.1088 Ag37 413.58 0.7888 0.6176 1.6191 2.9958 Ag43 444.09 0.62556 0.5263 1.9002 2.79
Peak location vs. 1/L : L=lenght of the cluster
4.5 4 3.5 3 Peak location vs. 1/L 2.5 y = 1.0466x + 2.3174 2 Linear (Peak location vs. 1/L) E(eV) R2 = 0.9494 1.5 1 0.5 0 0.5000 0.7000 0.9000 1.1000 1.3000 1.5000 1/L
Correlations of the maximum peak location (λ max) 34 Conference on Current Trends in Computational Chemistry 2008
with the total number of electrons of the clusters
Electrons Electrons beta Total electrons Absorption alpha Peak cluster number number number Maximum in eV size N α N β N 1/(N^(1/3)) Ag13 124 123 247 0.159380193 3.81723 Ag19 181 180 361 0.140442192 3.7662 Ag25 238 237 475 0.12816481 3.2392 Ag31 295 294 589 0.119296646 3.1088 Ag37 352 351 703 0.112464354 2.9958 Ag43 409 408 817 0.10696934 2.79
Peak location vs.(N)-1/3 : N = total number of electrons
4.5 4 3.5 3 2.5 2 E=f(1/N^(1/3) E(eV) 1.5 Linear (E=f(1/N^(1/3)) 1 0.5 0 y = 20.604x + 0.6534 0.1 0.11 0.12 0.13 0.14 0.15 0.16 R2 = 0.9194 1/N1/3
Conference on Current Trends in Computational Chemistry 2008 35
Correlations of the Gap with the maximum peak
CORRELATION of GAP with λ max for silver clusters
y = 311.34x0.1807 500 1.6 R2 = 0.9024 450 1.4 lambda nm 400 gap in eV 350 1.2 Power (lambda nm) 300 Power (gap in eV)
max 250 1
Gap Expon. (gap in eV) λ 200 y = 1.6391e-0.1583x 0.8 150 R2 = 0.9254 100 0.6 50 y = 1.5035x-0.4264 2 0 0.4 R = 0.8427 Ag13 Ag19 Ag25 Ag31 Ag37 Ag43
REFERENCES:
Vlasta Bonacic-Koutecky and all, J.Chem.phys, 115,22, (2001) 10450-10459. M.Yang and all,J.Chemical.Phys, 125, (2006) 144308-1 144308-8. René Fournier, Journal of chemical Physics, 115, (2001) 2165-2172. Shuang Zhao, J.Chem.Phys, 124, (2006) 184102-1 184102-10. M.N.Huda and all, Eur.Phys.J.D, 22, (2003) 217-227. Baibiao Huang and all, Int.J.Modern Physics B, Vol19,N° 15,16&17 (2005) 24042408. Martine.N.Blom and all, J.Chem.Phys, 124, (2006) 244308-1 244308-21. Chang Hyon Yu , Bull.Korean Chem.Soc, 21, 10,(2000) 1005-1010. V.Bonacic-Koutecky, Appl.Phys.A,82, (2006) 117-123. G.C.SCHATZ J.PhysChem 2008 36 Conference on Current Trends in Computational Chemistry 2008
Study of Cadmium Selenium Clusters: CdnSen for n=1 to 16 Spectroscopic and dynamic hyperpolarizability calculations
P.Bonifassi, Meng-Shen Liao, J.G.Watts, M.J.Huang, Y.Daoudi, P.C.Ray and J.Leszczynski
Chemistry Department, Jackson State University, Jackson, MS39217 Mississipi, USA
The structures of these clusters were build with the hyperchem program version 8 and the optimization calculations to find the stable geometries were using the gaussian program version 2003 with the functional b3lyp and the basis lanl2dzecp. The spectroscopic calculations with the TD DFT method and the static hyperpolarizabilities for some clusters with no symmetry are obtained with the same functional and the same basis. We were doing the Time Dependent Hartree Fock dynamic hyperpolarisabilities (TDHF) with hartree fock technic and the basis lanl2dzecp basis. The spectroscopic results are shown in the table below :
structure λ max oscillator strenght dipol moment λ max nm debyes Experiment homo(au) lumo(au) gap(au) gap(eV) CdSe 223 1.1038 5.75 227 -0.217 -0.16 0.057 1.550 Cd2Se2 585 0.022 0 -0.213 -0.133 0.08 2.176 Cd3Se3 364 0.0731 0.0551 359 -0.233 -0.114 0.119 3.237 Cd4Se4 524 0.068 0.0005 -0.236 -0.127 0.109 2.965 Cd5Se5 429 0.0721 2.12 -0.221 -0.127 0.094 2.557 Cd6Se6 395 0.07141 0 392 -0.238 -0.122 0.116 3.155 Cd7Se7 481 0.0353 0.994 -0.237 -0.127 0.11 2.992 Cd8Se8 455 0.068 0.0011 -0.239 -0.123 0.116 3.155 Cd9Se9 410 0.0378 0.0057 -0.242 -0.124 0.118 3.210 Cd10Se10 399 0.0993 0.0001 0 0.000 Cd13Se13 417 0.084 4.1432 410 -0.24 -0.128 0.112 3.046 Cd16Se16 457 0.0771 1.811 463 -0.223 -0.13 0.093 2.530
Spectroscopy of clusters CdnSen 700 3.500 600 3.000 500 2.500 400 2.000 l max(nm) 300 1.500 gap(eV) max in nm in max gap in eV in gap
λ 200 1.000 100 0.500 0 0.000 0 3 6 6 1 1 1 e e e e S S S S CdSe 6 0 1 Cd2Se2 Cd3Se3 Cd4Se4 Cd5Se5 Cd Cd7Se7 Cd8Se8 Cd9Se9 d d13 d16 C C C
Panaghiotis Karamanis and all, J.Chem.Phys, 124,071101 (2006). Panaghiotis Karamanis and all, Chemical Physics, 331 (2006) 19-25. Panaghiotis Karamanis and all , J.Chem.Phys, 127, 094706 (2007). Sabyasachi Sen and Swapan Chakrabarti, Physical Review B, 74, 205435 (2006). Sixin Wu, Honzeng Liu, Zuliang Du and all ,Nanotechnology 18 (2007) 485607-1485607-6 Rajan Jose,Hiroshi Fukumura and all, J.Am.Soc, 2006, 128, 629-636. Conference on Current Trends in Computational Chemistry 2008 37
38 Conference on Current Trends in Computational Chemistry 2008
(PCCP)2 Dimer: A New Prototype for Delocalized π-type Interactions
Bei Cao and Gregory S. Tschumper
Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848
Recently, the Tschumper Research Group has implemented two new prototypes, cyanogens and diacetylene, for studying delocalized π···π interactions. 1 The diacetylene and cyanogen dimers have similar properties to the larger delocalized π···π systems like benzene dimer. However cyanogen contains nitrogen atoms which are useful for investigating biological systems. In the present study, we extend these models to include the isovalent PCCP analog. The potential energy surface (PES) of the (PCCP)2 dimer has been studied at the MP2 and CCSD(T) levels of theory employing augmented correlation consistent basis sets (cc-pVXZ). Thus far five stationary points were found for the (PCCP)2 dimer, slipped-parallel (C2h), T- shaped (C2v), cross (D2d), rectangle (D2h), linear (D2h). In this study, we also examine the effect of higher-order correlation by calculating the difference between MP2 and CCSD(T) interactions energies. Initial results show that for the PCCP dimer the higher-order correlation effects are larger than for those of NCCN and HCCCCH dimers. P
PCCP C PCCP PCCP C PCCP PCCP P rectangle (D2h) slipped-parallel (C2h) cross (D2d)
PCCP
P
PCCPPCCP C
linear (D2h) C
P
T-shaped (C2v) 1. B. W. Hopkins, A. M. ElSohly and G. S. Tschumper, Phys. Chem. Chem. Phys., 2007, 9, 1550-1558 Conference on Current Trends in Computational Chemistry 2008 39
Enthalpies of Formation of TNT Derivatives by Homodesmotic Reactions
Erica Chong, Amika Sood and David H. Magers
Computational Chemistry Group, Mississippi College
TNT (2,4,6-trinitrotoluene) is a well known and widely used explosive. In the current study, we focus on the computation of the standard enthalpy of formation of TNT and similar aromatic compounds by homodesmotic reactions. In homodesmotic reactions the number and types of bonds and the bonding environment of each atom are conserved. One such homodesmotic reaction for TNT is shown below.
-O
N+ O -O -O + 3 N+ N+ + 3 O Toluene O
Nitrobenzene N+ O Benzene
- TNT O
The methods utilized involve the computation of the ΔfH of all of the reactants and products in each homodesmotic equation considered for a given compound using SCF theory and Density Functional Theory with the B3LYP functional. Two basis sets, 6-311G(d,p) and 6-311+G(d,p), are employed in each level of theory.
We first computed standard enthalpies of formation for certain smaller aromatics whose enthalpies are known to validate our method. We obtained excellent results for these systems with the exception of 3-nitroaniline for which our computed enthalpy was almost 3 kcal/mol too high. We then used different homodesmotic reactions to compute the standard enthalpies of formation of the TNT derivatives. Results are consistent with the exception of those obtained from reactions that utilize the experimental enthalpy value for 3-nitroaniline. Better convergence is obtained with our theoretical value for this system, leading us to believe that the reference value is incorrect. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.
40 Conference on Current Trends in Computational Chemistry 2008
Molecular Dynamics and Signal Transduction
Tim Clark
Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, Germany and Centre for Molecular Design, University of Portsmouth, Mercantile House, Hampshire Terrace, Portsmouth, UK
Long time-scale (50-100 nanosecond) molecular-dynamics simulations have revealed the mechanism of induction of the tetracycline repressor (TetR), which has become the archetypical signal-transduction system. TetR is responsible for the major mechanism of resistance of Gram- negative bacteria to the tetracycline class of antibiotics. It regulates its own expression and that of the tetracycline antiporter (TetA), a membrane-bound channel that pumps tetracyclines as their complexes with Mg2+ out of the bacterial cell and protons in. The available X-ray structures included a so-called flexible loop region that was not resolved, but proved to play a key role in the induction mechanism. [1] Remarkably, the TetR binding pocket shrinks by 40% of its volume on binding a tetracycline and becomes predominantly hydrophobic. [2]
Mutations of TetR are known that exhibit the reverse phenotype (i.e. they are induced in the absence of tetracyclines, but not in their presence). We were able to determine the origin of this effect for the G95E mutant, which shows the reverse phenotype. [3] Similarly, we have been able to deduce the mechanism of induction by the TetR-inducing peptide (TiP), which induces TetR by a different mechanism to that found for tetracyclines and can induce in the absence of Mg2+.
The simulations indicate that the time scale of the induction event in TetR is far shorter than originally thought, so that we can observe allosteric changes directly and reproducibly. The implications of these results for the pre-equilibrium mechanism of induction will be discussed.
[1] H. Lanig, O. G. Othersen, , F. R. Beierlein, U. Seidel and T. Clark J. Mol. Biol., 2006, 359, 1125-1136. [2] H. Lanig, O. G. Othersen, U. Seidel, F. R. Beierlein, T. Exner and T. Clark J. Med. Chem., 2006, 49, 3444-3447. [3] U. Seidel, O. G. Othersen, F. Haberl, H. Lanig, F. R. Beierlein and T. Clark, J. Phys. Chem. B, 2007, 111, 6006-6014.
Conference on Current Trends in Computational Chemistry 2008 41
Koopmans’ theorem for open shell systems
E. R. Davidson
University of Washington
Koopmans’ theorem is a variational principle for the ionization energy based on a limited form for the neutral and ion wavefunctions. This leads naturally to a definition of canonical Hartree-Fock orbitals. It is easy to generalize Koopmans’ original derivation to obtain variational approximations to the ionization energy and electron affinity from hihg-spin ROHF wavefunctions. This leads to two choices for the definition of canonical doubly-occupied, singly-occupied and virtual orbitals. The same derivation points out the fallacy in using UHF orbital energies even when there is no spin polarization. Although density function theory does not provide wave functions, use of approximate functionals should be expected to cause the same failings in TD-DFT for open-shell molecules as KT does for UHF for open shell systems. 42 Conference on Current Trends in Computational Chemistry 2008
Conformational Study of Oxacyclododecan-2-one by Dynamic NMR Spectroscopy and Computational Methods
Dalephine Davis, Gurvinder Gill, Diwakar M. Pawar, Sumona V. Smith, and Eric A. Noe*
Department of Chemistry, Jackson State University, Jackson, MS 39217-0510.
The low-temperature 13C spectrum of the twelve-membered lactone, oxacyclododecan-2- one, in 3:1 CHClF2/CHCl2F showed three peaks with chemical shifts of 176.32, 176.66, and 177.89 in the carbonyl region at -154.9 ºC, indicating the presence of three conformations with populations of 57.8, 38.1, and 4.1%. The proton NMR spectrum showed decoalescence for the CH2O protons at -89.7 ºC, resulting in multiplets of equal intensities. By -131.8 ºC, each of these multiplets split into three peaks, corresponding to three conformations. The NMR results were analyzed in terms of the conformations predicted by Allinger’s MM4 program, and the conformations are numbered 1a, 1b… in order of increasing MM4 strain energies. Molecular geometries, relative free energies, relative enthalpies, entropies, and lowest frequencies for the first ten conformations were obtained at the HF/6-311G* level and compared with the MM4 results. The calculated GIAO 13C chemical shifts show that the major, intermediate, and minor conformations are 1b, 1a, and 1j. A comparison with conformations of trans-cyclododecene and cyclododecane is also included.
This work was supported by NSF-CREST grant no. HRD-0318519 and NIH-SCORE grant no. S06GM-0084047. Conference on Current Trends in Computational Chemistry 2008 43
A Theoretical Study on Structures, Binding Energies and Vibrational Spectra of the Interactions of Alkali Metal Cations (Li+, Na+ and K+) with Mono- and Bi-cyclic Ring Fused Benzenes
T. C. Dinadayalane and Jerzy Leszczynski*
Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
Understanding of various kinds of noncovalent interactions is required since they are important in molecular recognition, designing molecular materials with desirable physicochemical properties, elucidation of enzymatic reaction mechanisms, design of nanomaterials, ion-selective ionophores and receptors. The interactions of alkali metal cations (Li+, Na+ and K+) with the cup-shaped molecules – tris(bicyclo[2.2.1]hepteno)benzene and tris(7-azabicyclo[2.2.1]hepteno)benzene have been investigated using MP2(FULL)/6- 311+G(d,p)//MP2/6-31G(d) level of theory. The geometries and interaction energies obtained for the metal ion complexation with the cup-shaped systems, trindene and benzotripyrrole are compared with the results for benzene-metal ion complexes to examine the effect of ring addition to the benzene on structural and binding affinities. The structures of ligands considered in this study are depicted in Scheme 1. The synthesis of cup-shaped molecules of benzotri(benzonorbornadienes) that possess high electron density within the cavity has been reported. The cup-shaped molecules exhibit a rigid geometry with π-cavities, which can be useful for alkali and alkaline earth metal cation extractions through cation-π interactions. Thus, they could be used as effective ionophores and molecular receptors, and could have practical applications in environmental chemistry and biology. The cup-shaped molecules possess two faces or cavities (top and bottom). The optimized structures of the complexes and the values of the pyramidalization angles indicate that the fused bi-cyclic rings undergo up or down flexible movement when the metal ion binds with the bottom or top face of the ligand. For all of the three cup-shaped ligands, the binding of Li+ with the top face leads to higher pyramidalization of the carbon of the central hexagon compared to Na+ and K+ complexes. Except for one of the conformers of tris(7-azabicyclo[2.2.1]hepteno)benzene), the metal ions prefer to bind with the top face over bottom face of the cup-shaped molecules. The selectivity of the top face is due to strong interaction of the cation with the π-cloud not only from the central six-membered ring but also from the π-electrons of rim C=C bonds. In contrast, the metal ions under study exhibit preference to bind with the bottom face rather than top face of tris(7-azabicyclo[2.2.1]hepteno)benzene) when the lone pair of electrons of three nitrogen atoms participates in binding with metal ions. This bottom face selectivity could be ascribed to the combined effect of the cation-π and strong cation-lone pair interactions. As evidence obtained from the values of pyramidalization angles, the host molecule becomes deeper bowl when the lone pair of electrons of nitrogen atoms participates in binding with cation. Molecular electrostatic potential surfaces nicely explain the cavity selectivity in the cup-shaped systems and the variation of interaction energies for different ligands. Vibrational frequency analysis is useful in characterizing different metal ion complexes and to distinguish top and bottom face complexes of metal ions with the cup-shaped molecules. This comprehensive study provides knowledge on the effect of fusing mono- and bi-cyclic rings to benzene on the strength of cation- π interactions. 44 Conference on Current Trends in Computational Chemistry 2008
H N
r2 r2
r1 r1 H N r1
N 1 2CH2 2NH H endo H H exo H H H N bottom bottom bottom N H H N N r2 r2 H r2 H H r1 r1 N N H r1 top top top H 3CH 2 syn-3NH anti-3NH
Scheme 1
Acknowledgements: This work was supported by the National Science Foundation (NSF) through CREST grant HRD-0318519 and Office of Naval Research (ONR) grant N00034-03-1-0116. Mississippi Center for Supercomputing Research (MCSR) is acknowledged for generous computational facilities.
References: T. C. Dinadayalane, D. Afanasiev and J. Leszczynski, J. Phys. Chem. A, 2008, 112, 7916- 7924. A. Hassan, T. C. Dinadayalane and J. Leszczynski, Chem. Phys. Lett., 2007, 443, 205-210.
Conference on Current Trends in Computational Chemistry 2008 45
Theoretical Calculation of Electronic Circular Dichroism of a Hexahydroxydiphenoyl-Containing Flavanone Glycoside
Yuanqing Ding, Xing-Cong Li, and Daneel Ferreira
National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, and Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA Email: [email protected]
Theoretical calculation of electronic circular dichroism (ECD) of a hexahydroxydiphenoyl (HHDP)-containing flavanone glycoside, mattucinol-7-O-[4",6"-O-(aS)-hexahydroxydiphenoyl]- β-D-glucopyranoside (2), was performed by time dependent density functional theory (TDDFT) at B3LYP/6-31G** level. It identified the roles of the (2S)-flavanone and (aS)-HHDP moieties in generating the ECD spectrum of 2, and provided theoretical evidence for the empirical ECD rules applicable to monomeric flavanones and HHDP-containing compounds. The experimentally observed high-amplitude positive Cotton effect (CE) around 240 nm in 2 is derived from the (aS)-HHDP chromophore, while the low-amplitude negative CE in the region of 260-300 nm is contributed by both the (aS)-HHDP and (2S)-flavanone moieties. The ‘linker’ glucosyl moiety has little effect on the overall ECD. It appears that the respective chromophores in 2 contribute additively to the overall ECD and the empirical rules are applicable for configurational assignment. However, if an (aR)-HHDP chromophore is present as shown in mattucinol-7-O-[4",6"-O-(aR)-hexahydroxydiphenoyl]-β-D-glucopyranoside (3), the dominant role of the (aR)-HHDP and interaction between the (aR)-HHDP and (2S)-flavanone moieties to its overall ECD may be confusing when applying the empirical rules to experimental ECD interpretation. Thus, theoretical calculation of the ECD that quantifies the contributions and interactions of different chromophores is essential for the assignment of the absolute configuration of such molecules.
40 2 (calculated) -1 3 (calculated) OH OH 2 (experimental)
mol 20
HO HO -1
O O cm O O OMe HO C OMe HO C 0 S O Me R O Me / O HO C O HO C O O S O O S Δε
HO HO O OH O OH -20 HO HO Me Me OH OH 2 OH O 3 OH O -40 200 250 300 350 400 λ / nm
46 Conference on Current Trends in Computational Chemistry 2008
Theoretical Studies on Addition Reactions between Norbornene and 2-Azoniaallene Cations
Yuanqing Ding, Shu-Lin Li, De-Cai Fang, Xing-Cong Li, Daneel Ferreira, and Ruo- Zhuang Liu
National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences and Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA and College of Chemistry, Beijing Normal University, Beijing 100875, China. Email: [email protected]
Density functional (B3LYP) calculations, using the 6-31G(d) basis set, have been employed to study the title reactions. The reaction between norbornene and 2-azoniaallene cations may proceed via both concerted and stepwise mechanisms. For the model reaction of norbornene with + 2-azoniaallene cation ( +H2C=N =CH2), three pathways could be located with two different approaching modes, one of which is the concerted process. However, the substituent effects are quite remarkable. When 2-azoniaallene is substituted by four chloro groups, the concerted mechanism is replaced by a stepwise one. If 2-azoniaallene is substituted by two chloro and two phenyl groups, the reaction will take place with a higher energy barrier due to increased steric repulsion leading to the formation of two different types of products.
Conference on Current Trends in Computational Chemistry 2008 47
Classical Molecular Dynamics Simulations Toward the Understanding of Nitroamine Binding within the NR1 S1S2 Domain
J. Ford-Green1,2, L. Gorb1,3, M. Qasim2, E. Perkins2, J. Leszczynski1,2
1Computationarl Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217, USA; 2US Army ERDC, Vicksburg, MS 39180, USA; 3US Army ERDC (SpecPro), Vicksburg, MS 39180, USA
Nitroamine compounds arising from explosive materials have proven to be harmful reagents, of which their biological activities trigger a cascade deleterious health within the nervous system of various model species. In conjuction with their highly conserved biologic responses these compounds continue to persist within various mediums of contaminated ecosystems. Thus, the study of the chemical end-points within mammalian neural networks may shed light upon nitroamine- binding pathways and preferred routes therein. This understanding may also be applied to biomonitoring rationals for the detection of exposives-contamination within within exposed organisms. It has been shown that after 48 hours of exposure 24mg/kg of the explosive-contaminant 1,3,5-Trinitro-1,3,5-triazacyclohexane (RDX) preferentially upregulates the transcripiton of the GRIN1 and GRIN2 genes. This highly conserved effect produces large amounts of the major, possibly minor, N-methyl-D-Aspartate receptor (NMDAR) subtypes NR1 and NR2 to position themselves on the post-synaptic neurilemma. Since these subtypes arrange in themselvese in an obligatory dimer-of-dimers stoichometry, it is of major interest for us to first study the direct binding routes of the natural inhibitors glycine (NR1) and L-glutamate (NR2) within the S1S2 main binding region. These sets of understandings will provide insight into direct, competitive, and allosteric binding within the major binding domains and the tetrameric NMDAR. Due to lack of protein crystal data regarding non-S1S2 binding domains on the NR1, we have carried out sequence homology studies with the program SwissModel’s “First Approach Mode” with a BLAST E-value limit of 1.0 X 10-5. After a 3-D model was constructed we applied the ff99 force field within the Amber8 package and compared various models of simulation to detect domain movement within the S1S2 model i.e. ~76 ps simulation in the Generalized Born (GB) solvent model @350K, 50 ps gas phase Simulated Annealing (SA) simulation @370K, and 50 ps SA simulation in the GB model @370K. Root Mean Square Deviations (RMSDs) of 30 amino acid segment positions were calculated and visualized with VMD molecular viewing software. The results show in SwissModel that the top five homologous protein sequences to the NR1 S1S2 are the holo-forms of the NR1 S1S2 binding domain complexed with various inhibtors from respective crystal studies. Our model was built from top candidate pdbid: 1y20 and showed 2.38e -173 e-value, and a 98% Sequence identity with our target sequence. Simulation efforts showed that the first 150 amino acids in the NR1 S1S2 model confer the main mode of the S1S2 domain opening (apo-form), while the last seventy amino acid segements are quite stationary after changing simulation conditions (moderately to severe). The 50 ps SA simulation in GB solvent proved to be the most severe treatment for domain opening, showing degradation of secondary and tertiary character within the NR1 S1S2 model. Of consequence, the 50 ps SA gas phase @ 370K and ~76 ps GB solvent @350K model show to be the most structurally stable upon domain opening. These two approaches will be applied to allosteric NR1 binding domains. 48 Conference on Current Trends in Computational Chemistry 2008
Conformational studies of Organophosphorus pesticides towards the discernment of their Esterase inhibition
Jason Ford-Green1, D. Majumdar1, Jerzy Leszczynski1
1Jackson State University, Departement of Chemistry, Jackson, MS 39217
In the modern age the exposure of humans to harmful organophosphorus (OP) agents has been shown to be exponentialy increasing. Due to the steady rise in deleterious health incidences more must be understood about the physico-chemical properties mediating such events in comprimised mammalian systems. Towards the elucidation of such events in neural networks, we have carried out ab initio conformational analysis on a certain class of OP agents which are manifest as pesticides i.e. parathion (PA), paraoxon (PO), and chloropyrifos (CP). All three of these OP pesticides act through the same mode of biological activity. Wherein an influx of the pesticide into the synaptic cleft or motor endplate arrests the binding event of acetylcholine to the enzyme Acetylcholinesterase (AchE). Similar competetive inhibitions have been shown in the X-ray crysallography studies of OP pesticides complexed with the AchE- similar enzymes Phosphotriesterase and Plant Carboxylesterase main active sites. To this end, we have compared the low-energy conformers of PA, PO, and CP to the existing analogous inhibitors embedded within their respective holoenzymes. We have carried out a rigorous partial-geometry leading to full-geometry optimization approach for achievement of the low-energy conformers for PA , PO, and CP which showed six, six, and four conformers respectively. For the discernment of electrostatic charge distribution we have mapped molecular electrostatic potentials (MEPs) on the isodensity surfaces of all low- energy conformers. The MEP comparisons between our low-energy conformers and that of the analogous inhibitors show not only geometrical homology between structures, but electronic structural homology as well. Thermochemical analyisis was conducted at the DFT and MP2 levels of theory within a 6- 31G(d,p) and more diffuse 6-31++G(d,p) basis set (same parameters for the geometrical analysis). These calculations reveal that all low-energy conformers are connected through certain bond-rotational transition states calculated by the second quadratic synchronous transit (QST2) method. Such transition states and low-energy conformers were verified through harmonic vibrational frequency analysis. Upon thermal correction populations of these rotomers were even more achievable than at 0 K, making such states thermally allowed. Lastly, the effects of water solvation on the low-energy conformational space were calculated using the CPCM polarized continuum model. Dipole moment magnitudes, relative solvation free energies, and relative free energies show that PA, PO, and CP each have preferred low-energy conformations that are consistent with conformations of analogous inhibitors in applicable Phosphotriesterase and Plant Carboxyesterase crystal structures. Acknowledgements: This work was facilitated by the support of the NSF CREST (grant no. HRD-0318519) and NSF EPSCOR (grant no. 440900 362427-02) grants. We would like to thank the Mississippi Center for Supercomputing Research for a generous allotment of computer time.
Conference on Current Trends in Computational Chemistry 2008 49
Singlet-Triplet Gaps and Rearrangements of 1,2-Dihydro-3H- pyrazol-3-ylidenes and 1,2,4,5-Tetrahydro-3H-pyrazol-3- ylidenes
= Fillmore Freeman* and Damilola A. Adepegba
*Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025 and = Department of Natural Sciences, University of Maryland Eastern Shores, Princess Anne, Maryland 21853
Aromaticity, conformational analysis, electronic and molecular structures, atomic charges, singlet-triplet gaps (∆EST), and the mechanisms of 1,2-rearrangements of 1,2-dihydro-3H- pyrazol-3-ylidene (7), 1,2,4,5-tetrahydro-3H-pyrazol-3-ylidene (8), and their respective 2- methyl- (9, 10), 2-(trifluoromethyl)- (11, 12), and 2-silyl- (13, 14) derivatives have been studied using complete basis set methods (CBS-QB3, CBS-Q, CBS-4M) and the hybrid density functional B3LYP, coupled-cluster theory [CCSD(T)], and the quadratic configuration interaction method [QCISD(T)] with the 6-311G(d,p), 6-31+G(d,p), 6-311+G(d,p), and cc-pVDZ basis sets. The singlet form is the ground state for the carbenes, the envelope or planar conformation is preferred by the unsaturated carbenes, and the envelope conformation is generally preferred over the half chair conformation by the saturated carbenes. CBS-QB3 and CBS-Q predict similar values for ∆EST, CBS-4M, CCSD(T) and QCISD(T) predict smaller ∆EST values than CBS-QB3 and CBS-Q, and B3LYP predicts the smallest values. The 1,2- rearrangements of the unsaturated carbenes proceed through out-of-plane three center transition states while the saturated carbenes rearrange through chair and boat transition states.
H H N N N NN NN SN SN NN NN N H H H H H H H H H H H 12 3 4 5 6 7
H H H H H H H N N N N N N N N N N N N N N H CH3 CH3 CF3 CF3 SiH3 SiH3 8 9 10 11 12 13 14
50 Conference on Current Trends in Computational Chemistry 2008
H
N H H N TS1 H N H N N N H N H H N H 7 H
H
TS1 TS1
H
H H H N N TS2 H N N N N N H H H H N H H 8 H
H H
H
TS2 TS2 Conference on Current Trends in Computational Chemistry 2008 51
Mechanisms of Insertion Reactions, 1,2-Rearrangements, and 1,2-Cycloadditions of Aminocarbenes: Three Center Transition States
Fillmore Freeman* and Vickie Tamdoan Bui
Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
Singlet-triplet gaps (∆EST), structural parameters, and the mechanisms of intramolecular rearrangements to imines, intermolecular insertion reactions, and cycloadditions of aminocarbenes to ethene have been studied using the complete basis set methods (CBS-QB3, CBS-Q, CBS-4M) and B3LYP, B3PW91, MP2, CCD, CCSD(T), and QCISD(T) with the 6- 31+G(d,p), 6-311+G(d,p), 6-311+G(3d,2p), cc-pVDZ, and cc-pVTZ basis sets. HCNH2 (1), HCN(CH3)2 (3), and HCN(CF3)2 (4) have singlet ground states and their predicted ∆EST values are 35.3, 41.0, and 26.4 kcal/mol, respectively. Singlet aminocarbene (HCNH2, S-1) is 36.4 kcal/mol higher in energy than its isomer methanimine (formaldimine, H2C=NH, 2) and the predicted barrier for the isomerization of (S-1) to (2) is 50.1 kcal/mol. The mechanism for the 1,2-rearrangements of the singlet aminocarbenes to the corresponding imines involve a three center transition state with decreasing positive atomic charge on the migrating group. The mechanism for the intermolecular insertions of aminocarbene (S-1) into the H—H bond of dihydrogen, the C—H bond of methane, the Si—H bond of silane, the N—H bond of ammonia, and the P—H bond of phosphine also proceed via three center transition states
H H H H H H C C H NCH NCH H C N C N H C N H 3 C C H H C H C H H H H H H C C H CH H H H H C H 3 H H H
S-3 T-3 (E)-5 (Z)-5 6
F F F F F F C C F NCF NCF C N F C F3C N H N F C C H C C H F H F F F F F C C H C F F F F CF3 F F F S-4 T-4 (E)-7 (Z)-7 8 52 Conference on Current Trends in Computational Chemistry 2008
Improvement of Molecular Mechanics Force Fields for Nucleic Acids. Ab Initio Based Amino Group Description
A. Furmanchuk1, V. I. Poltev2, E. Gonzalez2, A. Deriabina2, A. Martinez2, L. Gorb1, and J. Leszczynski1
1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS, USA and 2Physics and Mathematics Department, Puebla Autonomous University, Puebla, Mexico
The impressive progress in studying the fine structure of nucleic acid fragments have been achieved during the last two decades with use of X- ray diffraction1–4 and nuclear magnetic resonance (NMR) spectroscopy5–6. Unfortunately, the accuracy of these methods does not provide atomic level structures of nucleic acids olygomers. Therefore, an application of theoretical methods is inevitable both together with experimental data and also to predict rules which govern the three-dimensional structure of nucleic acids and their complexes. The present work is devoted to the description of conformational flexibility of amino groups in Nucleic Acid Bases. Since all known molecular mechanics force fields are not able to describe this phenomenon, we propose an ab initio based method to take it into account. Based on the extended MP2/6-31G(d,p) level calculations two-dimensional maps of energy and Figure. Approximated (continuous lines) amino group geometry parameters (as functions of and ab initio MP2/6-31G(d,p) (dots) two amino hydrogen torsions) have been Energy Maps for Guanine. Torsions 1 and constructed. Coefficients in analytical 2 are Used to Describe Positions of Two approximations to these maps have been refined Amino Hydrogens of the Base. at higher levels of theory. Resulting polynomial expressions7 can be used to improve existing level of molecular mechanics force field calculations for nucleic acids and their complexes. References: 1. Hays, F.A., Teegarden, A., Jones, Z.J.R., Harms, M., Raup, D., Watson, J., Cavaliere, E., Ho, P.S.: Proc. Natl. Acad. Sci. 102, 7157 (2005) 2. Chou, S.-H., Chin, K.-H., Wang, A.H.-J.: Nucleic Acids Res. 31, 2461 (2003) 3. Pallan, P.S., Lubini, P., Bolli, M., Egli, M.: Nucleic Acids Res. 35, 6611 (2007) 4. Parvathy, V.R., Bhaumik, S.R., Chary, K.V.R., Govil, G., Liu, K., Howard, F.B., Miles, H.T.: Nucleic Acids Res. 30, 1500 (2002) 5. Pfaff, D.A., Clarke, K.M., Parr, T.A., Cole, J.M., Geierstanger, B.H., Tahmassebi, D.C., Dwyer, T.J.: J. Am. Chem. Soc. 130, 4869 (2008) 6. Matsugami, A., Ohyama, T., Inada, M., Inoue, N., Minakawa, N., Matsuda, A., Katahira, M.: Nucleic Acids Res. 36, 1805 (2008) 7. Poltev, V.I., Gonzalez, E., Deriabina, A., Martinez, A., Furmanchuk, A., Gorb, L., Leszczynski, J. J. Biol. Phys., (2008). Article in Press. Conference on Current Trends in Computational Chemistry 2008 53
Density Functional Theory and Multiscale Simulations Combined With Spectroscopic Study of Barium/Strontium Ferrate/Cobaltate (BSCF) as a Promising Material For Solid Oxide Fuel Cell (SOFC)
Shruba Ganopadhyay,1 Talgat Inerbaev,1 Artëm E. Masunov,1, 2,3 Deanna Altilio, 4Nina Orlovskaya,4 Jaruwan Mesit,5 Ratan Guha,5 Ahmed Sleiti,4 Jayanta Kapat4
1Nanoscience Technology Center, 2Department of Chemistry, 3Department of Physics, 4Department of Mechanical, Materials, and Aerospace Engineering; 5School of Electrical Engineering and Computer Science, University of Central Florida, 12424 Research Parkway, Suite 400, Orlando, FL 32826; Email: [email protected]
Mixed oxides of the general formula ABO3 which crystallize in perovskite structures often have large mobility of the oxygen vacancies and exhibit strong ionic conductivity and used for several practical applications, including Solid Oxide Fuel Cells (SOFC). Barium/Strontium Ferrate/Cobaltate (BSCF) was recently identified as a promising candidate for cathode material in intermediate temperature SOFCs. [1] Oxygen defects and electronic structure of the cathode materials plays important role in electrical conductivity and ease of oxygen diffusion which is a key part of SOFC efficiency. In this study we employ plane wave density functional theory (DFT) combined with ultrasoft pseudopotentials in order to investigate the electronic structure of perfect BSCF, its oxygen vacant structure and the oxygen migration energetics in BSCF. Our calculations are based on the DFT with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional in the framework of Vanderbilt ultrasoft pseudopotentials [2] and plane wave basis set as it is implemented in Quantum-ESPRESSO program package [3]. The Brillouin-zone integrations were performed using Monkhorst-Pack grids using a 2×2×2 mesh for supercell calculations and 4×4×4 mesh for single unit. Spin polarized calculation with Marzari- Vanderbilt smearing is used throughout. The geometry optimization was performed using Broyden-Fletcher-Goldfarb-Shanno algorithim. The wave function and electron density representation are limited by kinetic energies of 40 and 360 Rydberg respectively. We treated the Ba(5s,5p,6s), Sr(4s,4p,5s), Co(4s,3d), Fe(3d,4s) and O(2s,2p) electrons as valence states, while the remaining electrons were kept frozen as core states. For Co+4 we used low spin (LS), intermediate spin (IS) and high spin (HS) states (spin of S=1/2, S=3/2, and S=5/2); for Fe4+ cations LS and HS states (S=1 and S=2) were considered. The accuracy of pseudopotentials was validated by computing the equilibrium lattice parameters (a) are compared with experimental value and bulk moduli (B) is also compared with available experimental value. First, we investigated different spin states of transition metal atoms Löwdin population analysis in BSCF supercell is presented in the Tab 1. It shows that the IS in Co and HS states in Fe are most stable with Boltzmann factor 98%. After structural relaxation of BSCF supercell, we observed, tetragonal Jahn-Teller distorted Co (Fig. 1) since elongation and contraction both are observed in simultaneous fashion overall symmetry of the structure remains cubic, from the spin state configuration it can be inferred that the IS state only, can show the Jahn-Teller distortion. This theoretical evidence reinforced by Raman spectroscopic data (Fig. 2) where disappearance of peak with increase of temperature is observed.
54 Conference on Current Trends in Computational Chemistry 2008
Table 1. Spin densitied on transition metal cations according to Löwdin population analysis for the different spin states of BSCF 2x2x2 superlattice, their relative energies and Boltzmann factors
Converted B Lowdin factor Multiplicity polarization ΔE % kcal Fe+4 Co+4 mol-1 Total (d4) (d5) Fe Co 23 2 3 3.61 2.59 9.66 2 27 4 3 3.62 3.12 0.00 98 35 2 5 4.31 4.16 35.23 0 39 4 5 4.6 4.58 101.37 0
Next we study the possibility of the cation ordering in BSCF. For modeling the mixed perovskite Ba0.5Sr0.5Fe0.2Co0.8O3 we used a 2×2×2 supercell [1]. One supercell has 4 Ba atoms, 4 Sr atoms, 2 Fe atoms and 6 Co atoms. For this structure all 9 possible symmetrically nonequivalent arrangements of Fe4+ and Co4+ cations at the transition metal atoms positions as well as Ba/Sr ion positions were taken into consideration. All these structures and their relative stability are listed in Tab. 2. From the Boltzmann factor it is evident there is no preferred cation arrangement.
Table 2. Different cation distributions, their relative energies (ΔE) and Boltzmann factors (B) ΔE B kcal factor M Fe Ba mol-1 % 27 ¼, ¼, ¼ ¼, ¼, ¾ ½, 0, 0 0, ½, 0 ½, 0, ½ ½, ½, ½ 0.00 18 27 ¼, ¼, ¼ ¾, ¼, ¾ ½, 0, 0 0, ½, 0 0,0, ½ ½, ½, ½ 0.10 18 27 ¼, ¼, ¼ ¾, ¾, ¾ ½, 0, 0 0, ½, 0 0,0, ½ ½, ½, ½ 0.76 13 27 ¼, ¼, ¼ ¼, ¼, ¾ ½, 0, 0 0, ½, 0 0,0, ½ ½, 0, ½ 1.42 10 27 ¼, ¼, ¼ ¾, ¼, ¾ ½, 0, 0 0, ½, 0 0,0, ½ ½, 0, ½ 1.41 10
Then we calculate the relative stability of oxygen deficient supercell, with respect to different vacancy positions. From experiment [1], the molar fraction of oxygen vacancies at 1150°C is δ=0.38. Therefore we examined different structures with up to 4 oxygen vacancies per supercell. We removed one, two, three and four oxygen atoms from 2x2x2 supercell, which corresponds to stoichiometry of Ba0.5Sr0.5Co0.8Fe0.2O3- δ (where δ = 0.125, 0.25, 0.375, 0.5). On Conference on Current Trends in Computational Chemistry 2008 55
the second step we remove one oxygen atom from the most stable stoichiometric configuration and calculate relative energy of different multiplicities. The multiplicity with the lowest energy is used to optimize geometry of that particular configuration and Boltzmann factor is calculated to check the probability of the particular orientation. The same procedure is repeated for the oxygen vacant configurations. In order to determine the multiplicity of the stoichiometric supercell, one of two spin states for Fe4+ cation were combined with one of three spin states for Co+4. As it is known from experiment the SrFe1-xCoxO3 compound is antiferromagnetic for x<0.10-0.15 and becomes ferromagnetic for x≥0.2. Our calculations confirm these results [4]. We observe two vacancies in cis-position to the same Fe/Co ion (L-shape vacancy ordering) to be the most stable. This is in agreement with the experimental fact that the BSCF structure remains cubic in the observed oxygen deficiency range, while with similar compound with no Ba forms brownmillerite structure with linear vacancy ordering [5]. The relaxed geometry of BSCF with 2, 3, and 4 oxygen vacancies also changes the coordination of one, two, or four transition metal cations, adjacent to the vacancy, from ideal octahedron with two vertices missing to distorted tetrahedron (Fig 3). For activation energy calculation we use different distribution in supercell with one vacancy. We perform two structural relaxation calculations, one is for oxygen vacant cubic supercell, another one with oxygen ion in the middle of the XYX plane and angle OYZ is 450. Activation energies for different cation orientations are listed in Tab. 3. Our results are in good agreement with the experimental value for activation energy of oxygen ion migration is c.a. 10.5 kcal/mol [1], except for one ion configuration, that has low Boltzmann factor and is infrequent. The present study demonstrates how plane wave DFT calculation can be used successfully to predict the electronic structure and oxygen transport property of doped perovskite BSCF. Our calculations predict the intermediate spin state and Jahn-Teller distortion for cobalt ions, both in agreement with experiment. The preferential vacancy arrangement is predicted to be L-shaped (for trimer) and square (for tetramer vacancies). This is in contrast with linear vacancy arrangement and phase transition to brownmillerite type of structure for similar material containing no Ba ions. The activation energy of oxygen migration was found in the range of experimental data. In the future we will intend to apply multiscale technique to determine the macroscopic vacancy diffusion coefficient. According to the protocol the small (atomic) scale Density Functional theory (DFT) is used to calculate activation energy barriers for oxygen migration in different local cation distribution. Activation barriers are used in Arrhenius equation to predict the rates for elementary steps in diffusion processes. These rates are then input into Kinetic Monte Carlo (KMC) at large (meso) scale simulations to obtain long time oxygen diffusivities and apparent activation energies. Since KMC method does not need energy evaluations, it is computationally inexpensive and allows treating millions of atoms explicitly. KMC approach can readily describe the macroscopic properties as a function of material morphology.
56 Conference on Current Trends in Computational Chemistry 2008
Table 3. Activation energies of different cation arrangement in BSCF supercell ΔΕ kcal Fe Ba Vacancy mol-1 ¼, ¼, ¼ ¾, ¾, ¾ ½, 0, 0 0, ½, 0 0, 0, ½ ½, ½, ½ ½ ,¼, ¼ ½, ¼, ¼ 9.06 ¼, ¼, ¼ ¾, ¾, ¾ ½, 0, 0 0, ½, 0 0, 0, ½ ½, ½, ½ ¼, ¾, ½ ¼, ½, ¾ 7.83 ¼, ¼, ¼ ¾, ¾, ¾ ½, 0, 0 ½, ½, 0 ½, 0, ½ ½, ½, ½ ¼, ¾, ½ ¼, ½, ¾ 12.49 ¼, ¾, ¼ ¼, ¼ , ¾ 0, ½, 0 ½, ½, 0 0, 0, ½ ½, 0, ½ ¼, ¾, ½ ¼, ½, ¾ 4.83
References [1]. Z. P. Shao, and S. M. Haile "A high-performance cathode for the next generation of solid-oxide fuel cells." Nature, 431 170 (2004) [2]. D. Vanderbilt, “Soft Self-Consistent Pseudopotentials in a Generalized Eigenvalue Formalism." Physical Review B, 41, 7892 (1990). [3]. S. Baroni, et al. Quantum-ESPRESSO. Available at http://www.pwscf.org (2006). [4]. I. R. Shein, K. I. Shein, et al. "Band structure and the magnetic and elastic properties of SrFeO3 and LaFeO3 perovskites." Physics of the Solid State, 47: 2082 (2005). [5]. S. J. McIntosh, F. Vente, et al. "Structure and oxygen stoichiometry of SrCo0.8Fe0.2O3-δ and Ba0.5Sr0.5Co0.8Fe0.2O3-δ." Solid State Ionics, 177 1737 (2006).
Conference on Current Trends in Computational Chemistry 2008 57
Application of New Pairwise Spin-Contamination Correction Approach to Study the Transition Metal Hydrides
Satyender Goel†‡ and Artëm E. Masunov†‡*
† Nanoscience Technology Center, ‡ Department of Chemistry, * Department of Physics, and University of Central Florida, Orlando, FL – 32826, Email: [email protected]
Chemical bond between transition metal atom and hydrogen is important in surface chemistry and nanoparticle cluster catalysis, as the energetics of this bond breaking plays a critical role in hydrogen transfer process. The studies of Transition Metal (TM) systems present a challenge for theoretical description due to the presence of several electronic states close in energy which results in strong electron correlation. For this reason molecules containing TMs serve as an important testing ground for various methods in theoretical chemistry and molecular physics. Density functional theory (DFT) is the method of choice to study large systems, due to relatively low computational cost. A clear advantage of unrestricted (also known as spin-polarized or broken spin-symmetry) solution is qualitatively correct description of bond dissociation process. Since exchange- correlation functionals used are approximate, unrestricted Kohn-Sham[1] (UKS) treatment improves them by taking part of the static electron correlation into account. The situation can be seen as localization of α and β electrons on the left and right atoms of the dissociating bonds, respectively (left-right electron correlation). Broken symmetry (BS) UKS thus describes the transition from closed shell system to biradical smoothly, which is not possible with restricted open shell KS (ROKS). A disadvantage of UKS approach is that spin-polarized Slater determinant is no longer an eigenfunction of the spin operator. Hence, the average value of <Ŝ2> is not, generally equal to the correct value of Sz(Sz+1) (Here Sz is ½ of the difference in total numbers of α and β electrons). This situation is known as spin contamination and <Ŝ2> is often used as its measure. As a result of spin contamination, molecular geometry may be distorted toward the high-spin state one, spin density often is incorrect, and electron energy differs from the pure spin state ones. Here we propose a variable spin-correction approach, based on canonical Natural Orbitals (NO). First, let us consider a two electron system such as stretched H2 molecule. We assume that restricted Kohn-Sham formalism yields higher energy for this system than unrestricted one, as the case of H2 molecule far from equilibrium. Unrestricted KS description produces the natural orbitals a, b as eigenvectors of the total density matrix with the orbital occupation numbers na, nb as corresponding eigenvalues. We further assume that na chemistry codes do not possess this property, which is why one has to produce the corresponding spin-polarized orbitals from NOs. BS solution can still be written as the Slater determinant in the basis of these corresponding orbitals as: 1 p1α1 p2α 2 1 λ BS = 1 2 pα qβ = = 2 S + 2 T (2) 2 q1β1q2 β 2 ()1+ λ ()1+ λ After some algebra, BS UKS energy can be written in terms of renormalized singlet and triplet state S0 ,T0 energies as: 2 ()1+ λ2 2λ2 E = E − E (3) S0 1+ λ4 BS 1+ λ4 T This energy includes the non-dynamic electron correlation effects arising from the mixing of b1α1b2 β 2 and a1α1a2 β 2 states. In order to relate the polarization parameter λ to the occupation numbers na, nb, we can expand the electron density matrix in the basis of a and b orbitals and obtain. λ = 2 nb −1 (4) 4 4n − 2n 2 E = E − b b E (5) S0 2 BS 2 T 2nb + 4nb + 4 2nb + 4nb + 4 Thus, for a system with one correlated electron pair one can obtain the pure singlet energy expressed in terms of energy of BS UKS solution, the occupation number of the bonding NO, and the energy of the triplet built on these bonding and antibonding NOs (as opposed to self- consistant KS orbitals). This expression is applicable to two-electron systems as well as to the systems which have in addition the unpolarized electron core or ferromagnetically coupled unpaired electrons. For the systems with two correlated electron pairs, BS energy can be written as: ˆ EBS= BS1 ⋅ BS2 H BS1 ⋅ BS 2 (6) After the substitutions and calculations UKS energy can be written in terms of renormalized singlet, triplet and mixture of triplet and BS state, S01S02, T01T02, T02BS1, T01BS2 as: 4 4 2 2 2 (1 + λ1 )(1 + λ2 ) ˆ 2λ2 (1 + λ1 ) ˆ EBS = S 01S 02 H S 01S 02 + T02 BS1 H T02 BS1 + 2 2 2 2 2 2 ()()1 + λ1 1 + λ2 ()()1 + λ1 1 + λ2 2 2 2 2 2 2λ1 ()1+ λ2 ˆ 4λ1 λ2 ˆ T01BS 2 H T01BS 2 − T01T02 H T01T02 2 2 2 2 2 2 ()()1+ λ1 1+ λ2 ()()1+ λ1 1+ λ2 (7) Then the energy ESo of the pure singlet S01S02 can be found from the above eq. 7 as: E = 1 S0 4 4 ()()1 + λ1 1 + λ2 2 2 2 2 2 2 2 2 2 2 2 2 (EBS ⋅ ()()1+ λ1 1+ λ2 − 2λ2 ()1+ λ1 ET BS − 2λ1 (1+ λ2 ) ET BS + 4λ1 λ2 ET T ) (8) 02 1 01 2 01 02 The above expression is derived[3] to extract the energy of the pure singlet state from the energy of the broken symmetry DFT description of the low-spin state and energies of the high- spin states: pentuplet and two spin-contaminated triplets. Thus, unlike spin-contamination correction schemes by Noodleman[2] and Yamaguchi,[4] spin-correction is introduced for each Conference on Current Trends in Computational Chemistry 2008 59 correlated electron pair individually and there fore is expected to give more accurate results. Spin-correction described above is implemented as a combination of unix shell script and FORTRAN code. It reads Natural Orbitals (NO) printout from Gaussian 03 job (keyword used was Punch=NO) and converts them into spin-polarized molecular orbitals according to eq (1). Script uses a threshold parameter to identify the correlated pair. The spin polarization of the electron core was neglected by adjusting the threshold value to consider natural occupations integer. The provision is made for the spin-up orbital p to be the one largely localized on metal atom and, so that spin-down orbital q is predominantly localized on H atom. The new alpha orbital set is made of doubly occupied NOs, orbital p, singly occupied NOs, and weekly occupied NOs. The new beta orbital set was identical, except that p was replaced with q. These orbitals were further used to evaluate the energy with single SCF step and verify that it is close to BS energy obtained at self-consistence. The energy of the triplet is calculated with another single SCF step using the original NOs only. It was used by the script to extract the energy of the pure singlet according to eq (3). The keywords used for single SCF step with the modified orbital set were SCF (MaxCycle=1) and Guess=Cards. We investigated bond energetics, electronic structures, dipole moments, and ionization potentials in gas-phase neutral hydrides, formed by 3d-transition metals from Sc to Cu. We found that BMK functional gives the best agreement with experiment, followed by two WFT methods. The other DFT methods range as follows. Among broken symmetry methods, the accuracy quickly deteriorates as the fraction of HF exchange decreases from BMK (42%) to B3LYP (20%) to TPSSh (10%) to TPSS (0%). Spin adapted (SA) formalism on the other hand, 25 20 BS-B3LYP 15 BS-TPSS BS-TPSS:DKH 10 SA-BLYP 5 BS-TPSSh MCPF BS-BMK 0 SA-B3LYP BS-BMK:DKH -5 MCSCF+SOCI Deviation in Binding Energy (kcal/mol) (kcal/mol) Energy Binding in Deviation -10 ScH TiH VH CrH MnH FeH CoH NiH CuH MH System Figure 1: Deviations in Binding Energies from experimental data for neutral TMH with various DFT and WFT methods show only marginal improvement from pure BLYP to hybrid DFT (B3LYP). SA-B3LYP gives 80% lower rms value than BS-B3LYP but it is still twice less accurate than BS-BMK. The individual values of deviations are plotted on Fig 1. One can see that BMK values are within 4 kcal/mol of experimental ones for almost all the systems (8 kcal/mol for CrH). Scalar relativistic correction does not improve the energies and deviations are similar to the one observed in non-relativistic BMK. TPSS strongly overbinds in all cases and the deviations are from 10 to 20 kcal/mol with ScH showing largest of all and 10% of HF exchange in TPSS does 60 Conference on Current Trends in Computational Chemistry 2008 not improve the situation. Small fraction of HF exchange (TPSSh) helps only in case of NiH, while larger fraction helps in most cases. Spin-adapted formalisms (BLYP and B3LYP) are close to each other for all systems, except for MnH, but have no systematic deviations otherwise. All DFT methods agree for full and half-full d-shells (CuH and CrH), although this consensus is ~10 kcal/mol away from experimental value in case of CrH. WFT and BMK are everywhere close to the baseline with MCPF slightly overbinding and MCSCF slightly underbinding. Unlike other studies employing spin-polarized (or unrestricted) KS formalism and ignoring spin contamination, the present study takes into consideration the new spin-correction approach detailed above. Spin contamination plays a major role in describing energy deviation of the systems with possibility of exhibiting more than one multiplicity, largely in complex systems involving TM compounds. MnH is found to have strong, more than 10%, spin contamination close to equilibrium bond length for M=5. The spin-contamination correction stabilizes this spin state by 3.5 kcal/mol below M=7, in disagreement with WFT. The corrected BMK dissociation energy is however, closer to the experimental value reported in Borane et. al.[5] Our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence. References [1] W. Kohn and L. J. Sham, "Self-Consistent Equations Including Exchange and Correlation Effects," Physical Review,140, 1133-&, (1965). [2] L. Noodleman, "Valence Bond Description of Anti-Ferromagnetic Coupling in Transition-Metal Dimers," Journal of Chemical Physics,74, 5737-5743, (1981). [3] S. Goel and A. E. Masunov, "Potential Energy Curves and Electronic Structure of 3d- Transition Metal Hydrides and their Cations," Journal of Chemical Physics,129 (2008). [4] K. Yamaguchi, et al., "Extended Hartree-Fock (Ehf) Theory of Chemical-Reactions .3. Projected Moller-Plesset (Pmp) Perturbation Wavefunctions for Transition Structures of Organic-Reactions," Theoretica Chimica Acta,73, 337-364, (1988). [5] V. Barone and C. Adamo, "First-row transition-metal hydrides: A challenging playground for new theoretical approaches," International Journal of Quantum Chemistry,61, 443-451, (1997). Conference on Current Trends in Computational Chemistry 2008 61 Gold Nanoparticle Based NSET Assay for Monitoring RNA Folding Kinetics Jelani Griffin, Uma Shanker Rai and Paresh Chandra Ray Department of Chemistry, Jackson State University, Jackson, MS, USA RNAs play critical functional roles in metabolism, replication, regulation, and development of cells. How RNA molecules fold into functional structures is a problem of great significance given the expanding list of essential cellular RNA enzymes and the increasing number of applications of RNA in biotechnology and medicine. RNA is the key enzymatic component in a number of essential cellular processes, such as translation and splicing. Aside from these fundamental roles, RNA also finds important applications in modern biotechnology and medicine This increasing appreciation of RNA as a crucial biopolymer demands more than ever a clear picture of how RNA molecules fold into their native structures, which are vital to their functional properties. Steady-state FRET measurements in solution allow one to measure the kinetics and requirements of docking of its two independently folding domains; time-resolved FRET reveals the relative thermodynamic stability of the undocked (extended, inactive) and docked (active) ribozyme conformations. However, the length scale for detection using FRET-based methods is limited by the nature of the dipole-dipole mechanism, which effectively constrains the length scales to distances on the order of <100 Å (R0 60 Å). Recently we have demonstrated that nanomaterial based surface energy transfer (NSET) is a technique capable of measuring distances nearly twice as far as FRET in which energy transfer from a donor molecule to a nanoparticle surface follows a predictable distance dependence; decrease in donor fluorescence intensity is translated into a measurable distance decrease between donor and acceptor. Here we want to demonstrate that gold nanoparticle based fluorescence resonance energy transfer (NSET) can be used to track the folding of RNA. As a model system, the conformational changes two- helix junction RNA molecules induced Mg2+ ions is studied by measuring time dependent fluorescence signal. The transition from an open to a folded configuration changed the distance between gold nanoparticles and the dye molecule attached to the ends of two helices in the RNA junction. So the folding process has been monitored from the change of fluorescence intensity. AU CG C G A U K dock GC A ------AC A GA----- K undock B B B A u c AU----- p G A-----A o C g o G c A ----- A L a A --- g C U A -- G ---- u A ------G A C G A ---- c p A U o G c C G o A u G C L U a C G A u C G A u A U A u 5’ 3’ A U 3’A U Domain B Domain A 5’ S S Cy3 Au Nanoparticle 62 Conference on Current Trends in Computational Chemistry 2008 The role of Metal Substrate Reconstruction in the Self- Assembly of Thiol Adsorbates Frank Hagelberg, and Georgi Nenchev, Bogdan Diaconescu, Karsten Pohl Department of Physics and Astronomy, East Tennessee State University, Johnson City, TN 37614 and Georgi Nenchev, Bogdan Diaconescu, Karsten Pohl, Department of Physics, University of New Hampshire, Durham, NH Self-assembled monolayer (SAM) formation has been the subject of intense computational research [1-3, and references therein]. Previous approaches have made allowance for local substrate irregularities, but not for any long-range dislocations. This premise may be problematic, since it is well known that the clean gold surface reconstructs into a very complex geometry which is described by a large unit cell of dimension Sqrt(3) x 22. According to traditional belief, the gold reconstruction coexists with thiol monolayers at only very low coverage levels up to approximately 0.1. For Dimethyldisulfid, it has been established that the Au(111) reconstruction is lifted already at a low coverage of 7.8 per cent [4]. A recent STM study, however, may lead to a revision of these views. For low coverage and also close to saturation coverage of methanethiol, novel short as well as long-range ordered structures were observed that form on top of the reconstruction. STM analysis reveals a two-row supercell which is due to a slight height variation between adjacent rows. In response to the experimental findings, thiol molecules in contact with the reconstructed Au(111) surface were modeled using Density Functional theory within three-dimensional boundary conditions. Specifically, thiol was studied in contact with the reconstructed surface, first focusing on a paired phase that was observed at sub-ML coverage. In accordance with the experimental finding, adsorption in the FCC regime was considered. Specifically, two methanethiol molecules were attached to adjacent hollow sites. Optimization yields an equilibrium structure involving an S-S distance of 4.0 Å which is compatible with the STM data. In this final geometry, one of the two paired molecules tends from its original position towards a bridge site, the other towards an on-top site. To assess the stability of this phase, a further computation for two methanethiol molecules at hollow positions with an initial S – S distance of 5.2 Å was carried out. This value remains nearly unaffected in the course of geometry optimization, implying negligible mutual influence of the two molecules on each other. Therefore, the adsorption energy difference between both configurations may be used as a measure for the interaction strength between an adsorbate pair. The result is 100 meV. From these calculations, the dimer phase impacts the geometry of the substrate. It reduces the reconstruction without removing it. Thus the amplitude of height modulation (“corrugation amplitude”) is found to be decreased by 30% from its value for the pure Au(111) surface. A close analysis of the long-range ordered phase that is observed at increased thiol exposure reveals a zigzag or step – profile with alternating bridge and particle sites. It is found that this solution has a distinct energy advantage of about 50 meV over the alternative pattern that involves straight parallel adsorbate rows. It is near-degenerate with a competing structure that comprises particle sites only, but it surpasses this configuration in by a very small stability margin of about 2 meV. The STM image recorded at a bias of 2 V is compatible with the partial electron density in the energy interval of 2 eV above the Fermi energy, as derived from our proposed equilibrium structure. Conference on Current Trends in Computational Chemistry 2008 63 [1] J.G.Zhou, Q.Williams, F. Hagelberg, Phys.Rev.B 77, 35402 (2008). [2] J.G.Zhou, Q.Williams, F. Hagelberg, Phys.Rev.B 76, 75408 (2007). [3] J.-G. Zhou, F.Hagelberg, Phys.Rev.Lett. 97, 45505 (2006). [4] C. Vericat et al., PCCP, 3258 (2005). 64 Conference on Current Trends in Computational Chemistry 2008 Structural Effects in Inorganic Chemistry Magdolna Hargittai Materials Structure and Modeling Research Group of the Hungarian Academy of Sciences, Budapest University of Technology and Economics, H-1111 Budapest, Szt. Gellért tér 4, Hungary Unexpected structures are still encountered in inorganic chemistry, especially in molecules of the d- and f-block metals, or, of large metals in general. Yet, their reliable determination, either by computations or by experiment in the gas phase, has been a formidable task. Lately, the ever-increasing potentials of computations have shown real success in this endeavor. In this talk, a few specific structural effects will be discussed based on joint computational and experimental (electron diffraction and vibrational spectroscopic) studies. The Jahn−Teller effect, while usually a small and subtle effect in organic chemistry, causes 1 major structural changes in transition metal complexes, among them in metal trihalides as MnF3 and the gold2 and silver3 trihalides illustrate. The Renner−Teller effect is a special case of the Jahn−Teller effect; as it is well known, it refers to linear molecules. Crystalline chromium dihalides are typical examples of the Jahn-Teller effect with their tetragonally distorted octahedral coordination, but their triatomic molecules in their vapors have been found linear by experiments. However, computations suggested that CrCl2 might be a case for the Renner−Teller effect.4 Recently, with a joint electron diffraction and computational study we showed the molecule unambiguously to have bent ground-state geometry due to Renner−Teller type 5 6 distortion. CrF2 is a similar case. The latter molecule is also interesting in that due to its extreme floppyness and its close-lying electronic states, it is a huge challenge for both experiments and computations. 15 10 5 5 A2 Relative enegy (kcal/mol) Relative 5 5 Πg B2 0 110 115 120 125 130 135 140 145 150 155 160 165 170 175 180 Cl-Cr-Cl Bond Angle (degrees) 5 Renner-Teller effect in chromium dihalides. The Πg electronic state splits into two 5 nondegenerate states, of which the B2 state is the ground state. Complexes of the lanthanides, especially their trihalides, have been studied by computations for decades. The early relatively low-level computations are now getting replaced by high-level, multiconfigurational calculations with small-core ECPs. However, the inclusion of the 4f subshell in the valence shell introduces new difficulties, not encountered by calculations using large-core ECPs. The effect of 4f orbitals on their bonding and spin-orbit effects will be discussed and the importance of using multiconfigurational calculations for these systems will be 7 demonstrated with the examples of dysprosium trihalides. Conference on Current Trends in Computational Chemistry 2008 65 Floppyness is probably the most typical characteristics of metal halide molecules, especially of their dimers and higher associates. The dimer structures have long been either determined by experiment or assumed based on similar systems. A growing body of evidence is emerging, mostly from computational studies that show that these assumed dimer structures were probably wrong. At the same time, some of the new computational results are also difficult to explain—so the question is still open. The tetramer of CuCl appears to be puckered in contrast to the expected planar ring as shown below. Two possible structures of Cu4Cl4. We will also look at the structural connections between the monomers and dimers of metal halide molecules, on the one hand, and between the vapor-phase molecular structures and their structures in the crystal, on the other. An example is CrCl2 that has antiferromagnetically coupled dimers and small oligomers in the vapor, whose structure is closely related to that of their crystal. Another series of examples will be the group 2 and 12 dihalides.8,9 Acknowledgement. Our work is supported by the Hungarian Scientific Research Fund (Grant OTKA K 60365). References 1. Hargittai, M.; Reffy, B.; Kolonits, M.; Marsden, C.J.; Heully, J.-L. J. Am. Chem. Soc., 1997, 119, 9042. 2. Reffy, B.; Kolonits, M.; Schulz, A.; Klapotke, T.M.; Hargittai, M. J. Am. Chem. Soc. 2000, 122, 3127; Hargittai, M.; Schulz, A.; Reffy, B.; Kolonits, M. J. Am. Chem. Soc. 2001, 123, 1449; Schulz, A.; Hargittai, M. Chem. Eur. J. 2001, 7, 3657. 3. -Rosing, H.C.; Schulz, A.; Hargittai, M. J. Am. Chem. Soc. 2005, 127, 8133. 4. Jensen, V. R. Mol. Phys. 1997, 91, 131. 4. Vest, B.; Varga, Z.; Hargittai, M.; Hermann, A.; Schwerdtfeger, P. Chem. Eur. J. 2008, 14, 5130. 5. Vest, B.; Schwerdtfeger, P.; Kolonits, M.; Hargittai, M. to be published. 6. Lanza, G.; Varga, Z.; Kolonits, M.; Hargittai, M. J. Chem. Phys. 2008, 128, 074301. 7.Donald, K.J.; Hoffmann, R. J. Am. Chem. Soc. 2006, 128, 11236. 8.Donald, K.J.; Hargittai, M.; Hoffmann, R. Chem. Eur. J. in press. 66 Conference on Current Trends in Computational Chemistry 2008 High-Accuracy ab initio Studies of Sn (n=1-4) Electronic Structure John A.W. Harkless Department of Chemistry, Howard University, 525 College St., NW, Washington, DC 20059 Quantum Monte Carlo methods are applied to the problem of conformer energetics of S4, and its decomposition products. The results presented here estimate the energy gap between the C2V and D4h conformers of S4, an important species in interstellar chemistry using variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC). VMC and DMC estimates of symmetric and asymmetric dissociation, selected electronic excited states of S3, S2, and S atom are also reported. The overall effectiveness and accuracy of the method is compared against other available theory and experiment. Conference on Current Trends in Computational Chemistry 2008 67 Theoretical Study on the Cation-π interactions of the Ring Fused Benzene Molecules Ayorinde Hassan, T. C. Dinadayalane, and Jerzy Leszczynski* Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR. Lynch Street, Jackson, MS 39217, USA A detailed understanding of cation-π interactions is important in chemistry and biology since lot of studies have shown their importance in protein structures and stability, protein- protein interactions, protein-enzyme interactions, and drug-receptor interactions. Tailoring of host molecules and/or binding sites by altering shapes is extensively being used in designing new drug targets, as well as in reoptimizing chemical agents that could be of medicinal value.1 Cation-π interactions play crucial role in the removal of radioactive and heavy metal ions from waste water streams.2,3 Recent studies revealed that ring addition to benzene significantly enhances the binding affinity of metal ions.4,5 Binding of alkali metal ions (Li+, Na+ and K+) with different ring fused benzene systems has been investigated at the density functional theory (B3LYP) and ab initio (MP2) method. The ligands and complexes were optimized at the B3LYP/6-31(d,p) level. Further, single point calculations were performed at the B3LYP/6- 311+G(2d,2p) and MP2/6-311+G(2d,2p) levels using the B3LYP/6-31G(d,p) level optimized geometries. The goal of the present work is to examine the effect of sequential ring annelation of monocyclic six-membered aromatic ring and bicyclo[2.1.1]hexene to the simplest aromatic benzene ring on the cation-π interactions. Benzene and ring annelated ligands considered in this study are shown in Scheme 1. Scheme 1: The host molecules for binding metal cation M+ The computed interaction energies clearly indicate that binding affinity of M+ ion with six membered aromatic ring is enhanced by tri-annelation of benzene or highly strained bicyclo[2.1.1]hexene ring. Substantial increase of interaction energy by bicyclo[2.1.1]hexene ring annelation may be attributed to the weak C-H…Li+ interaction in addition to M+-π 68 Conference on Current Trends in Computational Chemistry 2008 interaction. The strength of interaction decreases as the ionic radius increases from lithium to potassium. The same qualitative trend is observed for the interaction energies regardless of the levels of theory considered. The larger basis set with both B3LYP and MP2 method performs consistently better than smaller double-ζ basis set for binding energies. References: (1) Ma, J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303. (2) Amicangelo, J. C.; Armentrout, P. B. J. Phys. Chem. A 2000, 104, 11420. (3) Zhu, D.; Herbert, B. E.; Schlautman, M. A.; Carraway, E. R. J. Environ. Qual. 2004, 33, 276. (4) Hassan, A.; Dinadayalane, T. C.; Leszczynski, J. Chem. Phys. Lett. 2007, 443, 205. (5) Dinadayalane, T. C.; Afanasiev, D.; and Leszczynski, J. J. Phys. Chem. A 2008, 112, 7916. Conference on Current Trends in Computational Chemistry 2008 69 Exact Solutions of the Polyatomic Schrödinger Equations So Hirata,a Toru Shiozaki,ab Muneaki Kamiya,a and Edward F. Valeevc aQuantum Theory Project, University of Florida, Gainesville, Florida 32611-8435; bDepartment of Applied Chemistry, The University of Tokyo, Tokyo 113-8656; and cDepartment of Chemistry, Virginia Tech, Blacksburg, Virginia 24061-0002 An ultimate objective of electronic structure theory is to solve the Schrödinger equation of general polyatomic molecules and macromolecules within a controlled absolute accuracy, typically, 1 kcal mol–1, with even higher accuracy for relative energies. To achieve this without relying on statistical or empirical treatments, one must have rapidly converging series of approximations in both electron-correlation treatments and basis sets. Our efforts toward this objective are based on the grid-based, numerical solutions of the Hartree–Fock equations1 and on the high-rank, explicitly-correlated coupled-cluster methods with Gaussian basis sets,2,3 which are implemented by computer algebra. We will show that this combination yields the nonrelativistic total energies of Ne, BH, and H2O correctly within 2 kcal/mol. Hierarchical electronic and vibrational methods such as those based on coupled-cluster and perturbation theories are not yet applicable to macromolecules of any chemical compositions. However, when particular classes of macromolecules such as periodic insulators and molecular crystals are considered, one can apply these methods by exploiting known characteristics of their wave functions. We introduce such a scheme4–6 allowing the energies, structures, and phonons of molecular crystals to be predicted at correlated theoretical levels with a counterpoise basis-set superposition error correction. Reliable band assignments of the infrared, Raman, and inelastic neutron scattering spectra of solid formic acid are provided on this basis and the speculated polymorphism of solid formic acid is ruled out.6 This work has been supported by the U.S. Department of Energy, Office of Basic Energy Sciences through Grant DE-FG02-04ER15621. 1. T. Shiozaki and S. Hirata, Physical Review A (Rapid Communications) 76, 040503(R) (2007), “Grid-based numerical Hartree–Fock solutions of polyatomic molecules.” 2. T. Shiozaki, M. Kamiya, S. Hirata and E. F. Valeev, The Journal of Chemical Physics (Communications) 129, 071101 (2008), “Explicitly-correlated coupled-cluster singles and doubles (CCSD-R12) method based on complete diagrammatic equations.” 3. T. Shiozaki, M. Kamiya, S. Hirata, and E. F. Valeev, Physical Chemistry Chemical Physics 10, 3358–3370 (2008), “Equations of explicitly-correlated coupled-cluster methods.” 4. S. Hirata, M. Valiev, M. Dupuis, S. S. Xantheas, S. Sugiki, and H. Sekino, Molecular Physics 103, 2255 (2005), “Fast electron correlation methods for molecular clusters in the ground and excited states.” 5. M. Kamiya, S. Hirata, and M. Valiev, The Journal of Chemical Physics 128, 074103 (2008), “Fast electron correlation methods for molecular clusters without basis set superposition errors.” 6. S. Hirata, (submitted, 2008), “Fast electron-correlation methods for molecular crystals: An application to the α, β1, and β2 modifications of solid formic acid.” 70 Conference on Current Trends in Computational Chemistry 2008 Predicted NMR Shift Changes in the Aromatic Ring Due to Cation-π Interactions Estelle M. Huff, Peter Pulay, T.K.S. Kumar Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701 Much work has been done on finding the structure of proteins and other polypeptides based on their NMR shifts. Structure determinations of proteins that do not crystallize easily rely heavily on the NMR-derived atomic distances, using the chemical shift only to identify the atomic sites. The chemical shifts, however, also give information on the weak interaction between nearby amino acids. The presence of a cationic amino acid in close spatial proximity to an aromatic residue causes significant detectable changes in NMR shifts of the aromatic nuclei, predominately in the proton spectra. Modern ab initio techniques have been used to map the NMR shift changes of the aromatic ring due to the presence of a nearby cation, as a function of the distance and orientation of the cation relative to the ring. The accuracy of the calculations (~0.04 ppm) is much better than the magnitude of the predicted shifts changes (up to ~0.5 ppm). As cation-π interactions are of significant importance in drug design, protein folding, and receptor-ligand complexes, a better understanding of the cation-π interactions is critical. The knowledge gained on the orientation and strength of cation-pi interactions is expected to provide valuable clues for improving the accuracy of prediction of three-dimensional structures of proteins. Conference on Current Trends in Computational Chemistry 2008 71 Relative Stability of Isomers of a Dipseudoacid Peter J. Huwe1, Dmitriy V. Liskin2, Edward J. Valente2, and David H. Magers1 1Computational Chemistry Group, 2Structural Chemistry Group, Mississippi College Pseudoacids are cyclic oxocarboxylic acids. One example would be the cyclic lactol form of levulinic acid: O O OH O HO O However, the open form of this species is favored. Another example would be the cyclization product of 2-formylbenzoic acid: O O OH O H HO O Here the interacting groups are forced to be nearer to each other by the rigidity of the aromatic ring, and the cyclic form is favored. Recently Liskin and Valente reported the synthesis and characterization of the first dipseudoacid, an arylpyran dipseudoacid, C16H18O6 [Figure 1.]. Crystals of trans-4,4,8,8-tetramethyl-3,7-dihydroxy-1,2,3,4,5,6,7,8-octahydro-2,6- dioxaanthracen-1,5-dione occur in the monoclinic system and form linear hydrogen-bonded chains [J. Mol. Struc. 2007, in press]. This molecule has inversion symmetry, but an isomeric form with a two-fold rotation axis can be conceived [Figure 2.]. 72 Conference on Current Trends in Computational Chemistry 2008 Figure1. trans-4,4,8,8-tetramethyl-3,7-dihydroxy-1,2,3,4,5,6,7,8-octahydro-2,6 dioxaanthracen-1,5-dione Figure 2. isomeric form of the first dipseudoacid In the current study, we compare the relative stabilities of the two isomers and their ketone precursors to determine if the isomer with two-fold rotational symmetry might also be a candidate for synthesis. In addition, we investigate the relative energies of different derivatives of the two ketones and the two dipseudoacids to determine if different substitutions on the aromatic ring might alter the relative stability of the two isomers. We gratefully acknowledge support from the NSF (MRI-0321397). Conference on Current Trends in Computational Chemistry 2008 73 Prediction of Thermal Cycloreversion and Fatigue-resistance in Photochromic Compounds: A Density Functional Theory Study Pansy Iqbala,b, Ivan A. Mikhaylova, Kevin D. Belfieldb,d, Artëm E. Masunova,b,c aNanoscience Technology Center, bDepartment of Chemistry, cDepartment of Physics, dCREOL, College of Optics and Photonics, University of Central Florida 12424 Research Pkwy, Suite 400, Orlando, FL, 32829, USA, E-mail: [email protected] Photocyclization is a reversible process of isomeric transition between the open and closed forms upon irradiation of photochromic compounds accompanied by change in their color. The two isomeric forms differ in various physical and chemical properties and find prospective applications in optical switches and data storage applications with enhanced properties of interest. In particular dithienyl perfluorocyclopentenes are an important class of thermally irreversible (P-type) photochromic compounds (Fig.1). F F F F BLA 1 F F F F F F F F F F hν', Δ F F BLA 2 F F CH CH 3 hν CH3 3 S S S S H3C H3C SS CH3 (a) (b) (c) Closed Open Byproduct λ in nm λ in nm λ in nm Fig1: (a-c) Isomers of 1,2-bis(2-methyl-5-phenyl-3-thienyl) perfluorocyclopentene and (d-f) their absorption spectra: experimental (faint lines) and predicted at TD-B3LYP/6-31G*/PCM//M052x/6-31G*/PCM level of theory (bold lines) In order to be useful in design of various optoelectronic devices such as optical memory, optical switching, displays and nonlinear optics, the photochromic material has to satisfy certain requirements, such as 1. Thermal stability of both isomers; 2. Fatigue resistance; 3. Efficient photochromic reactivity: high sensitivity, rapid response; 4. High solubility in polymer matrices; 5. None-destructive readout capability; 6. Sensitivity at diode laser wave lengths [1]. Prediction of these properties based on the molecular structure of the chromophores is an important component of rational design strategy. In this contribution we apply Density Functional Theory (DFT) to predict the equilibrium geometry and absorption spectra. In order to predict accurate absorption spectra it is essential to obtain the correct geometry of the photochromic compound. In particular for 1,2-bis(2-methyl-5-phenyl-3- thienyl)perfluorocyclopentene (PFC-2) and one of its ethylene derivatives 1,2-bis(2-ethyl-5- 74 Conference on Current Trends in Computational Chemistry 2008 phenyl-3-thienyl)perfluorocyclopentene (PFC-2-et) we apply DFT to predict the equilibrium geometry (Table 1) and absorption spectra (Fig. 1) all the possible isomers. Table 1: Bond length alternation values (BLA (Ǻ)) and TD-DFT absorption wavelengths (λ (nm)) for PFC and PFC-2-et isomers at different DFT methods compared with the corresponding experimental values. PFC-2 Closed Open By-product BLA1 BLA2 λ BLA1 BLA2 λ BLA1 BLA2 λ Expa 0.085 0.055 575 -0.112 0.050 276 0.093 0.072 547 TD-BMK/6-31G*/PCM//BMK/6-31G*/PCM 0.083 0.057 566 -0.110 0.066 274 0.095 0.074 519 TD-B3LYP/6-31G*/PCM//BMK/6-31G*/PCM 0.083 0.057 620 -0.110 0.066 298 0.095 0.074 574 TD-B3LYP/6-31G*/PCM//BMK/6-31G* 0.100 0.074 590 -0.117 0.073 299 0.095 0.072 576 TD-B3LYP/6-31G*//BMK/6-31+G* 0.098 0.072 573 -0.116 0.072 276 0.095 0.072 565 TD-B3LYP/6-31G*//B3LYP/6-31+G* 0.083 0.055 608 -0.110 0.065 296 0.082 0.058 587 TD-B3LYP/6-31G*/PCM//B3LYP/6-31+G* 0.083 0.055 626 -0.110 0.065 298 0.082 0.058 600 TD-B3LYP/6-31G*/PCM//M052x/6-31G* 0.100 0.074 579 -0.114 0.068 292 0.097 0.077 569 TD-MO52x/6-31G*/PCM//M052x/6-31G*/PCM 0.100 0.076 521 -0.114 0.068 262 0.098 0.077 506 TD-B3LYP/6-31G*/PCM//M052x/6-31G*/PCM 0.100 0.076 581 -0.114 0.068 292 0.098 0.077 568 PFC-2-et Closed Open BLA1 BLA2 λ BLA1 BLA2 λ Expb 0.089 0.059 600 -0.115 0.068 286 TD-BMK/6-31G*/PCM//BMK/6-31G*/PCM 0.098 0.073 563 -0.121 0.069 277 TD-B3LYP/6-31G*/PCM//BMK/6-31G*/PCM 0.098 0.073 622 -0.121 0.069 302 TD-B3LYP/6-31G*/PCM//BMK/6-31G* 0.098 0.072 613 -0.121 0.070 303 TD-B3LYP/6-31G*//BMK/6-31+G* 0.098 0.072 609 -0.121 0.070 301 TD-B3LYP/6-31G*//B3LYP/6-31+G* 0.084 0.055 639 -0.111 0.066 299 TD-B3LYP/6-31G*/PCM//B3LYP/6-31+G* 0.084 0.055 657 -0.111 0.066 300 TD-B3LYP/6-31G*/PCM//M052x/6-31G* 0.102 0.077 605 -0.117 0.065 293 TD-MO52x/6-31G*/PCM//M052x/6-31G*/PCM 0.101 0.075 543 -0.116 0.067 263 TD-B3LYP/6-31G*/PCM//M052x/6-31G*/PCM 0.101 0.075 606 -0.116 0.067 294 a - ref [2], b - ref [3] From the above calculations, it is evident that the accurate equilibrium geometry comparison on the basis of bond length alternation (BLA1 and BLA2) values with that of the experimental X-ray geometry, is best reproduced at M052x/6-31G* level. The TD-DFT absorption spectra (λ) is closely comparable at the B3LYP/6-31G*/ PCM level. However the best agreement for both the parameters - BLAs as well as the λmax values is at TD-B3LYP/6-31G*/PCM//M052x/6- 31G*/PCM level of calculation suggesting that the basis set polarization is important to obtain the best geometry and also the spectral data is evaluated under solvent conditions so the TD-DFT method must employ polarization continuum model (PCM). Thermal cycloreversion process occurs through symmetry forbidden conrotatory electrocyclic mechanism, with transition state of strong diradical character. The activation barrier for thermal cycloreversion process was studied for a number of photochromic compounds (Fig. 2) and compared to the experimental value to validate a suitable exchange-correlation functionals in DFT method in the study of this phenomenon (Table 2). The mechanism for the byproduct formation in PFC-2 is also studied to provide a detailed mechanism. Conference on Current Trends in Computational Chemistry 2008 75 FF FF FF F F F F F F F F F F F F CH S CH3 CN CH3 CN 3 CN S CN S CHO S CN S SH3C OHC SH3C NC SH3C 2 10 11 FF NC CN FF F F F F F F F F R R2 2 S CH3 N N R1 S S CHO S S H3C S R1 DCN-2 13 R1=CH3, R2=H - PFC-2 R1=CH3, R2=CH3 - PFC-2-a Fig.2 : Set of photochromic compounds studied for calculation of activation barrier Table 2: Activation barriers for thermal cycloreversion process from open to closed isomers (in kcal/mol) Molecules 2 10 11 13 DCN-2 PFC-2 PFC-2-a Exp kcal/Mol 26.1 26.8 23.4 29.1 27.6 33.2 28.7 UAM1 30.1 29.5 29.8 29.9 24.3 27.1 24.8 UHF/MidiX 30.2 27.9 28.2 30.2 28.2 30.0 27.7 UB3LYP/MidiX 29.4 29.9 25.2 32.0 34.5 35.4 31.6 UB3LYP/MidiX(ZPE) 27.8 27.8 23.2 29.7 31.1 32.8 29.6 UBMK/MidiX 35.8 37.1 34.1 38.7 40.5 43.5 41.6 UBMK/MidiX(ZPE corr) 33.7 34.9 32.0 36.9 36.2 42.9 39.7 UM052x/6-31G* 31.5 31.4 26.6 34.5 39.3 38.2 35.8 UM052x/6-31G*(ZPE corr) 29.4 29.3 24.4 32.1 35.6 35.3 32.9 During the photochromic rearrangement, undesirable chemical reactions may also occur. This limits the number of cycles of photochromic reactions and contributes to photochemical fatigue. Fig. 1 depicts the closed, open and byproduct isomeric forms of PFC synthesized by Irie and coworkers [4]. The fatigue resistance reported as 73% decrease in the absorbance of the open form after 850 cycles. In order to predict the kinetics of photochemical fatigue in PFC-2, we investigated the mechanism of by-product formation. We hypothesized possibility of two different routes to form the by-product – thermally and photochemically (Fig. 3). The thermal by-product pathway involves the bicyclohexane (BCH) ring formation as a stable intermediate; while the photochemical by-product formation pathway may involve the methylcyclopentene diradical (MCPD) intermediate. In contrast to the electron recoupling process study by Celani et al.[5], we found the MCPD to be a stable intermediate potential energy surface of PFC-2. From our preliminary studies performed on the mechanism of byproduct formation, we have found that the by-product is only formed from the closed structure as suggested by the Irie et al. [4] with a barrier of 51.22 kcal/mol corresponding to TS2 between the closed form and the BCH intermediate and 16.16kcal/mol corresponding to TS3 between the BCH intermediate and the by- 76 Conference on Current Trends in Computational Chemistry 2008 product at UM052x/6-31G* level. Similar potential energy surface calculations for yet another derivative of PFC are done to compare the kinetics of the by-product formation. 1 6 1 6 5 2 5 TS1 2 3 . 3 4 4 S S S S 9 10 9 10 1 6 Open . Closed 5 2 Å . 2 .1 . 2 4 3 . TS2 Photo- S S by-product 9 2.22 Å 10 formation CIX 6 1 6 1 2 5 Thermal- 2 . 5 3 TS5 by-product 3 . formation 9 s 4 S 4 9 S10 S10 BCH MCPD TS6/7 1 6 TS3 2 5 3 SS4 9 10 bypdt Fig. 3 Possible routes to by-product formation The quantitative agreement between the experimental and the theoretical data suggests that DFT methods could be successfully employed in the prediction of three out of six properties essential for design of photoswitching and data storage applications: thermal stability, fatigue resistance and absorption spectra. References [1] M. Irie, Chem. Rev. 100, 1685 (2000). [2] M. Irie, T. Lifka, S. Kobatake, N. Kato, J. Am. Chem. Soc., 122, 4871 (2000). [3] S. Kobatake, K. Shibata, K. Uchida, M. Irie, J. Am. Chem. Soc., 122, 12135 (2000). [4] M. Irie, T. Lifka, K. Uchida, S. Kobatake, Y. Shindo, Chem. Commun., 747 (1999). [5] P. Celani, S. Ottani, M. Olivucci, et al., J. Am. Chem. Soc.,116, 10141 (1994). Conference on Current Trends in Computational Chemistry 2008 77 Structure and Properties of Bacterial Nitroreductase Olexandr Isayev,1 Leonid Gorb,1,3 Narimantas Cenas,2 Mo Qasim,3 and Jerzy Leszczynski1 1 Computational Center for Molecular Structure and Interactions, Jackson State University, P.O. Box 17910, Jackson, MS 39217; 2 Department of Biochemistry of Xenobiotics, Institute of Biochemistry, Vilnius, Lithuania; 3 US Army ERDC, Vicksburg, MS 39180 Because of the recalcitrance of nitroaromatics compounds (NACs), they have been accumulated in the locations of manufacturing, storage, and decommissioning over the past several decades. NACs and their metabolites are known to be toxic, mutagenic and carcinogenic to various organisms including humans, and therefore should be removed from contaminated sites. Recently, biodegradation of NACs has been proposed as inexpensive and environmentally clean way for their disposal. Although the major processes affecting the biodegradation of NACs have been investigated qualitatively, many issues regarding a reaction mechanism and enzymatic selectivity remain unsolved. Nitroreductase (NR) is a flavoprotein which catalyzes the pyridine nucleotide-dependent reduction of nitroaromatics. Previous studies established so called ping-pong kinetic mechanism. In order to clarify the poorly understood mechanisms of two-electron reduction of NACs by flavoenzymes, we examined the nitroreductase reactions by QM/MM approach at the M05- 2X/AMBER level of theory. We also concentrate on the role of electronic and structural parameters of nitroaromatic compounds in their reduction by the bacterial NAD(P)H niroreductase. In addition structural and dynamic properties of NR were obtained from classical MD simulation in the explicit water environment. The system has been carefully equilibrated using AMBER force field. After equilibration, statistical quantities were monitored during 50ns of NPT simulation under ambient conditions. 78 Conference on Current Trends in Computational Chemistry 2008 DFT study on the Glycine-(H2O)n and Protonated Glycine- (H2O)n (n=1 and 2) Jyothsna Kanipakam, T. C. Dinadayalane and Jerzy Leszczynski* Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA; E-mail: [email protected] Hydration of naturally occurring amino acids has attracted considerable attention due to the biological importance. Exploration of hydration of amino acids provides an understanding of the biomolecular properties and biophysical processes in the living systems.1-5 Protonation of α- amino acids has been the subject of experimental and theoretical interest.6-8 Hydration of amino acids, which are the building blocks of peptides and proteins, influences molecular structures. Naturally occurring α-amino acids are nonzwitterionic in the gas phase, whereas they exist predominantly in the zwitterionic form in aqueous solution at neutral pH. In order to have a detailed understanding of the hydration of amino acids and their structural preferences, we have examined the relative stability of zwitterionic versus nonzwitterionic glycine by adding 1 and 2 water molecules. In this work, we employed B3LYP/6-31+G(d,p) calculations to investigate the microsolvation of neutral, zwitterionic and protonated glycine (G). A thorough conformational analysis has been performed to find out the global minimum structure of glycine and protonated glycine; also we extended our search to locate the global minimum of hydrated non-zwitterionic, zwitterionic and protontated glycine. We computed the intermolecular charge transfer values in these solvated complexes. Scheme 1 depicts the optimized global minimum structures of nonzwitterionic glycine (G), zwitterionic glycine (G-zw), protonated glycine (GH). G G-zw GH Scheme 1 Acknowledgements: JK thanks Computational Center for Molecular Structure and Interactions (CCMSI) for participation in summer school. Mississippi Center for Supercomputing Research (MCSR) is acknowledged for generous computational facilities. References: (1) (a) Wincel, H. J. Phys. Chem. A 2007, 111, 5784-5791; (b) Wincel, H. Chem. Phys. Lett. 2007, 439, 157-161. Conference on Current Trends in Computational Chemistry 2008 79 (2) Kamariotis, A.; Boyarkin, O. V.; Mercier, S. R.; Beck, R. D.; Bush, M. F.; Williams, E. R.; Rizzo, T. R. J. Am. Chem. Soc. 2006, 128, 905-916. (3) Lemoff, A. S.; Wu, C. -C.; Bush, M. F.; Williams, E. R. J. Phys. Chem. A 2006, 110, 3662-3669. (4) Lemoff, A. S.; Bush, M. F.; Wu, C. -C.; Williams, E. R. J. Am. Chem. Soc. 2005, 127, 10276-10286. (5) Ye, S. J.; Moision, R. M.; Armentrout, P. B. Int. J. Mass Spectrom. 2005, 240, 233-248. (6) Dinadayalane, T. C.; Sastry, G. N.; Leszczynski, J. Int. J. Quantum Chem. 2006, 106, 2920-2933. (7) (a) Harrison, A. G. Mass Spectrom. Rev. 1997, 16, 201. (b) Bojesen, G. J. Am. Chem. Soc. 1987, 109, 5557. (8) Maksic, Z. B.; Kovacevic, B. Chem. Phys. Lett. 1999, 307, 497-504 80 Conference on Current Trends in Computational Chemistry 2008 Electronic Structure and Optical Properties of Si(111)/SiO2 Plane Interface Valentin V. Karasieva,b), Dmitri S. Kilinb) and Anatoli Korkinc) a)Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Apartado 21827, Caracas 1020-A, Venezuela; b)Quantum Theory Project, Departments of Physics and of Chemistry, University of Florida, Gainesville, FL 32611, USA; c)Nano &Giga Solutions, Gilbert, Arizona 85296, USA Interfaces between two materials, among them Si/SiO2, play an important role in the semiconductor industry, in particular for the complementary metal-oxide-semiconductor (CMOS) technology and for fabrication of light-emitting and light-absorbing Si-based nanostructured materials. Interaction of a semiconductor material with light is typically enhanced by impurities, interfaces, or spatial constraints. Thin films are nanostructured materials with one- dimensional (1D) spatial constraint. A silicon thin film in an oxygen containing atmosphere experiences formation of an oxide layer on its surface. Here we study such silicon - silicon dioxide plane interfaces with an atomic model computationally designed in Ref. [1]. In the present work we focus on the electronic structure of silicon dioxide interface with the (111) silicon surface. The interface model is shown in Figure; it is equivalent to the {Si66O40- 111} interface presented in Ref. [1], except that the Si-atoms in new model are placed inside the cell. The interface is designed for the purposes of atomic modeling of surface photovoltage, similar as it was done for the Si(111):H surface [2]. In the present study the calculations were carried out using density functional theory (DFT) in the generalized gradient approximation (GGA) with plane waves (PW) and pseudo-potentials (PP) as implemented in VASP [3]. Structural relaxation was performed without any symmetry constraints except that the lattice was kept orthorhombic during optimization. Kinetic energy cutoff used in PW basis set is 495 eV. The binding energy (in eV per SiOx unit, x=0.606 for our model) is found to be 10.25 eV which is very close to the value of 10.52 eV of the stress energy calculated in Ref. [1]. The lattice cell parameters are 7.529x6.601x36.081 Angstrom. The band structure was calculated using 11x11x1 Monkhorst – Pack uniform k-point grid. The band structure does not have dispersion in the direction of spatial confinement kz in accord with Refs. [4,5]. The band gap in interface is almost direct, 0.56 eV, the energy gap in Γ-point is 0.74 eV. Finally, optical properties, as given by the imaginary part of the dielectric function are calculated using numerical atomic orbital (NAO) basis set as implemented in SIESTA[6] and in plane wave basis set [7]. References 1Korkin, J.C. Greer, G. Bersuker, V.V. Karasiev, and R.J. Bartlett, Phys. Rev. B 73,165312 (2006). 2 D.S. Kilin, and D.A. Micha, Chem. Phys. Lett. 461, 266 (2008). 3Vienna ab initio simulation package (VASP), Version 4.5, http://cms.mpi.univie.ac.at/vasp/. See also G. Kresse, and J. Furthmüller, Comput. Mater. Sci. 6, 4136 (1996). 4P. Carrier, L.J. Lewis, and M.W.C. Dharma-wardana, Phys. Rev. B 65, 165339 (2002). Conference on Current Trends in Computational Chemistry 2008 81 5M.P. Punkkinen, T. Korhonen, K. Kokko, and Väyrynen, Phys. Stat. Sol. B 214, R17 (1999). 6Spanish Initiative for Electronic Simulations with Thousands of Atoms (SIESTA), Version 2.0, http://www.uam.es/departamentos/ciencias/fismateriac/siesta/. See also J.M. Soler, E. Artacho, J.D. Gale, A. García, J. Junquera, P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens. Matter 14, 2745 (2002). 7D. S. Kilin, K. Tsemekhman, E. I. Zenkevich, Ch. von Borczyskowski, and O. V. Prezhdo, J. Photochem. Photobiol. A 190, 342 (2007). 82 Conference on Current Trends in Computational Chemistry 2008 Prediction of Nitro Compounds Water Solubility by Modified COSMO-RS Method Yana Kholod1, Eugene Muratov1,4, Leonid Gorb1,2, Anatoly Artemenko1, Mohammad Qasim3, Victor Kuz’min4, Francis Hill3 and Jerzy Leszczynski1,3 1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA; 2US Army ERDC( SpecPro), Vicksburg, Mississippi, 39180, USA 3US Army ERDC, Vicksburg, Mississippi, 39180, USA, 4Laboratory of Theoretical Chemistry, Department of Molecular Structure, A.V. Bogatsky Physical-Chemical Institute, Odessa, Ukraine Water solubility is an extremely important property of chemical compounds. It plays a major role in definition of migration and ultimate fate of chemicals in the environment. In particular, high solubility leads to expeditious distribution in water. High water solubility is generally associated with very low affinity for adsorption to soil particles, and high accumulation of contaminants in living organisms. Recently we have predicted water solubility and several other physical-chemical properties of TNT and related nitro and amino aromatic species [1] using the COSMO-RS [2] technique. It has been found that simulated results are in very good agreement with experimental values (error is 0.3-1.0 logarithmic units). However, the original COSMO-RS applied to nitramines, e.g. RDX, HMX and CL-20 has shown much less accurate results for water solubility calculations (2.0- 3.0 LU). We have found that the error originates from incorrect prediction of Gibbs free energy of fusion (ΔGfus) for solid compounds, which is estimated by QSPR model implemented with COSMO-RS. In the current work we have modified the QSPR equations for ΔGfus estimation. Instead of using the fitting equation with predetermined parameters, QSAR approach has been constructed on the base of Simplex representation of molecular structure [3]. Training set of 130 compounds has been used for fitting. To check the accuracy of the modified method for water solubility prediction we have tested the set of 58 compounds with the known experimental values. The comparison of the calculated and experimental values has shown very good agreement (less then 0.8 LU). Therefore, the modified COSMO-RS method has been employed to predict water solubility of the compounds of our interest, e.g. nirtramines and nitroaromatics with unknown experimental values of water solubility. References: 1. Qasim M.; Kholod Y.; Gorb L.; Magers D.; Honea P.; Leszczynski J. Chemosphere; 2007; 69(7); 1144-1150 2. Klamt, A., Eckert, F. Fluid Phase Equilibr. 2000; 172; 43-72 3. Kuz’min V.E., Artemenko A.G., Muratov E.N. J. Comp. Aid. Mol. Des., 22 (2008) 403 Conference on Current Trends in Computational Chemistry 2008 83 Self-consistent Computations of Molecular Vibrational Spectra on a Base of Stable Numerical Methods I.V.Kochikova, G.M. Kuramshinab, V.M.Senyavinb aResearch Computer Center, Moscow State University, Moscow, 119992, Russia; bFaculty of Chemistry, Moscow State University, Dept. of Phys. Chem., Moscow, 119992 Russia A force constant matrix F (consisted from second derivatives of the molecular potential with respect to nucleus coordinates in the equilibrium configuration) is one of the most important information about the intramolecular dynamics. This matrix defines vibrational properties (including infrared and Raman spectra, vibration-rotational spectra, etc.). Molecular vibrations play an important role in energy transfer processes, chemical reactions, nonradiative transitions. Various spectral experiments are available for investigating molecules of different sizes up to biopolymers ana nanostructures with high accuracy and reliability. There are two main sources for the molecular force field determination. The first way is solving the inverse problem using an experimental data on molecular spectra and electron diffraction measurement. Both (vibrational or generalized structural) problems belong to the class of nonlinear ill-posed problems [1-2]. Other way is to estimate the molecular force field by carrying out quantum mechanical calculations with a goal to obtain the theoretical equilibrium configuration and force constants. These two approaches were joined in the unique statement based on joint treatment of experimental and quantum mechanical data. On this base the concept of regularized quantum mechanical force field (RQMFF) arose, and new formulations of inverse problems were given. Stable numerical methods for the solving corresponding inverse problems have been developed. New regularizing algorithms allow us to carry out a special modeling of matrix F based on the different constraints which take into account the relative order of intramolecular forces. Force fields of extended molecular systems (clusters, polymers etc.) are constructed on a base of synthesis of separate blocks of force constants. For the estimation of intermolecular force constants we use the quantum mechanical calculations and empirical data on the second virial coefficients. The next scheme for the calculations of vibrational spectra of the large size molecules such as biological systems, polymers, nanostructures, etc. can be proposed: 1) preliminary quantum mechanical analysis of moderate size molecules chosen as key or model molecules which are the fragments of large molecular systems; 2) joint treatment of ab initio and experimental data on vibrational spectra, ED and MW data for model molecules with stable numerical methods; 3) organization of a database on structural data and force field parameters transferable in a series of related compounds; 4) determination of intermolecular potential parameters of some model key molecules; 5) synthesis (construction) of molecular force field constant martrix of complicated molecular system on a base of regularized force field parameters and intermolecular potential of separate fragments, calculation of vibrational spectra and thermodynamical functions of analyzed system. Calculations 2)-5) are performed with software package SPECTRUM [1] (the scheme is presented below) which allows calculations of large molecules (up to a few hundreds of atoms). Regularized intermolecular potentials of the key molecules are determined from second virial coefficients within regularizing algorithm [3]. Advantage of this approach is a generalization of 84 Conference on Current Trends in Computational Chemistry 2008 all known empirical finite parameter potentials. Mathematical formulation of the problem is reduced to minimization of a non-quadratic functional on a set of linear constraints defining a concave-convex potential function with the fixed inflection point. Position of inflection point is determined using enumerative technique; functional is minimized by the projection of conjugate gradients method. This work was supported in part by the RFBR grant No 08-03-00415-a. References Conference on Current Trends in Computational Chemistry 2008 85 A.G. Yagola, I.V. Kochikov, G.M. Kuramshina, Yu.A. Pentin. Inverse Problems of Vibrational Spectroscopy. VSP Scientific Publishers: Zeist, 1999. Tikhonov, A.N., Leonov, A.S. and Yagola, A.G. (1998). Nonlinear Ill-posed Problems. Chapman&Hall, London. (Original Russian language edition: (1993) Nonlinear Ill-posed Problems. Nauka, Moscow). N.V. Anikeeva, I.V. Kochikov, G.M. Kuramshina, and A.G. Yagola. Numerical methods and programming, 2003, vol. 4, pp. 200-206. 86 Conference on Current Trends in Computational Chemistry 2008 The Power of the Sun Walter Kohn University of California, Santa Barbara, California 93106 As fossil fuels run out, the search for renewable sources of energy becomes more urgent. The documentary ”The Power of the Sun” is about the discovery of the power of light, the genesis of solar energy technologies and their vast and promising potential. It begins with the findings of Isaac Newton and other early visionaries, moving to the groundbreaking work in 1905 of Albert Einstein on photons, and the work at Bell Laboratories in the 1950s where the first silicon solar cell was produced. The Power of the Sun gives us insight into the clean logic of solar energy, its efficiency and many applications. Executive Producer Professor Walter Kohn, UCSB Nobel Laureate, worked with director/writer David Kennard and others to construct this optimistic and timely presentation. John Cleese serves as host and narrator, helping make the material accessible for all audiences. Conference on Current Trends in Computational Chemistry 2008 87 Stability of Single-Walled Carbon Nanotubes and Their Cut Ends Wojciech Kołodziejczyk1,2,3, Jakub Baran1, Peter Larsson4, Rajeev Ahuja4, J. Andreas Larsson1 1 Tyndall National Institute, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland.; 2 Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland; 3 Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA; 4 Division of Materials Theory, Department of Physics & Materials Science, Uppsala University, Box 530, SE-751 21 Uppsala, Sweden. A long-standing and elusive goal in technical exploitation of carbon nanotubes (CNTs) is controlling growth for the purpose of obtaining products with uniform properties, e.g. all metallic or all semiconducting CNTs. We have studied the stability of single-walled carbon nanotubes (SWNTs) of varying diameter and chirality, compared to the stability of cut ends of SWNTs, which are present at the interface of the catalytic metal particles used in growth experiments. We have found that SWNTs differ by < 1 eV in energy between different chiralities, which represents a challenge for property controlled growth. In addition, both zigzag and armchair tubes can be the most stable chirality of SWNTs, which is a fundamental obstacle for property controlled growth utilizing thermodynamic stability. In stark contrast, the most armchair-like open-ended/cut SWNTs are always the most stable, followed in sequence by chiral tubes up to zigzag SWNTs, which have the least stable cut ends. We explain this by triple bond stabilization of the carbon dangling bonds at the open ends. 1. P. Larsson, J. A. Larsson, R. Ahuja, F. Ding, B. I. Yakobson, H. Duan, A. Rosén, K. Bolton, Phys. Rev. B 75 (2007) 115419. 2. F. Ding, P. Larsson, J. A. Larsson, R. Ahuja, H. Duan, A. Rosén, K. Bolton, Nano Lett. 8 (2008) 463. 3. Z. Li, J. A. Larsson, P. Larsson, R. Ahuja, J. M. Tobin, J. O’Byrne, M. A. Morris, G. Attard, J. D. Holmes, J. Phys. Chem. C 112 (2008) 12201. 4. W. Kołodziejczyk, J. Baran, P. Larsson, R. Ahuja, J. A. Larsson, in prep. 88 Conference on Current Trends in Computational Chemistry 2008 Probing the Role of P=O Stretching Mode Enhsncement in Nerve-agent Sensors: Simulation of the Adsorption of Nerve- agents on the Model MgO and CaO Surfaces W. Kolodziejczyka,b, D. Majumdara, S. Roszaka,b, J. Leszczynskia aComputational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA and bInstitute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27,50-370 Wroclaw, Poland The interactions of nerve gases with model MgO and CaO surfaces have been investigated using density functional theory (DFT) and Møller-Plesset second order perturbation techniques. The geometries were fully optimized at the DFT level. Analyses of the calculated IR and Raman spectra point to the enhancement of the P=O stretching mode with respect to the isolated nerve agents and this property could be used to detect these toxic gases using surface-enhanced Raman spectroscopy. Conference on Current Trends in Computational Chemistry 2008 89 First Principles Non-Adiabatic Molecular Dynamics Study of the DNA-SWCNT System Dmytro Kosenkov1, Oleg V. Prezhdo2, Bradley F. Habenicht2, Leonid Gorb3, and Jerzy Leszczynski1 1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217; 2Contribution from the Department of Chemistry, UniVersity of Washington, Seattle, Washington 98195-1700; 3 Institute of Molecular Biology and Genetics, National Academy of Sciences, Kiev, Ukraine 03143 Recent results of the scanning tunnel microscopy (STM) investigations of the single-wall carbon nanotube (SWCNT) in complex with single strand DNA revealed that DNA can be coiled around the nanotube. This allows one to study the properties of DNA in the complex. The attractive idea about possibility to use STM as a tool for DNA sequencing has emerged. In order to check this possibility the first principles non-adiabatic molecular dynamics of DNA-SWCNT system (Fig.1) was performed. The state-of-the-art quantum-classical approach was used. This approach combines time-dependent density functional theory (TD-DFT) with fewest switches surface hopping (FSSH) in the Kohn-Sham basis. The interaction between CGCG DNA sequence and (6,4) SWCNT were investigated. The simulations were performed in VASP program augmented with the FSSH- TDKS functionality. The Perdew-Wang generalized gradient approximation (GGA), Vanderbilt ultrasoft pseudopotentials, periodic boundary conditions, and converged plane- wave basis sets were employed. To prevent spurious interactions between the images, 8Å of vacuum were added in the direction perpendicular to the axis of the nanotube. The structure of the nanotube and the dimension of the simulation cell along the tube were optimized to obtain the minimum energy Fig.1 DNA and SWCNT interactions. White structure. After heating the system to 300K by dotted surface represents HOMO-7 repeated velocity rescaling, a 1 ps molecular orbital localized on cytosine microcanonical trajectory was run in the nuclease. ground electronic state with a 1 fs time step. The HOMO-LUMO gap of the system was mainly determined by the electronic structure of the SWCNT and made up 1.13eV. Electronic bands localized solely on the SWCNT as well as the bands localized on the particular nucleobases (Fig.1) were observed. The preliminary results suggest that nucleobases of different nature (cytosine or guanine) and in different positions of the DNA sequence can be distinguished in SWCNT-DNA system. 90 Conference on Current Trends in Computational Chemistry 2008 The Analysis of Textures of Mesophases of Liquid Crystals by Fractal Structural Descriptors N.A. Kovdienko, L.N. Ognichenko, A.G. Artemenko, E.N. Muratov, N.S. Novikova, V.E. Kuz’min, and H.Novohatskaya Laboratory of Theoretical Chemistry, Department of Molecular Structure, A.V. Bogatsky Physical- Chemical Institute National Academy of Sciences of Ukraine, Odessa, Ukraine The analysis of structure-mesomorphic properties is an important and actual task. The results of such analysis could be used for the design of novel materials of liquid-crystal nature. Unfortunately, traditional QSPR approaches are not effective enough for the solution of such problems. The structure of individual molecules is analyzed in these methods, however mesomorphic properties are purely collective. Thus, the necessity of theoretical analysis of supramolecular structure becomes evident. Actually it is talked about investigation of graphical images of textures, surfaces, shears, etc which reflected the structure (supramolecular structure) of nanomaterials investigated. The set of quantitative indices reflecting individuality of investigated structures is required for characterization of nano-objects of interest. Actually such parameters are supramolecular structural descriptors. Mentioned descriptors could be used for the solution of structure – properties of liquid-crystal nanosystems problems. On the other hand it's possible to study relationship between structure of individual molecule and supramolecular structure of nanosystem. Such double-step analysis of relations molecular structure – supramolecular structure and supramolecular structure – properties of nanosystem will allow solving of all necessary tasks for the creation of novel nanosystems (liquid-crystal nanomaterials) and prediction of their properties. Obtained sets of supramolecular descriptors will be used for the solution of structure – properties of nanosystem problems. Mentioned tasks will be solved by two stages: 1. Supramolecular structure of nanosystem – its properties relationship analysis. Creation of the training set of nanosystems, generation of theirs nanostructure images. Calculation of supramolecular descriptors. Selection of supramolecular descriptors determining investigated properties. Development of the ensemble of PLS QSPR models. Validation of obtained models and estimation of their competence. 2. Molecular Structure – Supramolecular Structure of nanosystem Relationship analysis (QMSSSR). Simplex descriptors generation for training set compounds. Development of multiple PLS QMSSSR models for supramolecular descriptors selected on stage 1. Verification of QMSSSR models and estimation of their applicability domain. Thus, two sets of models (QSPR и QMSSSR) will allow ones to choose molecular and supramolecular structural descriptors of potential nanomaterials which are determining for their properties. These models will also useful for virtual screening and design of new nanosystems with desired properties. In the given work the database of liquid-crystal compounds which create cholesteric (Figure 1a), nematic (Figure 1b) and smectic (Figure 1c) mesophases has been gathered from literature [1-4]. It consists of 138 images of mesophases textures. The usage of fractal [5] and multifractal Conference on Current Trends in Computational Chemistry 2008 91 [6] descriptors of these images allow generation of quite adequate classification QSPR models applicable for prediction of type of mesophase by its image with 25-30% error for test set. QMSSSR analysis is planned on the next stage of the given work. a) b) c) Figure 1. Texture examples for a) cholesteric b) nematic and c) smectic liquid crystal mesophases References V. Novotna., M. Kasˇpar, V. Hamplova., M. Glogarova.,L. Lejcˇek, J. Kroupaa and D. Pociecha. J. Mater. Chem., 2006, 16, 2031–2038. R. Amaranatha and C. Tschierske. J. Mater. Chem., 2006, 16, 907–961 G. Pelzl, H. N. S. Murthy, Martin W. Schröder, S. Diele, Z.Vakhovskaya, H.Kresse and W. Weissflog . J. Mater. Chem., 2006, 16, 1702–1708 92 Conference on Current Trends in Computational Chemistry 2008 C.V. Yelamaggad, M. Mathews, S. A. Nagamani, D. S. S. Rao, S. K. Prasad, S. Findeisen and W. Weissflog. J. Mater. Chem., 2007, 17, 284–298 Kuz’min V.E., Kovdienko N.A. (1999) "Generating of structural parameters of molecules on a base fractal models". Dopovidi NAN Ukraini. № 8. 129-134. Artemenko A.G., Kovdienko N.A., Kuz’min V.E., Kamalov G.L., Lozitskaya R.N., Fedchuk A.S., Lozitsky V.P., Dyachenko N.S., Nosach L.N. (2002) "The analisys of “structure – anticancer activity” relationships in a set of macrocyclic pyridinophanes and their acyclic on the basis of lattice model of molecule using fractal parameters". Experim. Oncology. 24, 123-127. The SPSS AnswerTree 3.0 trial version program from http://www.spss.com L. Breiman, J.H. Friedman, R.A. Olshen, and C.T. Stone, Classification and Regression Trees, Wadsworth & Brooks/Cole Advanced Books & Software, Pacific Grove, CA, 1984. Conference on Current Trends in Computational Chemistry 2008 93 A Tetra-pirrolic Iron Molecular Biosensor to Detect Gas Pollutants Carlos Kubli-Garfias1†, Karim Salazar-Salinas1, and Jorge M. Seminario1,2 1Department of Chemical Engineering, 2Department of Electrical and Computer Engineering, Texas A&M University College Station, Texas, USA Pollution by dangerous gases is a common problem in public health. Among them, carbon monoxide (CO) and nitric oxide (NO) are associated to acid rain in large amounts [1, 2]. Therefore, detecting those substances to prevent their deleterious effect is an urgent task. The present work proposes a biosensor model based on the porphyrin nucleus of the soluble guanylate cyclase enzyme [3]. The model is tested with NO and CO as well as with molecular oxygen (O2) for comparison. Geometries, electronic structure, and second derivatives of the model are performed using density functional theory. Vibrational circular dichroism (VCD), infrared, and Raman spectra are obtained for the five-coordinated (5C) iron complex and for the six-coordinated complexes with gas moieties (6C). The sensor is capable of detecting the ligands to different extents. Figure 1 shows the frontier molecular orbitals when the moieties CO, NO and O2 are coordinated with the Fe porphyrin-histidine complex. Gold electrodes are used to approach the complex and to get the current-voltage electron transport characteristics using a modern theoretical procedure, GENIP as well as other experimental techniques [4-6]. a b c Fig 1. Energies of frontier orbitals of the ferrous porphyrin histidine complex with a) CO, b) NO and c) O2. HOMO (H) and LUMO (L) are expressed in electron volts. Level of theory, B3PW91 and basis set: 6-31G* for C, N, O, H and S; LANL2DZ for Fe and Au. The detection and sensing is based on the current-voltage and spectroscopic data. The conductance permits to distinguish between the iron 5C and 6C complexes, and VCD spectra show that CO is less detectable than NO due to the geometry of this gas in the sensor. Thus, CO is aligned with the iron atom, while NO and O2 bend with an angle detectable by VCD. It is 94 Conference on Current Trends in Computational Chemistry 2008 concluded that pollutants may be detected and measured successfully with the proposed biosensor. Acknowledgments We acknowledge financial support from the US Army Research Office and the US Defense Threat Reduction Agency (DTRA). References [1] B. Weinberger, D. L. Laskin, D. E. Heck, and J. D. Laskin, "The Toxicology of Inhaled Nitric Oxide," Toxilogical Sciences, vol. 59, p. 12, 2001. [2] D. A. Wink and J. B. Mitchell, "Nitric Oxide in Cancer Biology and Treatment," Free Radical Biology & Medicine, vol. 34, p. 4, 2003. [3] T. L. Poulos, "Soluble guanylate cyclase," Current Opinion in Structural Biology, vol. 2006, pp. 736-743, 2006. [4] J. M. Seminario, L. Yan, and Y. Ma, "Transmission of Vibronic Signals in Molecular Circuits," J. Phys. Chem. A, vol. 109, pp. 9712-9715, 2005. [5] J. He, H. Chen, A. K. Flatt, J. J. Stephenson, C. D. Doyle, and J. M. Tour, "Metal-Free Silicon-Molecule-Nanotube Testbed and Memory Device," Chem. Mater., vol. 17, pp. 4832- 4836, 2005. [6] M. F. Garcia-Parajo, J. Hernando, G. S. Monteiro, J. P. Hoogenboom, E. M. P. v. Dijk, and N. F. v. Hulst, "Energy Transfer in Single-Molecule Photonic Wires," ChemPhysChem, vol. 6, pp. 819-827, 2005. †Permanent address: Instituto de Investigaciones Biomédicas UNAM, México City. MEXICO. Conference on Current Trends in Computational Chemistry 2008 95 Hydrogen Bonded Complexes of Pyridoxale-5'-phosphate Derivatives with Water Molecules G.M. Kuramshinaa, S.A. Sharapovab,D.A. Sharapovb, Yu.A. Pentina aFaculty of Chemistry, bFaculty of Physics Moscow State University (M.V.Lomonosov), Moscow 119992, Russia Pyridoxal-5’-phosphate (PLP) and its derivatives (Vitamin 6 analogs) are very important biological systems and play the breakthrough role in the biological processes where they act as coenzymes catalyzing different reactions involved in the metabolism of amino acids. The hydrated media performs the special interest and it induced us to carry out the DFT investigations of more complex PLP derivatives including complexes of pyridoxale-5'-phosphate methylamine Shiff base with water molecules. The special attention to the hydration is explained by the importance of the surrounding water influence on the biological functions of the B6 derivatives. To simulate theoretically the hydration effects we use the modeling of the solvated compound by a complexation of the more stable isomer I with water molecules. Earlier the results of theoretical simulation of IR spectra of 1:1 and 1:2 complexes of I pyridoxale-5'-phosphate methylamine with water molecules were presented and conclusion was made that the hydration exerts influence both on structure and vibrational spectra of investigated systems. In the present investigation we turn next to the more complicated clusters of PLP and pyridoxal-5’-phosphate methylamine molecules with three and four water molecules. The IR and Raman spectra of pyridoxal-5’-phosphate methylamine Schiff base were investigated and interpreted on a base of DFT calculations [1]. It was proved that the enol-form (I) with skewed orientation of the phosphate group (Fig.1) is the most stable and preferred configuration from the total number of 30 possible conformers of pyridoxal-5’-phosphate methylamine in the gaseous form. The DFT calculations were performed with the program Gaussian 03 (Revision C.02) package. The fully optimized geometries for different configurations of enol-I – water complexes were calculated with 6-31G*, 6-31+G* and 6-31+G** basis sets and the B3LYP functional. The B3LYP/6-31+G** optimized structures of two complexes (II and III) with three water molecules and of one with four water molecules (IV) are presented in Fig.1 in comparison with structure of the enol-form . 96 Conference on Current Trends in Computational Chemistry 2008 a b c d Figure 1. Optimized B3LYP/6-31+G** structures of the enol form of pyridoxale-5'-phosphate methylamine (a) and of 1:3 (b and c) and 1:4 (d) complexes (bond lengths are in Å). The results on simulated with Lorentzian approximation (using B3LYP/6-31+G** frequencies and IR intensities) IR spectra of two different 1:3 (II) and one of 1:4 (III) systems are presented in Fig. 2. Theoretical IR spectra of complexes were compared to the experimental spectrum (see the embedded part in Fig. 1d). Conference on Current Trends in Computational Chemistry 2008 97 Figure 2. Theoretical B3LYP/6-31+G** spectra of pyridoxale-5’-phosphate methylamine (a) and its 1:3 (b, c) and 1:4 (d) complexes with water molecules. Imbedded in d is the experimental IR spectrum from [1]. Results of calculations show that the hydration has an influence both on structure and vibrational spectra especially in the CH-stretching and OH-stretching regions. E.g. one of remarkable changes is the significant lengthening up to 1.022 Å of the enol O-H bond in the complex with four H2O molecules in comparison with 1.001 Å in the pyridoxale-5’-phosphate methylamine molecule. This lengthening is accompanied by the shift of the enol OH-stretching from 3105 cm-1 in spectrum of PLP to 2730 cm-1 in the IR spectrum of 1:4 complex. In the high frequency region we should observe the additional bands due to the new OH- stretchings and results of calculations well correspond to all assumptions. Also very important changes are observed in the mid IR region which are connected mainly with the strong band intensities redistribution. On a base of calculations of a series of hydrogen bonded complexes of pyridoxale-5'-phosphate methylamine with water molecules on can observe that the increasing number of water molecules in surrounding of the PLP molecule leads to the better reproduction 98 Conference on Current Trends in Computational Chemistry 2008 of experimental IR spectrum of solid compound. Further inclusion of additional water molecules in the solvating surrounding should result in more adequate description of experimental data. The detailed assignment of vibrational spectra of the considered complexes was carried out with the software package SPECTRUM [2]. It was used for transformation of quantum mechanical Cartesian force constants to the matrix in redundant internal coordinates and for normal coordinate analysis and calculating potential energy distribution of II-IV. Acknowledgement This work was supported by the Russian Foundation for Basic Researches (Grant No 08-03-00415-a) References 1. G.M.Kuramshina, H.Takahashi. J. Mol. Struct., vol. 735-736, pp. 39-51, 2005. 2. A.G. Yagola, I.V. Kochikov, G.M. Kuramshina, Yu.A. Pentin. Inverse Problems of Vibrational Spectroscopy. VSP Scientific Publishers: Zeist, 1999. Conference on Current Trends in Computational Chemistry 2008 99 Toxicity of Benzene and its Derivatives toward Mammals: Development and Applications of QSAR Models Hrvoje Kušić1,2, Bakhtiyor Rasulev3, Danuta Lesczynska1,*, Jerzy Leszczynski3, Natalija Koprivanac2 1Civil and Environmental Engineering Department, Jackson State University, J.R. Lynch Street 1400, Jackson, Mississippi 39217, USA; 2Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia; 3Computational Center for Molecular Structure and Interactions, Jackson State University, J.R. Lynch Street 1400, Jackson, Mississippi 39217, USA The goal of the study was to develop reliable models that could be used for prediction of toxicity (in vivo) of varied aromatic compounds toward mammals. Compounds used as training, and test groups were derivatives of benzene (single benzene ring with different substitute groups such as hydroxyl-, nitro-, amino-, methyl-, methoxy-, etc,). A Genetic Algorithm and multiple regression analysis were applied to select the descriptors and to generate the correlation models. Evaluation of models was performed by calculating and comparing their model performances (r, R2, s, F, Q2) after splitting set of organic compounds to training and test sets. As the most predictive model is shown the 3-variable model having also a good ratio of the number of descriptors and their predictive ability to avoid overfitting. The main contribution to the toxicity showed MATS2p and C-026 descriptors, belonging to 2D autocorrelation and atom-centered fragments descriptors, respectively. The GA- MLRA approach showed good results in this study, which allows building simple, interpretable and transparent models that could be used for future studies of predicting toxicity of organic compounds to mammals. Acknowledgement: This work was supported by contracts # W912HZ-06-C-0057 and # W912HZ-06-C-096 funded by the DOD through US Army Engineer Research and Development Center, Vicksburg, MS 100 Conference on Current Trends in Computational Chemistry 2008 Hydrogen Generation Mechanism from Lithium Hydride + Ammonia Borane: An ab initio Study Tae Bum Lee and Michael L. McKee Department of Chemistry & Biochemistry, Auburn University, Auburn, Alabama 36849 Ammonia borane, BH3NH3, has received significant attention as a promising hydrogen storage material due to its high content of hydrogen, 12wt%. However, the activation barrier and kinetics for releasing hydrogen is still a bottleneck preventing practical applications. Here, we are motivated by some recent studies on the catalytic effect of LiH for hydrogen generation in BH3NH3. The stepwise mechanism and kinetics in the LiH/BH3NH3 system is studied at the CCSD(T)/6-311++G(3d,2p)// MP2/6-311++G(2d,p) level. Addition of LiH lowers the activation barriers compared with pure BH3NH3. Our stepwise mechanism coincides well with the experimental observations that show a gradual increase of hydrogen generation over time. Figure 1. Potential energy surface for the reaction of LiH + BH3NH3. Free energies (kcal/mol) are relative to LiH + BH3NH3 at 298.15 K Conference on Current Trends in Computational Chemistry 2008 101 Quantum Monte Carlo for Molecular Systems William A. Lester, Jr. Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720-1460 andChemical Sciences Division, Lawrence Berkeley National Laboratory,Berkeley, CA 94720 The quantum Monte Carlo method has become recognized for its capability of describing the electronic structure of atomic, molecular and condensed matter systems to high accuracy. This talk will summarize the approach and present recent developments connected with trial function construction and extension of the approach to a QM/MM (quantum mechanics/molecular mechanics) formulation for the inclusion of solvent. This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, Chemical Sciences Division of the U.S. Department of Energy under Contract No. DE- AC03-76SF00098, and by the CREST Program of the U. S. National Science Foundation. The calculations were carried out at the U. S. National Energy Research Supercomputer Center (NERSC). 102 Conference on Current Trends in Computational Chemistry 2008 Supramolecular Interactions of Fullerenes with (Cl)Fe− and Mn Porphyrins. A Theoretical Study Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang Department of Chemistry, P.O. Box 17910, Jackson State University, Jackson, MS 39217 The electronic structure and bonding in the noncovalent, supramolecular complexes of fullerenes (C60, C70) with (Cl)Fe− and Mn porphyrins [(Cl)FeP, MnP] were investigated in detail with DFT methods. A dispersion correction was made for the fullerene−porphyrin binding energy through an empirical method (J. Comput. Chem. 2004, 25, 1463). Several density functionals were employed in the calculations. The ground state of (Cl)FeP⋅C60 is predicted to be high spin (S = 5/2), in agreement with the experimental results which indicated that the electronic state of (Cl)FeP in the supramolecular complex is little perturbed by the coordination with the fullerene. MnP⋅C70 is calculated to have a high-spin (S = 5/2) ground state as well; this is similar to (Cl)FeP⋅C60, but at variance with the assignment of a low-spin (S = 1/2) state for this complex. According the calculations, C70 in MnP⋅C70 does not have sufficient ligand field strength to cause a high- to low-spin state change in MnP. More detailed experimental investigations are desirable, which might help to resolve the question of the MnP⋅C70 electronic structure. The estimated dispersion energies (Edisp) in the fullerene−porphyrin systems are rather large, ranging from 0.6 to 1.0 eV. Edisp improves the calculated binding energy considerably. (Cl)FeP⋅C60 MnP⋅C70 MnP⋅C70 High spin (S = 5/2) Low spin (S = 1/2) High spin (S = 5/2) Figure 1. Optimized molecular structures of (Cl)FeP⋅C60 and MnP⋅C70. Conference on Current Trends in Computational Chemistry 2008 103 Hydrogen Bonding in Complexes of Isocyanato or Isothiocyanato Compounds with Alcohols or Thiols Nannan Lin and David H. Magers Computational Chemistry Group, Mississippi College Isocyanato and isothiocyanato compounds have been of interest lately in photoinitialized polymerization studies. In the current study we build upon that interest by investigating the relative binding energies arising from hydrogen bonds formed in complexes of isocyanato or isothiocyanato compounds with alcohols or thiols. Specifically, the following systems are investigated: 2-isocyanato-propane (Figure 1.) and methanol, 2-isocyanato-propane and methanethiol, 2-isothiocyanato-propane (Figure 2.) and methanol, and 2-isothiocyanato-propane and methanethiol. Then the methyl groups in the alcohols and the thiols are replaced with ethyl and propyl groups to determine if the length of the carbon chain has any effect on the relative energetics of these systems. Energies for these systems are computed at the levels of SCF and DFT. The density functional used initially is Becke’s three-parameter hybrid functional using the LYP correlation functional. However, other functionals will be employed to investigate how different functionals behave in these extended systems. Correlation-consistent basis sets are employed and the basis-set-superposition errors are computed with the Counterpoise method. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. O C N Figure 1. 2-isocyanato-propane S C N Figure 2. 2-isothiocyanato-propane 104 Conference on Current Trends in Computational Chemistry 2008 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and silicon C. Davis Lofton, Crystal B. Coghlan, and David H. Magers Computational Chemistry Group, Mississippi College The conventional strain energies for three- and four-membered heterocycles of carbon and silicon are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include silacyclopropane, disilacyclopropane, silacyclobutane, 1,2-disilacyclobutane, 1,3- disilacyclobutane, and trisilacyclobutane. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth- order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Cross-sections of the electron density in the plane of the ring for each of the three- membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems. Results indicate that silicon substitution reduces the conventional strain energy of cyclobutane, but increases the conventional strain energy in cyclopropane by destroying the stabilizing factor of sigma delocalization. Electron-density plots show that only in cyclopropane is the electron density thoroughly delocalized in the sigma bonds of the ring. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. Conference on Current Trends in Computational Chemistry 2008 105 Are Conventional Strain Energies in Bicyclic Alkanes Additive? Andrew K. Magers, D. Brandon Magers, and David H. Magers Computational Chemistry Group, Mississippi College Conventional strain energies are computed for bicyclo[1.1.0]butane (Figure 1.), spiro[2.2]pentane (Figure 2.), bicyclo[2.1.0]pentane (Figure 3.), bicyclo[2.2.0]hexane (Figure 4.), spiro[2.3]hexane (Figure 5.), and spiro[3.3]heptane (Figure 6.) within the isodesmic, homodesmotic, and hyperhomodesmotic models. In addition, the conventional strain for the individual rings in each bicyclic system is computed with different hyperhomodesmotic equations to see if conventional strain energies might be additive. The electronic energies and corresponding zero-point-energy corrections are computed for all relevant molecular systems at the levels of self-consistent field theory, density functional theory, and second-order perturbation with both the cc-pVDZ and cc-pVTZ basis sets. The density functional employed is the common B3LYP hybrid functional. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. Figure 1. bicyclo[1.1.0]butane Figure 2. spiro[2.2]pentane Figure 3. bicyclo[2.1.0]pentane Figure 4. bicyclo[2.2.0]hexane Figure 5. spiro[2.3]hexane Figure 6. spiro[3.3]heptane 106 Conference on Current Trends in Computational Chemistry 2008 Are Conventional Strain Energies in Bicyclic Alkenes Additive? D. Brandon Magers and David H. Magers Computational Chemistry Group, Mississippi College Conventional strain energies are computed for spiro[2.2]pent-1-ene (Figure 1.), spiro[2.2]penta-1,4-diene (Figure 2.), bicyclo[2.1.0]pent-2-ene (Figure 3.), spiro[2.3]hex-1-ene (Figure 4.), spiro[2.3]hex-4-ene (Figure 5.), spiro[2.3]hexa-1,4-diene (Figure 6.), bicyclo[2.2.0]hex-2-ene (Figure 7.), bicyclo[2.2.0]hexa-2,5-diene (Figure 8.), spiro[3.3]hept-1- ene (Figure 9.), and spiro[3.3]hepta-1,5-diene (Figure 10.) within the isodesmic, homodesmotic, and hyperhomodesmotic models. In addition, the conventional strain for the individual rings in each bicyclic system is computed with different hyperhomodesmotic equations to see if conventional strain energies might be additive. The electronic energies and corresponding zero- point-energy corrections are computed for all relevant molecular systems at the levels of self- consistent field theory, density functional theory, and second-order perturbation with both the cc- pVDZ and cc-pVTZ basis sets. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. Figure 1. spiro[2.2]pent-1-ene Figure 2. spiro[2.2]penta-1,4-diene Figure 3. bicyclo[2.1.0]pent-2-ene Figure 4. spiro[2.3]hex-1-ene Figure 5. spiro[2.3]hex-4-ene Figure 6. spiro[2.3]hexa-1,4-diene Figure 7. bicyclo[2.2.0]hex-2-ene Figure 8. bicyclo[2.2.0]hexa-2,5-diene Figure 9. spiro[3.3]hept-1-ene Figure 10. spiro[3.3]hepta-1,5-diene Conference on Current Trends in Computational Chemistry 2008 107 Binding Energies in Dimers of N-methyl methyl carbamate, N-methyl S-methyl thiocarbamate, and N-methyl methyl dithiocarbamate Harley R. McAlexander and David H. Magers Computational Chemistry Group, Mississippi College Carbamates and thiocarbamates have been of interest lately in photoinitialized polymerization studies. In the current study we build upon that interest by investigating the relative binding energies in N-methyl methyl carbamate [Figure 1.], N-methyl S-methyl thiocarbamate [Figure 2.], and N-methyl methyl dithiocarbamate [Figure 3.]. Each dimer may be formed with one hydrogen bond or with two identical hydrogen bonds. In the dimmers with two hydrogen bonds, the hydrogen on the nitrogen of each monomer forms a hydrogen bond to either the oxygen of the carbonyl or the sulfur of the thiocarbonyl of the other monomer. Energies for the monomers and the dimmers are computed at the levels of SCF and DFT. The density functional used is the common B3LYP hybrid functional. Correlation-consistent basis sets are employed and the basis-set-superposition errors are computed with the Counterpoise method. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. O O O N S N H H Figure 1. N-methyl methyl carbamate Figure 2. N-methyl S-methyl thiocarbamate S S N H Figure 3. N-methyl methyl dithiocarbamate 108 Conference on Current Trends in Computational Chemistry 2008 Using computational Approaches for the Understanding, Design, and Predictions at the Nanoscale Vincent Meunier Oak Ridge National Laboratory A major role of fundamental research is to investigate how a new material can be employed most efficiently for practical applications. This is particularly important for nanoscience and energy applications since any new technology must display significant benefits and advantages over conventional approaches. As the size of practical systems is shrinking, unexpected physics emerges and new opportunities appear. At the same time, there is an unprecedented availability of computational resources, in terms of scalability and speed. The result is that the field is now rapidly approaching the point where typical length scales of systems investigated experimentally are becoming similar to the ones that can be treated accurately on state-of-the-art computers. It follows that computational sciences are evolving more and more in their role as science enabler and guide for development of new understanding in nanoscience. In this talk, I will expose a few examples where we used computational approaches successfully (1) to uncover the mechanisms associated with experimentally observed phenomena and (2) design new systems on the computer for subsequent experimental realizations. Conference on Current Trends in Computational Chemistry 2008 109 Computational Predictions of Partitioning Coefficients Values A. Michalkova,a L. Gorb,b F. Hill,b Mo Qasim,b and J. Leszczynskia aComputational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA; bU.S. Army Engineer Research and Development Center (ERDC), Vicksburg, MS 39180 Predicting and understanding properties and behavior of contaminants and the partitioning coefficient (KD) values is of great importance both from technological and academic points of view. The experimental measurement of KD is expensive, time consuming, and often hampered by considerable experimental error or noise. A literature search reveals that there have been neither QSPR nor quantum–chemical studies on the computational prediction of explosives log(KD) and their soil-water products of degradation. Therefore, a great need exists for reliable calculation methods that can be used to predict KD for explosives or to validate experimental data. The first part of work is devoted to the quantum-chemical study firstly of adsorption of selected polycyclic aromatic hydrocarbons (PAHs) and trinitrotoluene (TNT) on soot and TNT on clay minerals fragments and the energetics of such process. Second part of study is concentrated on quantum chemical predicting of logKd values. PAHs are chemical compounds that consist of fused aromatic rings and do not contain heteroatoms or carry substituents. As a pollutant, they are of concern because they have been identified as carcinogenic, mutagenic. An explosive material is a material that either is chemically or otherwise energetically unstable or produces a sudden expansion of the material. The most studied types of explosives are nitroaromatic explosives (NACs). They are widely used as pesticides, herbicides, solvents, and intermediates in the synthesis of dyes. The development of efficient technologies, which can expedite the cleanup of NAC-contaminants, is a high Department of Defense (DoD) priority and has received considerable public attention. TNT (C6H2(NO2)3CH3) is an NAC compound best known as a part of explosive mixtures for military and industrial applications. Clays are layered aluminosilicates showing a large variety of important physicochemical properties: sorption ability, catalytic properties and surface acidity. The minerals of the kaolinite group can adsorb polar organic molecules relatively easily. Dickite is a typical representative of minerals of the kaolinite group with a dioctahedral 1:1 layer structure consisting of an octahedral aluminum hydroxide sheet and a tetrahedral silica sheet with the ideal chemical formula Al2Si2O5(OH)4. Soot is a general term that refers to the black, impure carbon particles resulting from the incomplete combustion of a hydrocarbon (coal, oil, wood, or other fuels). Some soots have been used for many years as common pigments used in paints and inks. The interactions of PAHs and TNT with soot and clay mineral (see Figure below) have been studied applying the density functional theory (DFT) in conjunction with the M05-2X functional and 6-31+G(d,p) basis set. The studied complexes were fully optimized. The soot was modeled by a single coronene (C24H12) molecule. The models of clay mineral were simulated by representative cluster model of the tetrahedral sheet of dickite that contains three tetrahedral rings containg the silicon central cation. The structure of adsorbed complexes and their interaction energy has been calculated. These calculations will yield thermodynamic parameters related to adsorption: ΔHads ΔSads ΔGads. The hydration was taken into account by using the PCM method. 110 Conference on Current Trends in Computational Chemistry 2008 A B Figure. Initial structure of TNT adsorbed on cluster model of soot (A) and clay mineral (B). Conference on Current Trends in Computational Chemistry 2008 111 The Effects of Ionic Strength and pH on the Thermal Stabilities of DNA Aptamers Brandon Mitchell, G. Reid Bishop, and David H. Magers Computational Chemistry Group, Mississippi College The effects of ionic strength and pH on the thermal stabilities of three structurally distinct deoxyribonucleic acid (DNA) aptamers were examined. Each aptamer is related by its binding activity to derivatives of the amino acid arginine and by virtue of a general stem-loop secondary structure. However, each aptamer has a unique sequence which influences their absolute folded structure. DNA aptamers are deoxyoligonucleotides that are selected from random sequence libraries for their binding affinity to a target molecule (ligand). The aptamer under investigation is 1OLD (24mer, 7.84 kDa) binds to derivatives of L-Arg. Each was studied by optical UV spectroscopic methods to determine their van=t Hoff thermal stability properties in a variety of different ionic solution conditions. We hypothesized that each of these aptamers adopt a stem-loop structure at low ionic strengths but convert to a more stable stem-loop-bulge structure at higher ionic strengths. To test this hypothesis series of thermal denaturation experiments were carried out on both the native forms of each aptamer as well as selected sequence mutants. In addition, both the stem-loop structures and the stem-loop-bulge structures are computed using molecular mechanics to determine approximate relative energies. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. 112 Conference on Current Trends in Computational Chemistry 2008 Conventional Strain Energy in Boracycloproane, Diboracyclopropane, Boracyclobutane and Diboracyclobutane Elizabeth Mobley, Brandon Magers, Harley McAlexander, and David H. Magers Computational Chemistry Group, Mississippi College The conventional strain energies for boracyclopropane (Figure 1.), diboracyclopropane (Figure 2.), boracyclobutane (Figure 3.), 1,2-diboracyclobutane (Figure 4.), and 1,3- diboracyclobutane (Figure 5.) are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Results are compared to the conventional strain energies of cyclopropane and cyclobutane to determine what effect boron substitution has on the conventional strain energies of these prototypical homocycles. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. H B HB HB Figure 1. Boracyclopropane Figure 2. Diboracyclopropane BH HB BH Figure 3. Boracyclobutane Figure 4. 1,2-Diboracyclobutane HB BH Figure 5. 1,3-Diboracyclobutane Conference on Current Trends in Computational Chemistry 2008 113 Hydration of Urea and Trimethylamine-N-oxide Katherine Munroe, J. Chase Burns, and David H. Magers Computational Chemistry Group, Mississippi College Both urea and trimethylamine-N-oxide (TMAO) (Figure 1.) are small molecules with large dipole moments, and both are easily dissolved in water. Urea is commonly used to denature biological macromolecules such as proteins and DNA. In contrast, TMAO is known to induce structure in these same molecules. Each of these small polar molecules is thought to interact differentially with water. Water also plays a role in stabilizing macromolecular structure. In the current study results are presented investigating the theoretical water binding properties of urea and TMAO to understand their differential activities. Specifically, the binding energies of both systems with three and with six water molecules are investigated, and the free energy of solvation for each system is computed using a polarizable continuum model. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies for all complexes are computed using SCF theory and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. Figure 1. trimethylamine-N-oxide 114 Conference on Current Trends in Computational Chemistry 2008 Reaction Force Analysis of the Effect of the Solvent Chloroform on the Markovnikov and Anti-Markovnikov Addition Reactions of HCl + Propene Jane S. Murray,1,2 Jaroslav V. Burda,3 Alejandro Toro-Labbé,4 Soledad Gutiérrez- Oliva,4 and Peter Politzer1,2 1Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA; 2Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA; 3Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 112 16 Prague, Czech Republic; 4Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile The reaction force F(R) of a chemical or physical process is given by the negative derivative of the potential energy V(R) along an appropriate reaction coordinate R. The maxima, minima and zeroes of F(R) divide the process, naturally and unambiguously, into well- defined stages. In particular, an activation barrier is found to be composed of two components, one of which reflects preparative structural factors while the other corresponds to the first part of the transition to products. By computing the magnitudes of these contributions both in the presence and absence of an external agent, such as a solvent or a catalyst, it is possible to determine whether the effect of that agent is primarily upon early structural changes or upon the transition portion of the activation barrier. In this poster is presented an analysis of the effects of the solvent chloroform upon both the Marknovikov and anti-Markovnikov addition reactions of HCl + propene. Conference on Current Trends in Computational Chemistry 2008 115 Structure and Geometry of Isomers of Nano N20 Clusters Jamshid Najafpour*, Farrokh Roya Nikmaram, Maryam Kordi Peykani Department of Chemistry, Faculty of science, Islamic Azad University Shahr-e-Rey Branch, Tehran, P.O. Box: 18735/334, Iran, Email: [email protected] Among the high-energy density materials, nitrogen clusters have been the subject of intense interest in the past 20 years [1–20]. In these investigations, the studies of stability and bonding have received great attentions. There has been a continuing interest in the homopolyatomic nitrogen compounds (Nn), in part due to their curiosity molecular shape and properties. Until recently, known stable polynitrogen species were rather rare consisting only of molecular nitrogen (N2), isolated in 1772 − by Rutherford, Scheele and Cavendish [21], and azide anion ( N3 ), first synthesized in 1890 by Curtius [22]. Other nitrogen compounds, being much less thermodynamically stable than N2 with its very strong N–N triple bond, tend to decompose into N2 fragments. The short-lived transient + N3 radical and the N3 cation have also been detected and spectroscopically characterized [23]. Quite recently, Christie and coworkers [24] reported a surprisingly simple preparation and + − characterization of the salt [ N5 ][As F6 ], which contains the third stable member of the + polynitrogen family, N5 . It has been predicted that the ground state of pentanitrogen cation has an open V-form (C2v) and is a singlet state [24]. Since large polynitrogen molecules are likely to be unstable with respect to decomposition to N2 relevant experimental studies are more numerous than by theoretical investigations. Calculations have suggested that both the N4 and N6 species have a clear preference for acyclic forms, the former having an open triplet structure [25] and the latter a singlet diazide form (N3–N3) [2,26,27]. Regarding the N8 species, although theoretical calculations [2,28–30] pointed out that azidopentazole [N3–N5] is the lowest energy species and is stable with respect to fragmentation, it has not yet been observed experimentally. Theoretical studies have also been reported for the larger polynitrogens N7 [31], N10 [2], N12 [2], N18 [32] and N20 [33–37]. Semiempirical [33–35] as well as ab initio MO and DFT studies [36,37] of the N20 species previously reported considered only the cage form as a possible stable structure. In the next work, Ab initio MO method at HF and MP2 levels and DFT method with popular hybrid B3LYP functional in conjunction with 6-31G(d) and 6-31G+(d) basis sets are reported three isomers of N20 clusters [38]. They are the fullerene-type cage form of Ih symmetry, a corannulene-like bowl form of C5v symmetry, and a ring isomer with D5 symmetry of which the cage form turns out to be the highest energy form. It is shown that both methods provide a conclusive indication that the bowl and ring forms are more stable than the cage form by about 200 kcal/mol in contrast to the case of the C20 species where the relative stability is quite sensitive to the method employed in the quantum chemical studies In the present study, we report new quantum chemical calculations for two interesting N20 nitrogen clusters (Figure 1) by the density functional theory (DFT) with the exchange-correlation potential that constructed from Becke’s three parameter formula for exchange (B3) [39] along with the Lee-Yang-Parr parameterization for correlation (LYP) [40]. These calculations were performed within a valence double-z basis set augmented with both diffuse and polarization functions (aug-cc-pVDZ). This basis set was contracted as: (10s5p2d/4s3p2d) and used pure spherical harmonic (i.e. 5 d-type), one-particle Gaussian functions. Also atom in molecules (AIM) quantum theory were carried out to study the bonding of the nano N20 isomers (Figure 2 and Table 1). All ab initio calculations have been performed using 116 Conference on Current Trends in Computational Chemistry 2008 Spartan’06 [41] and WinGAMESS.08 [42] and QTAIM calculations have been done using AIM2000 package [43]. The total energies of two isomers for cage and bowl forms with B3LYP/aug-cc-pVDZ level have obtained -1093.564 a.u. and -1093.850 a.u. respectively. The thermodynamic stability order of the bowl form is more than the cage form by about 180 kcal/mol. cage form bowl form Figure 1. Optimized geometry of cage and bowl isomers at the N20 species at level of theory of B3LYP/aug-cc-pVDZ Figure 2. Critical points of bonds, rings and cage of the N20 isomers. (Red points are Bond Critical Points: BCPs; Yellow points are Ring Critical Points: RCPs; Green point is Cage Critical Point: CCP. The lines are Bond Paths: BPs.) The AIM analysis [44] for the optimized structures has been performed to obtain the 2 topological properties of the bonds, such as the Laplacian of ρb (∇ ρb ) at bond critical points, the bond critical points (BCP), ring critical points (RCP) and cage critical points (CCP) and also 2 the bond paths (BP). As is known, the ∇ ρb identifies whether the charge of the region is 2 2 locally depleted (∇ ρb > 0) or concentrated (∇ ρb < 0 ). The former is typically associated with interactions between closed-shell systems (ionic bonds, hydrogen bonds, and van der Waals molecules), whereas the latter characterizes shared interactions (covalent bonds), where the electron density concentrates in the internuclear region [45]. Obviously, the latter is required for 2 bond formation. So, the critical points with ∇ ρb < 0 are discussed in this work. The complete list of bond critical points of electron density (where ∇ρ = 0 ) and their mathematical characters have been gathered in table 1 for two N20 isomers. According to table 1, in all cases shared interactions exist between N-N atoms. In attention to Gillespie-Popelier discussion [46] and table 1, represent the following bondings natures: some of N-N bonded Conference on Current Trends in Computational Chemistry 2008 117 ∇2 ρ < 0 interactions in two isomers are shared non polar covalent ( b , equal atomic charge and ρ ∇2 ρ < 0 b order of 10-1 a.u.) and some of them are shared polar covalent ( b , different atomic ρ charge and b order of 10-1 a.u.). 2 Table 1. Bond lnghts (Å), ρb and ∇ ρb of the bonds in two N20 isomers at the B3LYP/aug-cc-pVDZ BCP’s Connected Bond 2 N isomers ρ ∇ ρ 20 number Atoms lenghts b b Cage 1 N-N 1.493 0.275 -0.105 N1-N2, N4-N5, N7-N8, Bowl 1 1.264 0.454 -0.262 N10-N11, N13-N14 N2-N3, N5-N6, N8-N9, 2 1.386 0.347 -0.171 N11-N12, N14-N15 N3-N4, N6-N7, N9-N10, 3 1.387 0.346 -0.171 N12-N13, N15-N1 N3-N17, N6-N18, N9-N19, 4 1.515 0.259 -0.085 N12-N20, N15-N16 N16-N17, N17-N18, N18-N19, 5 1.455 0.302 -0.134 N19-N20, N20-N16 References 1. W.J. Lauderdale, J.F. Stanton, R.J. Bartlett, J. Phys. Chem. 96 (1992) 1173. 2. M.N. Glukhovtsev, H. Jiao, P.v.R. Schleyer, Inorg. Chem. 35 (1996) 7124. 3. J.S. Wright, J. Am. Chem. Soc. 96 (1974) 4753. 4. S.A. Perera, J.R. Barrlett, Chem. Phys. Lett. 314 (1999) 381. 5. M.N. Glukhovtsev, P.v.R Schleyer, Chem. Phys. Lett. 198 (1992) 547. 6. T.M. Klapo¨tke, J. Mol. Struct. (THEOCHEM) 499 (2000) 99. 7. M.T. Nguyen, T.K. Ha, Chem. Phys. Lett. 335 (2001) 311. 8. A.M. Tian, F.J. Ding, L.F. Zhang, Y.M. Xie, H.F. Schaefer III, J. Phys. Chem. A 101 (1997) 1946. 9. L. Gagliardi, S. Evagelisti, B.O. Roos, P.O. Widmark, J. Mol. Struct. (THEOCHEM) 428 (1998). 10. L.J. Wang, Q.S. Li, J. Li, J. Comput. Chem. 22 (2001) 1334. 11. Q.S. Li, L.J. Wang, J. Phys. Chem. A 105 (2001) 1979. 12. T.M. Klapo¨tke, R.D. Harcourt, J. Mol. Struct. (THEOCHEM) 541 (2001) 237. 13. Y.M. Wang, K.C. Sun, C. Chen, Huaxue 54 (1996) 31. 14. C. Chen, K. Sun, S. Shyu, J. Mol. Struct. (THEOCHEM) 459 (1999) 113. 15. Y. Ren, X. Wang, N.B. Wong, A.M. Tian, F.J. Ding, L.F. Zhang, Int. J. Quant. Chem. 82 (2001) 4. 16. D.L. Strout, J. Phys. Chem. A 106 (2002) 816. 17. R. Ponec, J. Roithova, X. Girones, K. Jug, J. Mol. Struct. (THEOCHEM) 545 (2001) 255. 18. Y.D. Liu, P.G. Yiu, J. Guan, Q.S. Li, J. Mol. Struct. (THEOCHEM) 588 (2002) 37. 19. M.F. Cheng, H.O. Ho, C.S. Lam, W.K. Li, J. Serb. Chem. Soc. 67 (2002) 257. 20. M.T. Nguyen, L. Thanh, A.M. Mebel, R. Flammang, J. Phys. Chem. A 107 (2003) 5452. 21. N.N. Greenwood, A. Earmshaw, Chemistry by the Elements, Pergamon Press, Oxford, 1984. 22. T. Curtius, Ber. Dtsch. Chem. Ges. 23 (1890) 3023. 23. J.M. Dyke, N.B.H. Jonathan, A.E. Lewis, A. Moris, Mol. Phys. 47 (1982) 1231. 24. K.O. Christie, W.W. Wilson, J.A. Sheehy, J.A. Boatz, Angew. Chem. 111 (1999) 2112. 25. M.N. Glukhovtsev, P.V.R. Schleyer, Int. J. Quantum Chem. 46 (1993) 119. 26. T.K. Ha, M.T. Nguyen, Chem. Phys. Lett. 195 (1992) 179. 118 Conference on Current Trends in Computational Chemistry 2008 27. H. Huber, T.K. Ha, M.T. Nguyen, J. Mol. Struct. (Theochem) 105 (1983) 351. 28. M.T. Nguyen, T.K. Ha, Chem. Ber. 129 (1996) 1157. 29. R. Engelke, J.R. Stine, J. Phys. Chem. 94 (1990) 5689. 30. M.L. Leininger, C.D. Sherrill, H.F. Schaefer III, J. Phys. Chem. 99 (1995) 2324. 31. Q.S. Li, X. G. Hu, W.G. Xu, Chem. Phys. Lett. 287 (1998) 94. 32. J.D. Gu, K.X. Chen, H.L. Jiang, J.Z. Chen, R. Y. Ji, Y. Ren, A. M. Tian, J. Mol. Struct. (Theochem) 424 (1998) 183. 33. M. Shulman, R.J. Disch, J. Am. Chem. Soc. 100 (1978) 5677. 34. I. Alkorta, J. Elguero, I. Rozas, A.T. Balaban, J. Mol. Struct. 228 (1992) 47. 35. C. Chen, L.H. Lu, Y.W. Yang, J. Mol. Struct. (Theochem) 253 (1992) 1. 36. A.A. Blizuyuk, M. Shen, H.F. Schaefer III, Chem. Phys. Lett. 198 (1992) 249. 37. J.S. Wright, D.J. McKay, G.A. Dilabio, J. Mol. Struct. (Theochem) 424 (1998) 47. 38. T.K. Ha, O. Suleimenov and M.T. Nguyen, Chem. Phys. Lett. 315 (1999) 327. 39. A.D. Becke, J. Chem. Phys. 98 (1993) 5648. 40. C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785. 41. Spartan'06. B.J. Deppmeier, A.J. Driessen, T.S. Hehre, W.J. Hehre, J.A. Johnson, P.E. Klunzinger, J.M. Leonard, W.S. Ohlinger, I.N. Pham, W.J. Pietro, Jianguo Yu. Wavefunction, Inc., Irvine, CA 2006 42. M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A.Nguyen, S.J. Su, T.L. Windus together with M. Dupuis, J.A. Montgomery, j. comput. Chem. 14 (1993) 1347. F. Biegler-Kِnig, J. Schِnbohm, D. Bayles, AIM2000 - A Program to Analyze and Visualize Atoms in .43 Molecules, J. Comp. Chem., 22, (2001) 545. 44. R.F.W. Bader. Atoms in Molecules, A Quantum Theory; International Series of Monographs in Chemistry; Oxford University Press: Oxford, vol. 22, 1990. 45. P.L.A. Popelier, Atoms in Molecules, Prentice Hall, UMIST, 2000. 46. R.G. Gillespie, P.L.A. Popelier, Chemical Bonding and Molecular Geometry, New York, Oxford, 2001. Conference on Current Trends in Computational Chemistry 2008 119 Shape Dependent Nonlinear Optical Properties of Nanomaterials Adria Neely, Anant Kumar Singh, Jelani Griffin, Gopala Krishna Darbha, Uma Shanker Rai, and Paresh Chandra Ray Department of Chemistry, Jackson State University, Jackson, MS, USA Shape-controlled synthesis of metal nanostructures has opened many new possibilities to design ideal building blocks for future nanodevices. By solution-based method, three kinds of silver colloids, nanospheres, triangular nanoprism and nanorods, have been synthesized. First hyper-polarizabilities of silver nanostructures of various shapes were measured using hyper- Rayleigh scattering technique, and their shape-dependent properties were evaluated. We have shown the B is the smallest for the silver nanoparticle and nanoprisms exhibits highest Bs. We provide experimental evidence for higher multipolar contribution to NLO response for silver nanoprism as well as silver nanoparticles. The great differences of the B values for different shape Ag colloids confirmed that like electromagnetic enhancement, retardation effect and morphology effect play very important roles on NLO properties of silver nanomaterials. 120 Conference on Current Trends in Computational Chemistry 2008 Conformational Study of Oxacyclotridecan-2-one Eric A. Noe, Gurvinder Gill, and Diwakar M. Pawar Department of Chemistry, Jackson State University, Jackson, MS 39217-0510 Abstract. Low-temperature 13C NMR spectra of oxacyclotridecan-2-one showed the presence of two conformations, with populations of 55.5 and 45.5 % at -162.4 °C. Populations were estimated at the coalescence temperature by assuming that the free-energy difference is constant, and rate constants of 172.1 and 141.1 s-1 and free-energy barriers of 5.63 and 5.68 kcal/mol were obtained at -151.9 °C. In the proton NMR spectra, the CH2O hydrogen signal decoalesces into two peaks which are still exchange broadened at -155.9 °C. A search of conformational space was done using Allinger's MM4 molecular mechanics program, and the coordinates for 1a-1d, numbered in order of increasing strain energies, were used for ab initio calculations. From the free energies and chemical shifts calculated at the HF/6- 311G* level, populations of 55.5 and 45.5 % at -162.4 degrees were assigned to conformations 1b and 1a, respectively, These two conformations are similar to the [337] conformation of cyclotridecane, which is favored for this cycloalkane. This work was supported by NIH SCORE, grant no. S06GM-0084047, and NSF CREST, grant no. HRD-0318519. Conference on Current Trends in Computational Chemistry 2008 121 The Strange Case of the Cyclopropenyl Anion Brandice Nowell,1 Willard Collier,1 Pornpun Rattananakin,2 and Charles U. Pittman Jr.1 1Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 and 2Department of Chemistry, Maejo University, Chiang Mai, Thailand 50290 Organic chemistry textbooks often cite the cyclopropenyl anion as an example of a 4 π electron antiaromatic molecule. Recent reports have cited the cyclopropenyl anion as a failure of the nucleus independent chemical shifts (NICSs) criterion of aromaticity since NICSs appears to indicate the cyclopropenyl anion is in fact aromatic. Since the reliability of NICSs is crucial to our research interests in unique aromatic molecules, the question of the aromaticity/antiaromaticity of the cyclopropenyl anion must be answered. The first phase of our research compared the NICS scans of the cyclopropenyl anion, benzene, the cyclopropenyl cation, the cyclopentadienyl anion, cyclobutadiene, and the cyclopentadienyl cation calculated at the HF, B3LYP, and MP2 levels of theory using the 6-31+G(d,p) basis set. NICS scans were constructed by calculating the NICSs at the center of the ring and every 0.1 Å along a line perpendicular to the plane of the carbon ring, extending 3.5 Å both above and below the plane of the ring. The data, B3LYP/6-31+G(d,p) illustrated below, contradict the claim that the cycolopropenyl anion is aromatic according to the NICSs criterion as the NICSs behavior does not mirror the NICSs of the aromatic reference molecules benzene, the cyclopropenyl cation, and the cyclopentadienyl anion. B3LYP/6-31+G(d,p) NICS Scans 100.0 Cyclopropenyl anion 90.0 Cyclobutadiene 80.0 Cyclopentadienyl cation 70.0 Benzene Cyclopentadienyl anion 60.0 Cyclopropenyl cation 50.0 40.0 30.0 20.0 NICS Values 10.0 0.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 -10.0 -20.0 -30.0 -40.0 Distance from Center of the Molecule (Å) 122 Conference on Current Trends in Computational Chemistry 2008 The Quantum-Chemical Investigation of Diphenyl Chlorophosphate Aminolysis by Cage Amines S.I. Okovytyy,1,2 A.V. Tokar,1 G.V. Gryn’ova,1 L.I. Kasyan,1 J. Leszczynski2 1Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine and 2Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217, USA Phosphoryl transfers from phosphate monoesters and diesters are an important class of reaction that is involved in many aspects of chemistry and biochemistry ranging from organic synthesis through enzyme catalyzed reactions such as DNA replication and repair. Consequently, the theoretical and experimental research of nucleophilic substitution processes, which occur near the tetracoordinated phosphorus atom, has a great interest. In this work the potential energy surface of diphenyl chlorophosphate aminolysis by amines, which contain one of the following cage fragments – exo/endo-norbornyl, exo/endo-norbornenyl or 1-adamantyl have been investigated: R (CH2) n NHR CHNH2 CH2NH2 R=H, CH R=H (n=0-2), CH (n=0) 3 3 The calculations have been performed in gas phase and in solution (acetonitrile, ε=36,64) at CPCM/B3LYP/6-31G(d)//B3LYP/6-31G(d) level of theory. The solvation effects have been evaluated by single-point calculations, i.e. with unrelaxed gas-phase isolated reactants (I, II) and transition states (III) geometries. O R" O R' N P R'R''NH + ClP(O)(OC6H5)2 O H Cl R' - substituent with the cage fragment, R'' = H, CH Bond lenghts: 3 P-N 1.936-2.014 A P-Cl 2.470-2.529 A H-Cl 2.110-2.288 A I II III The results of calculations have shown the preferable front side attack of amino-group on phosphorus atom in comparison with corresponding back side approach. Some important regularities in correlation “structure – nucleophilic reactivity” for cage amines have been established. Thus, the entrance of withdrawing C=C-bond in norbornyl fragment as well as exo/endo-isomerism of starting amines don’t have any appreciable effects on calculated values of activation energy. On the contrary, the length of carbon chain (CH2)n between the cage fragment and amino-group as well as the presence of substituent R’’ near nitrogen atom have a great importance for activation barriers of aminolysis reaction: these values have become much more high with decrease of n and introduction of R’’= CH3-group. So, the obtained calculating data have demonstrated, that the major factor of cage amines nucleophilic reactivity is the sterical factor. Conference on Current Trends in Computational Chemistry 2008 123 Determination of internuclear distances in binary ionic crystals Valentin V. Oshchapovsky Lviv State University of Life Safety, P.O.Box 10676, Lvov, 79000, Ukraine E-mail: [email protected] On the basis of the mathematical theory of graphs the expression for calculation of binary ionic crystals lattice energy was received [1]. In this case a molecule (the formula unit of MeX crystal) was presented in the form of complete and finite graph. The method is founded on establishment of functional (matrix) interconnection between ions radii and U magnitudes of binary inorganic compounds of MX type, where M is metal; X is halogen, hydrogen. A new formula for calculation of crystalline lattice energy was obtained being based only on the magnitudes of ions radii without the additional insertion of arbitrary factors (parameters). Later the expression for calculation of Ulat ionic crystals lattice energy was refined and corrected: average error of theoretical determination of U for the crystals of alkali metal halides makes up 0.49% [2]. Additionally this formula was modified for multi-atomic systems as well [2]. The analysis of obtained formula for the calculation of lattice energy of ionic crystal has showed that there is a term that characterizes the radius value of the overlapping area of electron clouds of interconnected ions. On this basis the formulas are proposed for calculation of internuclear distances in molecules of different types in crystalline state. Average error of R12 calculation for the crystalline alkali metal halides (with the structural of NaCl type) makes 1.225 %. For the calculation of internuclear distances the Shannon’s system of ionic radii (in VI- coordination) was used [3]. The mentioned formula confirms an adequacy of molecular structure model of Stewart- Briegleb. [1] Oshchapovsky V.V. "Scientific Israel – technological advantages", 1999, Vol.1, No 2, pp.37- 40. [2] Oshchapovsky V.V. J. of General Chemistry, 2008, Vol. 78, No. 4, pp.549-559. (in Russian). [3] Shannon, R.D. Acta Crystallogr. 1976. A32. Part 5. pp. 751-767. 124 Conference on Current Trends in Computational Chemistry 2008 Molecular-to-nano-biomaterials: Understanding and Design by Computation R. Pachter Air Force Research Laboratory Materials & Manufacturing Directorate Wright-Patterson Air Force Base, Ohio 45433-7702 In this talk, we present a perspective on computational approaches for studying materials for applications of interest. First, to accurately predict the photophysical properties of molecular structures that exhibit multiphoton absorption, we applied density functional theory (DFT)/time- dependent DFT (TDDFT) for the calculation of one-photon absorption (OPA) and two-photon absorption (TPA) spectra for series of molecular chromophores of relevance, including biological chromophores. Validation of TDDFT regarding the functional to be used for molecules that exhibit charge-transfer characteristics, application of quadratic response for the calculation of TPA, and inclusion of solvent effects, will be discussed. Furthermore, photophysical properties of semiconductor quantum dots and functionalized metal nanoparticles will be assessed. In addition, for requirements in autonomous energy, aspects of the biocatalysis of hydrogen production in [Fe-Fe] hydrogenases by applying QM/MM simulations will be reported. Finally, we address structural aspects of nano-biostructures for sensing, in which biological moieties bind inorganic surfaces, and suggest design for multifunctionality. Conference on Current Trends in Computational Chemistry 2008 125 Enthalpies of Formation of Furan and Pyrrole Derivatives by Homodesmotic Reactions Yunfeng Pan, Alison Cochran, and David H. Magers Computational Chemistry Group, Mississippi College Furan is a heterocyclic aromatic compound that is highly volatile. Due to its aromaticity its chemistry is quite different from most heterocyclic ethers. A derivative, 2,5-dimethylfuran (Figure 1.) has been proposed as a possible biofuel. In the current study, we focus on the computation of the standard enthalpy of formation of 2,5-dimethylfuran and other furan and pyrrole derivatives by homodesmotic reactions. The enthalpy of all of the reactants and products in each homodesmotic equation is computed by various levels of theory and basis sets. From the resulting enthalpy of reaction, the desired enthalpy of formation is determined by use of reference values for all other systems in the reaction. When possible, more than one homodesmotic equation is used for a particular system to demonstrate the reliability of the method. We gratefully acknowledge support from the NSF (MRI-0321397) and from the Mississippi College Catalysts. O Figure 1. 2,5-dimethylfuran 126 Conference on Current Trends in Computational Chemistry 2008 Theoretical Investigations of the Structure and Bonding of Several Transition Metal Complexes to Probe their Carbon monoxide (CO) Releasing Properties Biswarup Pathak, D. Majumdar, Jerzy Leszczynski Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA The structural and bonding characteristics of several CO-releasing molecules (CORMs) have been investigated using state of the art density functional (DFT) theories. Based on the nature of the physiological buffer compositions used in experiments, several isodesmic reactions − 2− involving chloride (Cl ), hypophosphate (HPO4 ) and nitrosyl (NO) ligands are set up to find out whether the ligand substituted products, which could have direct influence in CO releasing mechanism, are thermodynamically feasible or not? The isodesmic equations involving the Cl− 2− and HPO4 ligands are exothermic whereas it is endothermic with the NO ligand. CO CO CO CO CO CO OCCl CO OC Mn Mn CO Ru Ru OC OC OC Cl CO CO CO CO CO Dimanganeses decacarbonyl Tricabonyldichloro ruthenium(II) dimer [Mn2(CO)10] [Ru(CO)3Cl2]2 CORM-1 CORM-2 CO OC NH Ru O OC O Cl Tricabonylchloro(glycinato)rruthenium(II) [Ru(CO)3Cl(glycinate)] CORM-3 Conference on Current Trends in Computational Chemistry 2008 127 Quantitative Structure – Activity Relationship Study of Organophosphorus Pesticides, Nerve Agents and their Derivatives Y. Paukku1, E.N. Muratov1,2, A.G. Artemenko2, N.A. Kovdienko2, V.E. Kuz’min1,2, and J. Leszczynski1 1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS; 2Laboratory of Theoretical Chemistry, Department of Molecular Structure, A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Odessa, Ukraine Organophosphorus compounds (phosphorus-containing organic chemicals) are often used as pesticides and warfare agents. These compounds exhibit their toxic behavior through the inhibition of acetylcholinesterase (AChE), an enzyme that normally relaxes the activity of acetylcholine, a neurotransmitter. Organophosphates cause behavioral and psychological changes in humans, which include irritability, nervousness, fatigue, insomnia, memory loss, impaired judgment, slurred speech, and depression. Many of them are acute toxins which irreversibly inhibit AChE. Therefore, current work is devoted to the investigation of structure – acute toxicity relationship for organophosphorus compounds, revealing of structural features responsible for toxic effect and development of new QSAR equations which will accurately predict toxicity for organophosphorus compounds. Therefore, the aim of this study is to find a relationship between structure and acute toxicity of organophosphates by application of quantum-chemical techniques and QSAR approach followed by subsequent validation of obtained results using broad spectrum of available experimentally determined data and the usage of QSAR models developed for virtual screening of toxicity for new compounds of interest. All toxicity data have been collected from literature sources. The following types of acute toxicity for organophosphorus compounds are considered in this study: - Oral Lethal Doses (LD50, mg/kg) values for rats. - Dermal Lethal Doses (LD50, mg/kg) values for rabbits. Many organophosphates are chiral, therefore (R) - and (S)-isomers are taken into account. Quantum-chemical calculations have been performed by density functional theory (DFT) at B3LYP level with conjunction of 6-311G (d, p) basis set for geometries optimization with further evaluation of electronic properties of target molecules. Acknowledgement: This work was facilitated by the support of the NSF EPSCoR (Experimental Program To Stimulate Competitive Research) grant #440900 362427-02. 128 Conference on Current Trends in Computational Chemistry 2008 Quantum-chemical Investigation of the Interaction of Organophosphorus Compounds with Zinc Oxide Surfaces Y. Paukku, A. Michalkova, and J. Leszczynski Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS Organophosphorus compounds (OPs), powerful inhibitors of the enzymes involved in nerve function, are widely used as insecticides as well as nerve agents. Due to their high toxicity there is a serious demand for more sophisticated and useful techniques for detection and destruction of toxic substances. Among the most dangerous nerve agents used as chemical warfare agents is OP named tabun (GA, ethyl dimethylphosphoramidocyanidate). However, due to its toxicity experimentalists work with simulants of organophosphonates, such as dimethyl methylphosphonate (DMMP), since it is non toxic and possesses necessary elemental composition. Zinc oxide (ZnO) nanoparticles have received much attention due to a various applications such as UV absorption, decomposition, deodorization, and antibacterial treatment. It is a well- known catalyst, adsorbent, toxic gas sensor, etc. Zinc oxide has attracted research interest for its unique properties and applications in electronics, cosmetics, food industry, pharmaceutical and chemical industries. Therefore, this study is devoted to the investigation of adsorption and decomposition of organophosphorus simulant DMMP and nerve agent tabun on the zinc oxide surfaces. Ab initio calculations at the density functional theory, second order Møller-Plesset perturbation theory levels and using the n-layered integrated molecular orbital and molecular mechanics (ONIOM) method have been carried out for adsorption of DMMP and GA on (ZnO)n n=4, 18, 60 molecular clusters of (1010) and (0001) zinc oxide surface. Different adsorption sites and DMMP orientations were considered. The geometry of target molecule is fully optimized while the geometry of the oxide fragments is kept frozen. The structure, interactions, atomic charges and interaction energy (corrected by the basis set superposition error) of the adsorption systems have been investigated. Different methods and different size and surface type of the ZnO fragments are considered. The optimized structure of GA and DMMP adsorbed on Zn18O18 and Zn60O60 fragments of zinc oxide is displayed in Figures 1-2. Molecular adsorption proceeds as chemisorption via formation of a Zn…O chemical bond in the case of the DMMP adsorption complex and a P…O covalent bond or Zn…N chemical bond for tabun adsorption complexes. The type of the surface affects largely the strength of the intermolecular interactions and the interaction energies. All complexes are also stabilized by the formation of hydrogen bonding interactions of the C-H…O type. The difference in the geometrical parameters and atomic charges of adsorbed and isolated DMMP and GA has been analyzed. The changes of bond lengths in target molecules caused by the adsorption are proportional to the strength of formed intermolecular interactions. Overall, GA was found to interact more strongly with the surface of ZnO than DMMP. Conference on Current Trends in Computational Chemistry 2008 129 Figure 1. The optimized structure of GA and DMMP adsorbed on Zn18O18 fragment of zinc oxide. Figure 2. The optimized geometry of DMMP adsorbed on Zn60O60 surface obtained using the ONIOM(B3LYP/LAL2DZ:PM3) method. 130 Conference on Current Trends in Computational Chemistry 2008 Hierarchical Feedback Control and Reverse Engineering of Transcriptional Networks involved in Sex Hormone Synthesis in Ovaries Edward J Perkins, Natàlia Garcia-Reyero2, Sandy Brasfield1, Daniel L Villeneuve3, Xin Guan4, Dalma Martinovic3, Nancy Denslow2, Youping Deng 4,5, Ying Li5, Tanwir Habib5, Jason Shoemaker6, and Francis Doyle III6 1US Army Engineer Research and Development Center, Vicksburg, MS, USA; 2 University of Florida, Gainesville, FL, USA; 3US EPA Mid-Continent Ecology Division, Duluth, MN, USA; 4 SpecPro, US Army ERDC, Vicksburg, MS, USA; 5 University of Southern Mississippi, MS, USA;6 University of California at Santa Barbara, CA, USA; Sex steroid synthesis is controlled through a highly conserved and complex interplay within the endocrine pathway comprised of the hypothalamus-pituitary-gonad (HPG) axis. We investigated regulation of steroid synthesis in ovaries of the experimental fish model Pimephales promelas upon exposure to chemicals using a combination of microarrays, PCR, hormone monitoring, dynamic simulation and reverse engineering of transcriptional interactions. The HPG axis could compensate for chemical inhibition of steroid synthesis in exposed whole fish, however ovary tissue exposed in vitro could not. In the absence of hormonal feedback control from the HPG axis, local responses in gene expression and enzyme inhibition dominated in ovary tissues resulting in limited hormone production. Sensitivity analysis of an ovary metabolic model suggested local regulatory events would occur rapidly after stimulation. Consistent with this prediction, oscillatory behaviors in expression of key metabolic genes, StAR and CYP 11, were revealed within 60 min of substrate addition characteristic of feedback control systems. The transcriptional interactions in ovaries were further investigated by inference of a transcriptional interaction network in ovaries. Microarray data was generated for ovaries functioning in over 180 different conditions including time series exposure to various chemicals, in vitro vs in vivo exposures, and stages of ovary maturation. Differentially expressed genes were identified within each condition. The union of all differentially expressed genes across all conditions was used to infer transcriptional interaction networks in ovaries. 2000 genes plus 55 genes known to be involved in steroid metabolism were used in network inference. The inferred network revealed novel interactions within the ovary and provide the basis for understanding local control strategies. Overall, these experiments reveal distributed control of steroid synthesis where global control compensates for local regulatory inhibition of metabolic gene expression to optimize hormone production and prevent adverse impacts on reproduction. Conference on Current Trends in Computational Chemistry 2008 131 Theoretical Study of RDX and TATP Interactions with MOF-5 T. Petrova, A. Michalkova and J. Leszczynski Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA Metal-organic frameworks (MOF’s, also known as coordination polymers) represent a relatively new family of regular nanoporous materials that as formed by a network of metal ions linked by bridging ligands other than oxygen. MoF-5 has a highly symmetric periodic structure with 106 atoms per primitive unit cell. This crystal is formed by 1,4-benzenedicarboxylate (BDC) to link together Be4O clusters. The resulting framework with formula unit Be4O(BDC)3 consists of cubic pores, where BDC forms the edges of the cubes and the Be4O clusters form the vertexes. The width of each pore is approximately 13 Å. Due to a finely controlled pore structure, functionalized MOFs are likely to have considerable advantages over other microporous materials such as zeolites and microporous carbons, which are currently utilized for adsorption separations, enantioselective catalysis and gas storage. Also they can be used as sensors and serve as templates for creation of molecular species architectures. 1,3,5-trinitro-s-triazine (RDX) is a highly symmetric, energetic compound often used as a secondary explosive. It is important energetic material that releases large amount of energy upon bulk decomposition. 3,3,6,6,9,9-hexamethyl-1,2,4,5,7,8-hexaoxacyclononane (TATP) is an organic peroxide and a primary high explosive. TATP is highly susceptible to heat, friction, and shock. The explosion of TATP involves entropy burst, which is the result of formation of one ozone and three acetone molecules from every molecule of TATP in the solid state. Just a few hundred grams of the material produce hundreds of liters of gas in a fraction of a second. The design of functionalized MOF-5 to be highly specific for given explosive compounds will be guided by extensive computational analysis. The adsorption of RDX and TATP on representative fragments of MOF-5 containing berillium metal atoms has been studied at the density functional theory (DFT) level to understand the strength and character of the binding (see Figure 1). The B3LYP functional has been used in conjunction with the LANL2DZ basis set. The representative cluster models of MOF-5 were prepared as cut offs from the periodic structure. The MOF-5 models were divided into three groups based on Figure 1. The optimized TATP (right) and RDX (left) structures interacting with the MOF-5 fragments. which part of MOF-5 they contain: linker (L), connector (C) and connector-linker (CL) fragments. The geometries of organic explosives (RDX and TATP) have been fully optimized while the geometry of the MOF-5 fragment was kept frozen. 132 Conference on Current Trends in Computational Chemistry 2008 Mechanisms of the Aryl Azide Addition to Substituted Norbornene Imides. Computational Study T. Petrova,a,b S.Okovytyy,a,b L. Gorb,a I.Tarabara,b J.Leszczynski a aDepartment of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217-0510, USA and bDepartment of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk 49625, Ukraine The functionalization of olefins with heteroatoms provides direct entry to formation of various heterocyclic systems with a wide range of applications. For example, aziridination of C=C bond in some norbornene derivatives results in generation of polycyclic triazolines and/or aziridines possessing antineoplastic and antiviral acitivities. Development of synthetic approaches and theoretical investigation of mechanisms for the reactions of new biologically active nitrogen containing norbornene derivatives due to transformation of different reaction centers of molecules is one of important problems of organic chemistry of heterocyclic compounds. The addition of aryl azide (p-NO2C6H4N3) to norbornene imide containing ester (1) or imide (2) substituents afforded exo-triazolines in exellent yield. Unexpectedly, reaction of imide (3) with aryl azide resulted in formation of azidine polycyclic system. The exo stereochemistry and character of products were confirmed experimentally. A theoretical investigation of possible mechanisms of the aziridination process is very important to understand the nature of transformations. O O N p-NO2C6H4N3 N N N CHCl3 C OCH3 N C OCH3 O O O O 1 O2N O O p-NO2C6H4N3 N N N N CHCl 3 N C NHCH C H C NHCH C H 2 6 5 2 6 5 O O O O 2 O2N O O p-NO2C6H4N3 N O2N N N CHCl3 COOH COOH O O 3 Conference on Current Trends in Computational Chemistry 2008 133 In the present work a quantum-chemical investigation of the potential energy surface for the aryl azide addition to endic imides (1-3) has been carried out. The calculations have been performed at the B3LYP/6-31+G(d) level of theory in the gas phase. All possible reaction pathways were discussed. R' = R' O R' O O N N N [3+2] + R N N R N N R N + N cycloaddition N N N O O O INT TS1 [2+1] cycloaddition O = R' = O O R' N R N N N N R N N R' R N + C N O N O O TS3 TS2 R = -CH COOH; R' = - p-C H NO 2 6 4 2 The addition of azides to bicyclic imides affords an exo-triazolines or exo-aziridine depending of imide substuituent nature. The steric bulk of the azide does not appear to play a significant role in the course of the reaction; however, the reactivity of the azide was varieted significantly due the presence of carboxylic group in endic imide (3). The presence of protic acid might favor an intermediate aminodiazonium formation (in TS2) over the concerted [3+2] cycloaddition to produce triazoline, but protonation of the azide would be reversible to get aziridine products. 134 Conference on Current Trends in Computational Chemistry 2008 Gas Phase and Solution Structures of 1-Methoxyallenyllithium Lawrence M. Pratt,1 Darryl D. Dixon2 and Marcus A. Tius2 1Department of Chemistry, Fisk University 1000 17th Ave. N., Nashville, TN 37208 and 2Department of Chemistry, 2545 The Mall, University of Hawaii, 1236 Lauhala St,Honolulu, HI 96813 The structure of 1-methoxyallenyllithium was examined by ab initio and density functional theory (DFT) calculations. This compound could potentially exist as a monomer, one of two isomeric dimers, or a tetramer. Unlike halovinyllithium carbenoids, DFT calculations generated a reasonable geometry for 1-methoxyallenyllithium with the 6-31+G(d) basis set, compared to the MP2 optimized structure with the same basis set. Therefore, all geometry optimizations of the monomer, dimers, and tetramer were performed at the B3LYP/6-31+G(d) level, followed by frequency calculations at the same level of theory. The frequency calculations verified that the structure were stationary points, and also provided thermodynamic information to calculate the free energy of each species. The geometries were then re-optimized at the MP2/6-31+G(d) level. Approximate free energies were calculated from the MP2 electronic energy and the B3LYP thermal corrections, which include the zero point energy. In the gas phase, both the B3LYP and MP2 calculations predicted the tetramer to be the most stable aggregate. The structures were also modeled in THF solution, using explicit THF ligands to represent the inner solvation sphere. Care was taken to correctly represent the standard state of each species in solution. There was some disagreement between the two methods concerning the number of THF ligands coordinated to each lithium atom, with MP2 predicting higher coordination numbers than B3LYP. Both methods predicted the monomer to dimerize in THF solution. The dimer was predicted to further aggregate to the tetramer by the B3LYP method, but not by MP2. Conference on Current Trends in Computational Chemistry 2008 135 Dynamics on the Nanoscale: Time-Domain ab initio Studies of Quantum Dots and Carbon Nanotubes Oleg Prezhdo Department of Chemistry, University of Washington, Seattle, WA 98195-1700 Device miniaturization requires an understanding of the dynamical response of materials on the nanometer scale. A great deal of experimental and theoretical work has been devoted to characterizing the excitation, charge, spin, and vibrational dynamics in a variety of novel materials, including carbon nanotubes, quantum dots, conducting polymers, inorganic semiconductors and molecular chromophores. We have developed state-of-the-art non-adiabatic molecular dynamics techniques and implemented them within time-dependent density functional theory in order to model the ultrafast photoinduced processes in these materials at the atomistic level, and in real time. Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of molecular and bulk properties. As a result, QDs exhibit new physical properties such as carrier multiplication, which has the potential to greatly increase the efficiency of solar cells. The electron-phonon and Auger relaxation in QDs compete with carrier multiplication. Our detailed studies of the competing processes in PbSe QDs rationalize why carrier multiplication was first observed in this material. The electron-phonon interactions in carbon nanotubes (CNT) determine the response times of optical switches and logic gates, the extent of heating and energy loss in CNT wires and field- effect transistors, and even a superconductivity mechanism. Our ab initio studies of CNTs directly mimic the experimental data and reveal a number of unexpected features, including the fast intrinsic intraband relaxation and electron-hole recombination, the importance of defects, the dependence of the relaxation rate on the excitation energy and intensity, and a detailed understanding of the role of active phonon modes. 136 Conference on Current Trends in Computational Chemistry 2008 Graphene Terahertz Generators for Molecular Circuits and Sensors Norma L. Rangela, b and Jorge M. Seminarioa, b, c aDepartment of Chemical Engineering, bMaterials Science and Engineering Graduate Program, and cDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA Graphene is a “novel” material recently proposed as one of the main alternatives to overcome the performance limitations of materials such as silicon and carbon nanotubes. Graphene was first isolated in 2004 by Novoselov et al. [1]. The coupling of layers is due to the weak van der Waals forces between layers in either Bernal or hexagonal stacking (ABABAB…) or the rhombohedral stacking (ABCABC…), which can be considered as a planar defect of the Bernal stacking or simply no stacking order also known as turbostratic graphite. With mobilities that are five times larger in suspended graphene [2] than in silicon, graphene offers faster devices with lower energy dissipation due to its ballistic behavior [3], and with less noise than most semiconductors by using the bilayer graphene [4]. The possibility of using graphene as a molecular sensor has been experimentally proven by Scheding et al. [5], resulting in a change in conductivity when gas molecules such as NO2, NH3, H2O and CO with different concentrations are adsorbed on a graphene surface. This was later theoretically demonstrated by Hwang et al. for NO2 and NH3 [6] with a high sensitivity, low noise, and a room-temperature operated sensor. The sensing with graphene nanoribbons is done using molecular vibrations (vibronics). Vibronics can be used to sense or transport signals, using molecules. Theoretical simulations have shown graphene as a possible sensor able to identify single molecules with modes in the terahertz (THz) region [7]. Thus the vibrational spectrum of monolayer and multilayer graphene, characterization along with its applications as part of a molecular circuit are the main topics focused in this presentation. The optimized structure of the single, double and triple layered graphene nanoribbons are obtained using the hybrid functional M05-2X, which has an improved performance for nonbonded interactions and π-π stacking [8]. Once the optimized geometries are found, the Raman spectrum is calculated. All calculations are performed with the 6-31G(d) basis using the program Gaussian 03 [9]. The Raman intensities for a single graphene layer are shown in Figure 1 (pink line), and the vibrational mode values are shown with vertical lines. In the terahertz region (less than 100 cm-1) there are neither visible nor hidden modes for the graphene monolayer, but due to the presence of an extra layer or a molecule in its neighbourhood, visible modes appear in the spectrum. Therefore, clusters of graphene can be used as potential sources of molecular signals in the terahertz region. Conference on Current Trends in Computational Chemistry 2008 137 Figure 1. Frequency spectrum for graphene nanoribbons performing as sensors based on terahertz fingerprints of single O2 molecules. Both hydrogen passivated and non-passivated structures show that the frequency spectrum for single graphene layer onsets at frequencies greater than 300 cm-1, while the second and third layered cluster structures shows Raman intensities in the terahertz region (less than 100 cm-1) An application of the modes generated at low frequencies, is the identification of single molecules using graphene, characteristic peaks for each different molecule are generated in at the low frequency region, acting as THz-fingerprints, that can be identify suggesting graphene as a potential sensor based on molecular vibrations. The effect of the edges, passivation and number of graphene layers is considered for the sensing approach. Signals at the molecular level are still unreadable and un-addressable by any present technology, thus, an interface from the nano and molecular world to microtechnology is strongly needed to allow the implementation of current molecular devices. The amplification of the signals processed at the molecular level either with the vibronics or the MEP scenarios is proposed using monolayer graphene as an amplifier performing in molecular circuits. Thanks to the two dimensional morphology of graphene, the capability of having a molecular membrane (one atom thick) interacting within molecular circuits, and at the same time with lengths in the micrometer scale promises graphene to be the perfect interface from the molecular and nanotechnology to the microtechnology. 138 Conference on Current Trends in Computational Chemistry 2008 Figure 2. Graphene nanoribbons as molecular interfaces to read signals from MEPs (left) and from vibrational frequencies (right) and translate them into current voltage characteristics. Graphite (black bulk) and gold (green bulk) are used as electrodes for both new scenarios. The partial density of state (DOS), and the sets for each bias voltage of the Hamiltonian and overlap matrices are entered in our in situ developed program, GENIP [10-12]. The information is used to calculate the electron transport characteristics using a Green’s functions approach that considers the local nature of the graphene molecule as well as the non-local features of the contacts, graphite or gold. In summary, the signals at the molecular level are amplified by graphene membranes into currents that can be read by standard microelectronics circuits. References [1] K. S. Novoselov, A. K. Geim, S. V. Morozov, D. Jiang, Y. Zhang, S. V. Dubonos, I. V. Grigorieva, and A. A. Firsov, "Electric Field Effect in Atomically Thin Carbon Films " Science, vol. 306, p. 666, 2004. [2] K. I. Bolotin, K. J. Sikes, Z. Jiang, M. Klima, G. Fudenberg, J. Hone, P. Kim, and H. L. Stormer, "Ultrahigh electron mobility in suspended graphene," Solid State Communications vol. 146, pp. 351-355 2008. [3] D. Gunlycke, H. M. Lawler, and C. T. White, "Room-temperature ballistic transport in narrow graphene strips," Physical Review B (Condensed Matter and Materials Physics), vol. 75, p. 085418, 2007. [4] Y.-M. Lin and P. Avouris, "Strong Suppression of Electrical Noise in Bilayer Graphene Nanodevices," Nano Lett., 2008. [5] F. Schedin, A. K. Geim, S. V. Morozov, E. W. Hill, P. Blake, M. I. Katsnelson, and K. S. Novoselov, "Detection of individual gas molecules adsorbed on graphene," Nat Mater, vol. 6, pp. 652-655, 2007. [6] E. H. Hwang, S. Adam, and S. D. Sarma, "Transport in chemically doped graphene in the presence of adsorbed molecules," Physical Review B (Condensed Matter and Materials Physics), vol. 76, p. 195421, 2007. Conference on Current Trends in Computational Chemistry 2008 139 [7] N. L. Rangel and J. M. Seminario, "Graphene terahertz generators for molecular circuits and sensors," J. Phys. Chem. A, Submitted, 2008. [8] Y. Zhao, N. E. Schultz, and D. G. Truhlar, "Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions," J. Chem. Theory Comput, vol. 2, pp. 364-382, 2006. [9] M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, T. Vreven Jr, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, "Gaussian-2003, Revision E.01," Pittsburgh PA: Gaussian, Inc., 2003. [10] P. A. Derosa and J. M. Seminario, "Electron Transport through Single Molecules: Scattering Treatment using Density Functional and Green Function Theories," J. Phys. Chem. B, vol. 105, pp. 471-481, 2001. [11] J. M. Seminario, A. G. Zacarias, and P. A. Derosa, "Analysis of a Dinitro-Based Molecular Device," J. Chem. Phys., vol. 116, pp. 1671-1683, 2002. [12] J. C. Sotelo, L. Yan, M. Wang, and J. M. Seminario, "Field Induced Conformational Changes in Bimetallic Oligoaniline Junctions," Phys. Rev. B, vol. 75, p. 022511, 2007. 140 Conference on Current Trends in Computational Chemistry 2008 Excitation Energies of Small Planar Polycalicenes Pornpun Rattananakin,1 Willard Collier,2 Steven R. Gwaltney,2 and Charles U. Pittman Jr.2 1Department of Chemistry, Maejo University, Chiang Mai, Thailand 50290 and 2Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 The ground states of calicene 1 and small planar polycalicenes 2-8 have been investigated with both Hartree-Fock (HF) theory and density functional theory (DFT) using the B3LYP functional. Both methods agree that the singlet-state of calicene 1 and small planar polycalicenes 2-5 and 7-8 are the ground state. DFT results show that the differential between singlet-state and triplet-state energies of calicene 1 and small planar polycalicenes 2, 4-5 and 7-8 are 67.3, 54.9, 31.8, 17.3, 29.1, and 31.8 kcal mol-1, respectively. On the other hand, both methods indicate that the triplet-state of bicalicene 3 is the ground state. DFT results give a differential between singlet-state and triplet-state energies of bicalicene 3 is 20.5 kcal mol-1. However, results from the two methods differ for system 6, which contains three calicene units bonded with head-to- head. The excitation energies of calicene 1 and small planar polycalicenes 2-8 have been investigated with time-dependent density functional theory (TDDFT). Data indicate that the number of conjugated double bonds in the head-to-tail systems is the major factor to decrease the excitation energy and to increase the oscillator strength. The difference between the excitation energies in system 2 and system 4, between system 4 and system 7, and between system 7 and system 8 are 0.39 eV, 0.34 eV, and 0.21 eV, respectively. TDDFT results indicate that the difference between the highest oscillator strengths in system 2 and system 4, between system 4 and system 7, and between system 7 and system 8 are 0.049, 0.371, and 0.623, respectively. When two isomeric polycalicenes are compared, e.g. the head-to-tail system 4 and the head-to- head system 6, the number of conjugated double bonds is equal. TDDFT results indicate that the excitation energy of the head-to-head system is 0.18 eV greater than that of the head-to-tail system. On the other hand, the TDDFT results are that the oscillator strength of the head-to-tail system is 0.023 higher than that of the head-to-head system. 1 23 45 6 7 8 Conference on Current Trends in Computational Chemistry 2008 141 Modeling Polyamides and DNA Binding Joshua M. Rodgers and Steven R. Gwaltney Department of Chemistry, Mississippi State University, Mississippi State, MS 39762 This project is a study of the interactions of amide linked molecules with specific stands of DNA base pairs. The ligands are composed of imidazole and pyrrrole units linked by amide bonds. While these polyamides occur naturally in life, research is ongoing based on constructing synthetic molecules of this type that will bind to DNA and ultimately repress certain gene sequences. This research project is an attempt to use computational modeling to reproduce the results of binding DNA and one of these polyamides in order to verify the applicability of this modeling approach. These polyamides have specificity for sequences on the DNA strand. This allows them to be used to target certain sites. For example, a molecule may be synthesized in the lab with the affinity for the sequence, “TGTTA”. This molecule would then attach to this site, impeding other attachment near its position, blocking the use of that target site. Autodock 4 has been used to predict the binding energies at certain locations on specific strands of DNA. Currently, Netropsin, a natural antibiotic, has been bound into the minor groove of a DNA strand containing the sequence “ATAT”. Ultimately, we expect this research will provide synthetic chemists the foresight they need to understand how these molecules will function in the human body. Results of the predicted structures of Netropsin bound to DNA will be presented. 142 Conference on Current Trends in Computational Chemistry 2008 Molecular Hydrogen Storage in Spherophanes A. Saal,a,b,c O. Ouamerali,a C.A. Daul,b T. Jarrossond a PCTCI Laboratory, Faculty of Chemistry, USTHB 16111 Dar El Beïda, Algiers Algeria; b Dpt of Chemistry, University of Fribourg, Suisse; c Dpt of Chemistry, UMMTO university, Algeria;d Ecole ENSCM, Montpellier, France. The design and synthesis of new materials for hydrogen storage is a great challenge. Scientists look for materials with high storage capacity, favorable thermal and chemical stability for everyday use, and fast kinetic. The storage of hydrogen may be done either in molecular or atomic form. Atomic hydrogens are maintained in the substrate by covalent bonds, this makes theirs desorption difficult and energy demanding. However, the VdW weak interactions that maintain the hydrogen molecules inside the material facilitate their desorptions at moderate pressures and temperatures. Numerous experimental and theoretical investigations have been made on the study of hydrogen storage capacity in carbon nanotubes, fullerenes, zeolites, and clathrates. In this investigation, we have considered a set of spherical molecules: the spherophanes, and studied the energy barriers of the insertion/desorption of hydrogen molecules into/from these cage molecules. Since the interactions that control the system (H2, spherophane) are noncovalent, the empirical correction scheme introduced by Grimme to take into account the VdW interactions is used. Conference on Current Trends in Computational Chemistry 2008 143 Odor Detection Based on DNA for Nitroaromatic Compounds Karim Salazar-Salinas1, Carlos Kubli-Garfias1, † and Jorge M. Seminario1,2 1Department of Chemical Engineering, 2Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA Nitroaromatic amines and nitroaromatic explosives are related to high cancer risk mainly of colon, breast and prostate [1, 2]. Toxicological essays in Salmonella have showed the relationship among direct-acting mutagenicity and the orientation of the nitro group with the generation of radicals by enzymatic reduction [3]. During the attack of these compounds, the DNA is in a one-electron oxidative state. Studies found that the first product of the attack is the 8-oxo-7,8-dihydroguanine (8-oxo-gua) through long-range hole migration. This product is chemically stable, thus measurements during its formation are possible. We evaluate the oxidation of the guanine nucleotides by the action of nitroaromatic compounds (Fig.1). The proposed mechanism of the reaction is based on cation formation, whereby C8 is surrounded by a positive region. The complementary nucleotide cytosine-guanine (C-G) and cytosine- 8oxoguanine (C-8oxoG) are detected by observing the reduction of the bandgap of the complementary nucleotide C-G when it is exposed to a nitroaromatic amine, from 1.93 to 1.63 eV. DNA is known to act as a sensor for detecting volatile compounds by the immobilization of a single strand or double-strand DNA on the electrode [4] or by the fluorescent changes [5]. We propose here the detection of this DNA damage by nitrocompounds by observing the transversal current response to the application of a transversal voltage applied through gold electrodes. Our goal in this study is to find out methods for detecting and assessing the sensing capacity of models based on current-voltage (I-V) characteristics and spectroscopic data. We use density functional theory based techniques for proving the concept [6-12]. O NH2 7 4 6 5 N O 7 5 3 1 HN N 6 5 H 8 N 6 2 1 HN 8 H N 2 N 4 N 9 O O O N 1 O 2 3 5 5 O P O- H N 2 N 4 N 9 O -O P O O 2 O 3 5 1 H H 4 O- O P O- O- 4 H H 1 O H H H H H OH 14H H O- OH H 23 H H a 3 2 b H OH Figure 1. Schematic structure of a) complementary nucleotide citosyne-guanine (C-G), and b) the 8-oxo-guanine (8- oxoG) representing the damaged part of the DNA pair. Acknowledgments We acknowledge financial support from the US Army Research Office and the US Defense Threat Reduction Agency (DTRA). †Permanent address: Instituto de Investigaciones Biomédicas UNAM, México City. MEXICO. References [1] A. Nemeikaitė-Čėnienė, V. Miliukienė, J. Šarlauskas, E. Maldutis, and N. Čėnas, "Chemical aspects of cytotoxicity of nitroaromatic explosives: a review," Chemija, vol. 17, p. 8, 2006. [2] P. A. Thompson, F. Seyedi, N. P. Lang, S. L. MacLeod, G. N. Wogan, K. E. Anderson, Y.-M. Tang, and F. F. K. B. Coles a, "Comparison of DNA adduct levels associated with 144 Conference on Current Trends in Computational Chemistry 2008 exogenous and endogenous exposures in human pancreas in relation to metabolic genotype," Mutation Research, vol. 424, p. 12, 1999. [3] P. P. Fu, D. Herreno-Saenz, L. S. V. Tungeln, Y.-S. Jack O. Lay, J.-S. L. Wu, and F. E. Evans, "DNA Adducts and Carcinogenicity of Nitro-Polycyclic Aromatic Hydrocarbons," Environmental Health Perspectives, vol. 102, p. 8, 1994. [4] D.-P. Zhang, W.-L. Wu, H.-Y. Long, Y.-C. Liu, and Z.-S. Yang, "Voltammetric Behavior of o-Nitrophenol and Damage to DNA," Int. J. Mol. Sci, vol. 9, p. 10, 2008. [5] J. White, K. Truesdell, L. B. Williams, M. S. AtKisson, and J. S. Kauer, "Solid-State, Dye-Labeled DNA Detects Volatile Compounds in the Vapor Phase," PLoS Biology, vol. 6, p. 7, 2008. [6] R. M. Tovar, K. P. Johnson, K. Ashline, and J. M. Seminario, "Effects of Substituents on Molecular Devices," Int. J. Quantum Chem., vol. 108, pp. 1546-1554 2008. [7] J. C. Sotelo and J. M. Seminario, "Local reactivity of O2 to Pt3 on Co3Pt and related backgrounds," J. Chem. Phys., vol. 128, pp. 204701 (1-11), 2008. [8] P. F. Salazar and J. M. Seminario, "Identifying Receptor-Ligand Interactions through an ab Initio Approach"," J. Phys. Chem. B, vol. 112, pp. 1290-1292, 2008. [9] N. L. Rangel and J. M. Seminario, "Nano-micro interface to read molecular potentials into current-voltage based electronics," J. Chem. Phys., vol. 128, p. 114711 2008. [10] L. A. Jauregui and J. M. Seminario, "A DNA sensor for sequencing and mismatches based on electron transport through Watson-Crick and non-Watson-Crick base pairs," IEEE Sensors, vol. 8, pp. 803-814, 2008. [11] S. Hong, L. A. Jauregui, N. L. Rangel, H. Cao, S. Day, M. L. Norton, A. S. Sinitskii, and Jorge M. Seminario "Impedance measurements on a DNA junction," J. Chem. Phys., vol. 128, pp. 201103 (1-4) 2008. [12] E. J. Bautista and J. M. Seminario, "Harmonic force field for glycine oligopeptides," Int. J. Quantum Chem., vol. 108, pp. 180-188, 2008. Conference on Current Trends in Computational Chemistry 2008 145 Hydrogen Storage in Boron/Carbon Systems Julia Saloni1, Wojciech Kolodziejczyk1,2, Szczepan Roszak1,2 and Glake Hill1 1The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217 USA; 2Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland Studies on the properties, application and storage of alternative fuel such as hydrogen become crucial in present world due to rapid consumption of fossil fuels, raising oil prices and the bad impact of fossil fuels use on environment. Hydrogen as a fundamental element, widely used in chemical and space industries becomes perfect candidate for an inexpensive alternative fuel. However, development of efficient, durable and inexpensive hydrogen storage systems is necessary. Boron Doped Single Walled Carbon Nanotubes, BDSWCNTs, seems to be a perfect candidate for this cause due to their properties (low operating temperature, low cost, simple design and low volumetric). These studies are devoted to design hydrogen storage device. Applying ab initio methods variety of calculations has been performed to obtain molecular structures and interactions of H2- BDSWCNTs systems. Fig1. Adsorption of H2 on the surface of BDSWCNT 146 Conference on Current Trends in Computational Chemistry 2008 Theoretical Study of Interactions of Thymine and Uracil and their Tautomers with Tetrahedral Edge Clay Minerals Fragments B. Sanders, A. Michalkova, and J. Leszczynski Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street, Jackson , MS 39217 DNA, also known as deoxyribonucleic acid, is a double stranded molecule found in all forms of life. The shape of DNA is in the form of a double helix. Thymine (C5H6N2O2) is a nitrogenous base of DNA. DNA has also the nitrogenous bases adenine, guanine, and cytosine. In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds to assist in stabilizing of the nucleic acid structures and cytosine (C) binds with guanine (G). RNA, also known as ribonucleic acid, is one stranded molecule that is also found in all forms of life. RNA is found in three forms, r(ribosomal)RNA, m(messenger)RNA, and t(transcriptive)RNA. The nitrogenous bases found in RNA are uracil (C4H4N2O2), adenine, guanine, cytosine. Uracil pairs with adenine through hydrogen bonding, while guanine pairs with cytosine just like it does in DNA. Uracil can also bind with a ribose sugar to form a ribonucleoside, uridine. When a phosphate attaches to uridine, uridine 5'-monophosphate is produced. Tautomers are interconvertible organic compounds that undergo a chemical process called tautomerization. Usually, a hydrogen atom along with the switch of a single or double bond migrates to where tautomerization is possible. In thymine, the hydrogen bonded to the first nitrogen atom migrates to the second oxygen atom and the double bond between the second carbon atom and the second oxygen atom has now become a single bond (C-O). The double bond migrates between the first nitrogen and the second carbon now creating a double bond (N=C). In uracil, both hydrogen atoms migrate to the oxygen atoms, creating hydroxide ions and moving the double bond. Two new double bonds are formed, between the second carbon and third nitrogen and between the fourth and fifth carbons. The clay minerals are a part of a general but important group within the phyllosilicates. There are many important uses and considerations of clay minerals. They are used in manufacturing, drilling, construction and paper production. They have great importance to crop production as clays are a significant component of soils. They include the following groups: kaolin group which includes the minerals, kaolinite, dickite (it is the subject of this work), halloysite, and nacrite, serpentine group, smectite group, illite group, and chlorite group. Dickite (Al2Si2O5(OH)4) is a phyllosicate clay mineral, with the same composition as kaolinite, nacrite, and halloysite but with a different crystal structure. It is a layered silicate mineral with one tetrahedral sheet linked through oxygen atoms to one octahedral sheet of alumina. Bonding between the tetrahedral and octahedral sheets requires that the tetrahedral sheet becomes corrogated or twisted, causing ditrigonal distortion to the hexagonal array, and the octahedral sheet is flattened. This minimizes the overall bond-valence distortions of the crystallite. In the ideal composition of the tetrahedral and octahedral sheets, the layers have no charge. If the layers are charged this charge is balanced by interlayer cations such as Na+ or K+. In each case the interlayer can also contain water. The calculations of the interactions of thymine, uracil and their tautomers were performed at the density functional theory level with the B3LYP functional applying the 6-31G(d) basis set. This study was carried out in order to understand how these target molecules interact with the clay mineral fragments and to study the differences in their interactions. The studied systems were fully optimized. The tetrahedral edge mineral fragments were simulated using a single Conference on Current Trends in Computational Chemistry 2008 147 tetrahedra with the Si or Al central cation. Several different positions of the target molecule were tested in order to find the most stable orientation. The fragment was terminated by the oxygen atom and by the hydroxyl group. We have studied the geometrical parameters and ESP charges, the interaction energies corrected by the basis set superposition error and topological characteristics of the studied systems applying the AIM analysis according to the Bader’s theory. Figure: The optimized structure of tautomer of thymine interacting with the tetrahedral clay mineral fragment (Si(OH4)). 148 Conference on Current Trends in Computational Chemistry 2008 A Theoretical Analysis of Non-Covalent Interactions in Isolated and Associated Forms G. Narahari Sastry Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 007, AP, India In recent years the emphasis on understanding the interaction of non-covalent interactions in a quantitative fashion has become important for both experimentalists and theoreticians. Among the non-covalent interactions hydrogen bond has been recognized as the most important and is one of the most vividly explored and widely understood phenomenons. Among the other non- covalent interactions, cation-π and π−π interactions have emerged as interactions of strategic biological importance and have become of the focus of several investigations. In comparison to the hydrogen bonding π−π are considered weaker and usually cation-π are stronger. Here we undertake a systematic analysis to analyze and quantify how various factors such as the size and nature of the π-acceptor system, the curvature, nature of metal ion involved, the effect of solvent modulate the cation-π interaction. Protein data bank and Cambridge structural database analyses were made to understand the occurrence and relevance of the cation-π interactions in biology and chemistry. The current study is mainly concerned with delineating how cation-π interactions effect other non-covalent interactions such as π−π stacking and hydrogen bonding. The cooperativity of a pair of non-covalent interactions when they operate simultaneously involving a common moiety is defined. The causes and consequences of cooperativity on non-covalent interactions in the structure, stability and function of the macromolecular systems are explored. References: + + + + + 2+ + + (a) Cation [M=H , Li , Na , K , Ca , Mg , NH4 , and NMe4 ] interactions with the aromatic motifs of naturally occurring amino acids: A theoretical study, A. S. Reddy and G. N. Sastry, J. Phys. Chem. A 2005, 109, 8893-8903; (b)On the Cooperativity of Cation-π and Hydrogen Bonding Interactions, D. Vijay, H. Zipse and G. N. Sastry, J. Phys. Chem. B, 2008, 112, 8863-8867; (c) From Subtle to Substantial: Role of Metal Ions on π−π Interactions, A. S. Reddy, D. Vijay, G. M. Sastry, G. N. Sastry, J. Phys. Chem. B, 2006, 110, 2479-2481; (d) A computational study on π and σ modes of metal ion binding to heteroaromatics (CH)5-mXm and (CH)6-mXm (X = N and P): contrasting preferences between nitrogen and phosphorous substituted rings, D. Vijay, G. N. Sastry, J. Phys. Chem. A, 2006, 110, 10148-10154; (e) Cation – Aromatic Database (CAD), A. S. Reddy, G. M. Sastry, G. N. Sastry, Proteins: Structure, Function, and Bioinformatics, 2007, 67, 1179-1184; (f) Metal ion binding with dehydroannulenes - Plausible two dimensional molecular sieves, B. Sateesh, Y. Soujanya and G. N. Sastry, J. Chem. Sci., 2007, 119, 509-515; (g) Cation-π interactions of bare and coordinately saturated metal ions: Contrasting structural and energetic characteristics, A. S. Reddy, H. Zipse and G. N. Sastry, J. Phys. Chem. B, 2007, 111, 11546–11553; (h) Cation-π Interactions of Curved Polycyclic Systems: M+ (M = Li and Na) Ion Complexation with Buckybowls, U. D. Priyakumar and G. N. Sastry, Tetrahedron Lett., 2003, 44, 6043-6046; (i) A Computational study of cation-π interactions in polycyclic systems: Exploring the dependence on the curvature and electronic factor, U. D. Priyakumar, M. Punnagai, G. P. Krishna Mohan and G. N. Sastry, Tetrahedron, 2004, 60, 3037-3043; (j) Exploring the size dependence of cyclic and acyclic π–systems on cation-π binding, D. Vijay and G. N. Sastry, Phys. Chem. Chem. Phys., 2008, 10, 582-590. Conference on Current Trends in Computational Chemistry 2008 149 Graphene Structures for New Scenarios for Molecular and Nano Electronics Jorge M. Seminario Department of Chemical Engineering, Materials Science and Engineering Graduate Program, Department of Electrical and Computer Engineering, Texas A&M University College Station, Texas, USA Graphene materials have been proposed as one of the main alternatives to overcome the performance limitations at the nanoscale of materials such as silicon and carbon nanotubes. Our interest in the use of grapheme centers on its potential suitability for two new scenarios that we have developed for molecular and nano electronics based on molecular potentials and vibronics. We will show an introduction to the new scenarios and analyses of a few layered graphene nanoribbons. 150 Conference on Current Trends in Computational Chemistry 2008 Size and Distance Dependence NSET Ruler for Selective Sensing of Hepatitis C virus RNA Dulal Senapati, Jelani Griffin, Anant Kumar Singh, and Paresh Chandra Ray Department of Chemistry, Jackson State University, Jackson, MS, USA We report size and distance dependent NSET properties of gold nanoparticles for recognizing hepatitis-C virus HCV RNA sequence sensitively and selectively (single-base mutations) in a homogeneous format. We have demonstrated quenching efficiency increases by three orders of magnitude, as the particle size increases from 5 nm to 70 nm. Due to this extraordinarily high KSV, NSET detection limit can be as low as 300 fM concentration of RNA depending on the size of gold nanoparticle. We have shown that the distance dependent quenching efficiency is highly depend on the particle size and the distance at which the energy transfer efficiency is 50%, ranges all the way from 8 nm, which is very closer to the accessible distance of conventional FRET, to about 40 nm by choosing GNPs of different diameters. Our result points out that the DMPET and NSET model provides a better description of the distance dependence of the quenching efficiencies for 8 nm gold nanoparticle, but agrees poorly for 40 and 70 nm gold nanopartciles, where the measured values were always larger than the predicted one. Conference on Current Trends in Computational Chemistry 2008 151 Interaction of Gold Clusters with Guanine and Watson-Crick Guanine-Cytosine Base Pair: A Theoretical Investigation Manoj K. Shukla1, Madan Dubey2, Eugene Zakar2 and Jerzy Leszczynski1 1Computational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Ms 39217 (USA), and 2US Army Research Laboratory, Sensors and Electron Devices Directorate, AMSRD-ARL-SE-RL, Adelphi, MD 20783 (USA) Particles at the nanoscale range have physical and chemical properties significantly different than the corresponding bulk structure. The size-dependent physico-chemical properties of nanomaterials are being utilized in novel applications in different fields such as in electronics devices, drug delivery system, space applications and many more. The novelty of nanomaterials has been also a cause for potential concern for environmental toxicity. It has been suggested that nanoparticles upon significant and prolonged exposure may cause allergic reactions and may lead to disease similar to asbestosis. It has shown that the intracellular uptake and kinetics of gold nanoparticles significantly depend on their physical dimension. Recent results suggest that longer multiwalled carbon nanotubes (MWCN) have toxic effects similar to those from asbestos. Further, it was suggested the shape and size of nanoparticles have paramount role compared to their chemistry in relation to their toxicity. The gold nanoparticles have been found to form gold aggregates in living system. Since in nucleic acids, the N7 site is the major groove site and therefore it is expected that gold clusters would interact to DNA via the major groove site. Geometries of the guanine-gold (G-Aun; n =2, 4, 6, 8, 10, 12) and guanine.cytosine-gold (GC-Aun; n =2, 4, 6, 8, 10, 12) complexes, where gold clusters were coordinated at the N7 site of guanine, were optimized at the B3LYP/6-31G(d)∪LANL2DZ level. It was found that gold clusters would form more stable complexes with the GC base pair than the guanine base alone. It was also revealed that consequent to the interaction with gold clusters the GC base pair may slightly open the hydrogen bond (O6(G)…(NH2(C)) belonging to the major groove site of DNA. Consequent to the gold binding a substantial amount of electronic charge was transferred from the guanine and guanine-cytosine base pair to the gold cluster. Further, the amount of the electronic charge transferred to gold cluster is more for the GC-Aun than that in the G-Aun complexes. The electron attachment as well as ionization processes in the complexes will take place at the gold cluster. Further, these processes are also supplemented by the charge transfer from the guanine and GC base pair especially in the smaller complexes. Acknowledgements: MKS and JL are thankful to financial support from Army Research Laboratory BAA# DAAD19-03-R-0017, section # 2.41" Contract No. W911QX-07-C-0100, NSF-CREST grant No. HRD-0318519, ONR grant No. N00014-08-1-0324 and the Mississippi Center for Supercomputing Research (MCSR) for the generous computational facility. 152 Conference on Current Trends in Computational Chemistry 2008 A Theoretical Study of the Interactions of In+ and In+3 with Stone-Wales Defect Single-Walled Carbon Nanotubes Tomekia Simeon1*, Krishnan Balasubramanian2-4 and Jerzy Leszczynski1 1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA, 2Department of Mathematics and Computer Science, California State University, East Bay, Hayward, CA, United States, 3University of California, Chemistry and Material Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808 L-268, Livermore, CA 94550, United States, 4Glenn T Seaborg Center, Lawrence Berkeley Laboratory, University of California, Berkeley, CA 94720, United States Experimental techniques [1] have demonstrated the controllable, reversible and mass transport exchange of indium nanocrystals along surfaces of multi-walled carbon nanotubes (MWCNTs). In particular, at certain sites robust nucleation occurs suggesting preferred locations for controlled manipulation. We believe these site locations represent structural defects, like rehybridization, incomplete bonding and topological defects within the carbon network. Although minute, these defects can drastically modify the electrical, chemical and mechanical properties of CNTs. This study was devoted to understand the role of structural defects, specifically a Stone- Wales (SW) defect in the surface transport and interaction properties of the In+ and In+3 for both the singlet and triplet state. The effects of CNT surface curvature on In+ and In+3 is also studied and compared to graphite. Geometries of complexes were optimized at the B3LYP level. The standard 6-31G(d) basis set was used for carbon and hydrogen atoms while an effective core potential (ECP) was used for indium. All calculations were performed using the Gaussian 03 suite of programs. The computed Mulliken charges and HOMO-LUMO gap energies, interactions and interaction energy (corrected by the basis set superposition error) of the systems have been studied and will be discussed. Figure 1 represents the comparison of the molecular electrostatic potential maps for a) In+ and b) In+3 with a SW defect CNT. Reference: 1. A. Zettl, B. C. Regan, S. Aloni, R. O. Ritchie, U. Dahmen, Nature, 428, 924, (2004). Conference on Current Trends in Computational Chemistry 2008 153 a b Figure 1. Comparison of the molecular electrostatic potential surfaces for the ground state configurations of a) In+ and b) In+3 interacting with a SW-defect CNT. Acknowledgements This work was supported in part by the U.S. Army Engineer Research and Development Center under contract W912HZ-05-D-0012 , “High Performance Computational Design of Novel Materials”, and by the U.S. Department of Defense High Performance Computing Modernization Office. This work was also supported by the U.S. Department of Energy under Grant No. DE-FG02-04ER15546. The work at LLNL was performed under the auspices of US Department of Energy under Contract No.W-7405-Eng-48. 154 Conference on Current Trends in Computational Chemistry 2008 Hydrogenated Gallium-Oxide Clusters [Ga2O2H2]2+ as Models of Catalytic Sites for the Ethane Dehydrogenation in Oxidized Ga/ZSM-5: a DFT Study Vitaly Solkan N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr. 47, Russian Federation; E-mail: [email protected] The reaction mechanism of the ethane dehydrogenation was investigated using DFT calculations for binuclear gallium-oxide cluster as the active site in oxidized Ga-exchanged + ZSM-5 zeolite. Our previous study [1] has shown that gallyl species [GaO] easily rotate around a zeolite aluminium tetrahedron with the activation barrier of 18.6 kcal/mol. It could lead to mutual orientation of both [GaO]+ dipoles to each other, and this could result in a capture of one 2+ GaO moiety by another thus giving condensed gallium-oxide particle [Ga2O2] . One can assume another mechanism of quasi-square particle formation by oxidation of gallium-exchanged + zeolite. At the first step one of the Ga cations is oxidized to the [GaO2] particle, which could be formed either by adsorption of molecular oxygen on the gallium atom or by consecutive + oxidation with two N2O molecules [2]. Then residual gallium cation migrates to the [GaO2] particle to give the resultant tetraatomic cyclic cluster. We have employed the cluster approximation to model catalytic sites in Ga/HZSM-5. The basic lattice cluster consists of two neighboring zeolite rings, containing five silicon T-atoms each. Exact Si and O atom coordinates were taken from ZSM-5 structure (orthorhombic MFI), obtained by model building, single crystal and powder X-ray data [3]. One of silicon atoms in each ring was substituted with aluminium atoms. The cluster we constructed employed H termination, and dangling O-Si and O-Al bonds were terminated with H atoms, placed initially at respective distances of 1.47 and 1.58Å from Si and Al atoms, that were optimized later at the first step. Quantum-chemical calculations have been carried out within density functional theory (DFT) using the GAUSSIAN 03 program. The hybrid B3LYP functional was used, involving D95 basis set for hydrogen, silicon and aluminium atoms, and biexponential 6-31G* basis set for gallium and oxygen atoms. Transition states were found using the quadratic synchronous transit QST2 and QST3 methods, implemented with frozen zeolite lattice atoms. Validity of the transition states was confirmed by imaginary frequency mode visualization and relaxation by perturbing transition states geometry along assumed reaction coordinate. It was found that the binuclear cyclic tetratomic flat Ga2O2 cluster with formal charge 2+ is stabilized on single aluminium tetrahedron, while remote second cationic position remains empty. This gallium-oxide cluster adsorbs hydrogen molecule with ease giving dihydrides, which acts as active catalytic site for the reaction of alkane dehydrogenation. It is important that pure gallium-oxide cluster cannot support this process due to very high hydrogen affinity and thus H2 removal prohibition. But the situation is changed for partially hydrogenated cluster, for example, for the dihydride species. Ethane dehydrogenation reaction activation energies were estimated relying on activation energy of ethane dissociated adsorption and ethylene elimination. One should notice also that the active site regeneration by hydrogen molecule elimination, as it was found earlier, proceeds with activation energy of 43.3 kcal/mol, which allows closing catalytic cycle (Fig.1). By comparing obtained results with literature data [4-6] it was proposed that this dehydrogenation reaction can proceed on the suggested cluster, thus explaining high activity of oxidized gallium-exchanged ZSM-5 zeolites in alkane dehydrogenation reactions. Conference on Current Trends in Computational Chemistry 2008 155 Figure 1. Catalytic cycle for the ethane hydrogenation mechanism over partially hydrogenated 2+ 2+ gallium-oxide cluster. One can consider [Ga2O2H4] as initial structure with [Ga2O2H2] and 2+ [Ga2O2H3C2H5] as less stable intermediates. Acknowledgements. Financial support of RFBR through the project 05-03-33103 is gratefully acknowledged. We thank Prof. G. Zhidomirov for advice on the methodology of cluster approach and thank Dr. E. Kuzmin for performed calculations. References. 1. I. V. Kusmin, G. M. Zhidomirov, V. N. Solkan, Int. J. Quant. Chem. 2007, 107, 2434. 2. V. N. Solkan, G. M. Zhidomirov, V. B. Kazansky, Int. J. Quant. Chem. 2007, 107, 2417. 3. H. Lermer, M. Draeger, J. Steffen, K. K. Unger, Zeolites 1985, 5, 131. 4. E. J. M. Hensen, E. A. Pidko, N. Rane and R. A. van Santen, Angew. Chem., Int. Ed. 2007, 46, 7273. 5. E. A. Pidko, E. J. M. Hensen, R. A. van Santen, J. Phys. Chem. C 2007, 111, 13068. 6. G. M. Zhidomirov, A. A. Shubin, M. A. Milov, E. J. M. Hensen, V. B. Kazansky, R. A. van Santen, J. Phys. Chem. C 2008, 112, 3321. 156 Conference on Current Trends in Computational Chemistry 2008 Protonated Molecular Oxygen and Sulfur Dioxide as Chemical Precursors in the Conversion of SO2 to SO3 by Oxygen in super acid: A Theoretical Study on Mechanism of Acid-Catalyzed oxidation of SO2 with Molecular Oxygen Vitaly Solkan N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow,Leninskii pr. 47, Russian Federation; E-mail: [email protected] Fluorosulfonic acid catalyzes the rate of oxidation of SO2 to SO3 with molecular oxygen at room temperature [1]. The mechanism for this process is not fully understood, and it has been argued that the superacid only catalyze the formation of singlet oxygen or peracids [2]. Indeed, Olah and co-workers [3] have successfully achieved hydroxylation of branched chain saturated hydrocarbons in "magic acid" media containing FSO3H. In order to understand this level of catalytic activity we undertook a computational study to examine the overall mechanistic pathway for SO2 oxidation by oxygen in super acid FSO3H. Geometries of the stationary points (minima and transition states) involved in the reactions have been optimized at the B3LYP/6- 31++G** level. The stationary points have been further characterized by vibrational frequency analysis at the same level of theory. In some cases we also found it necessary to confirm that a transition state connected the correct minima by performing intrinsic reaction coordinate (IRC) calculations. For comparison, we have therefore also computed MP2/6-31++G** energies at the B3LYP/6-31++G** optimized geometries. It is generally considered that MP2 produce relative energies for closed shell systems of similar accuracy as B3LYP. To estimate the accuracy of B3LYP and MP2 approaches for the systems studied here, the energies of the stationary points have also been calculated using a G3 type of extrapolation scheme. Considering the experimental setup, it must be assumed that the initial step of the reaction is the interaction between SO2 and the fluorosulfonic acid. This will lead to the formation of an initial complex as shown in Figure 1 1. This complex is considerably stronger bound than the initial complex of singlet O2 ( O2) with FSO3H (Fig.2). Several pathways are possible: (i) An addition of HOO(+) cation to the S=O bond of SO2 initially yields a HOOSO2 (+) cation. According to our proposal, the latter may add sulfur dioxide to yield a (HOO)(OSO)SO2 (+) cation. (ii) An alternative would be the reaction of 1 singlet oxygen ( O2) with the protonated sulfur dioxide followed by proton transfer. The strategy consists of a series of ab initio and density functional quantum chemical calculations of a number of hydrogen-sulfur-oxygen species. These calculations are used to examine the potential energy surface and the kinetics of the reaction of SO2 with molecular oxygen. The geometry of reactants, transition states, and possible products of reactions are fully optimized using the full second-order Moller-Plesset many-body perturbation theory and B3LYP functional using the 6-31++G(d,p) and 6-311++G(d,p) basis sets, respectively. All of the methods employed predict exothermic heats of reaction for the product channels 1-2. It is found that the most stable structure is the (HOO)(OSO)SO2 (+) cation, followed by cyclic isomer (OO)(OSO)SO2 H (+). The formation of SO3 from cyclic isomer (OO)(OSO)SO2 H (+) involves the formation of the unstable intermediate. Conference on Current Trends in Computational Chemistry 2008 157 Fig. 1. Optimized structure of complex between SO2 and two molecule of the fluorosulfonic acid at B3LYP/6-31++G(p,d) level. Fig. 2. Optimized structure of complex between singlet O2 and two molecule of the fluorosulfonic acid at B3LYP/6-31++G(p,d) level. Acknowledgment This work was supported in part by the RFBR (Project 08-03-00388-a). References: Vishnetskaya M.V., et al. Russ. J. Phys. Chem., 2006, 80, Iss. 2, 236. (Engl. Trans.). Vishnetskaya M.V., Romanovsky B.V., Catal. Lett., 1994, 29, 3256. Olah, G.; Parker, D. G.; Yoneda, N. Angew Chem., Int. Ed. Engl. 1978, 17, 909. 158 Conference on Current Trends in Computational Chemistry 2008 Post-Hartree-Fock Study on Decomposition of Nitrous Oxide on Ga–ZSM-5 Vitaly Solkan and Jerzy Leszczynski N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr. 47, Russian Federation; and Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Str., Jackson, MS 39217, USA. E-mail: [email protected] Recently we presented DFT/B3LYP study of the interaction of nitrous oxide with Ga/ZSM- 5 and GaO/ZSM-5 [1]. The active centers were taken to be mononuclear [Ga]+ and [Ga=O]+. We + shoved that the first step of N2O decomposition involves the formation of [GaO] and the release of N2. The metal-oxo species produced in this step then reacts with N2O again, to release N2 and + form [GaO2] . The calculated activation energies for N2O dissociation in Ga-ZSM-5 and GaO- ZSM-5 are 22.2 and 24.9 kcal/mol, respectively. In the present work we have performed a detailed theoretical study of the mechanisms of nitrous oxide dissociation in Ga-ZSM-5, GaO-ZSM-5, and GaO2-ZSM-5 using post-Hartree- Fock calculations at MP2 computational level. The catalytically active center and a portion of the zeolite framework are represented by a 3T-cluster. The standard 6-31+G(d) basis set was used + + + for N2O molecule and for all active centers [Ga] , [Ga=O] , and [GaO2] . For 3T cluster we used standard 6-31G(d) basis set. This mixed basis set (BS-I) was used for geometry optimization at MP2 level. All stationary points were characterized by harmonic vibrational analyses employing energy Hessians at two levels: MP2/BS-I and B3LYP/6-31+G(d). To check the effects of basis set superposition errors (BSSEs), the counterpoise correction method was applied to the addition complexes. The stationary point energies (well-depth corresponding to the reactant complex, ERC, transition state (TS) energies with respect to the reactant complex, E ) were evaluated at the B3LYP and MP2 levels. These energies were then corrected for zero-point vibrational energies ( EZPVE) and for thermal energies ( H), and applied entropies to obtain free energies ( G) at 298 K. An activation barrier estimation ( E#) was calculated as follows: E# = V# + # EZPVE + E(T), where V is the potential energy barrier at 0 K, and EZPVE and E(T) are differences of zero-point vibrational energy (ZPVE) and thermal corrections between the TS and the corresponding reactant complex. To obtain more reliable values of the energies for the different stationary points on the PES, a number of single-point calculations using MP4(SDTQ) was performed. To verify the relevance of the transition states found, intrinsic reaction coordinate IRC calculations were performed starting from the transition states. Theoretical Ea(MP2) and Ea(MP4) values (see Table 1) represent potential energy barriers without zero-point vibrational energy and thermal corrections at MP2 and MP4 levels, respectively. Results and Discussion The dissociation of N2O at a single gallium center in zeolite ZSM-5, (Z), can be envisioned to proceed via the following sequence of steps: - + - + N2O(g) + Z [Ga] = Z [Ga(N2O)] (1) - + - + Z [Ga(N2O)] = N2(g) + Z [GaO] (2) - + - + N2O(g) + Z [GaO] = Z [GaO(N2O)] (3) - + - + Z [GaO(N2O)] = N2(g) + Z [Ga(O)2] (4) - + - + N2O(g) + Z [GaO2] = Z [GaO2(N2O)] (5) - + - + Z [GaO2(N2O)] = N2(g) + Z [Ga(O)3] (6) - + - + Z [Ga(O)3] = O2(g) + Z [GaO] (7) Conference on Current Trends in Computational Chemistry 2008 159 - + - + Z [Ga(O)2] = O2(g) + Z [Ga] (8) 1. Energetics of Nitrous Oxide Adsorption and Decomposition on 3T-Ga The calculated binding energies ( Eads) at MP2 level for N2O adsorption on the 3T-Ga is equal to 7.39 kcal/mol. This value with the BSSE correction ( Ebsse) decreases up to 2.22 kcal/mol. An activation barrier at MP2 level, E# = +15.7 kcal/mol, exist for reaction 2 at T=298 K (Table 1). The imaginary frequency associated with the transition state mode is 447i cm-1 along the r(O-N) reaction coordinate that connects reactants to products. Taking into account that the enthalpy of reaction is HR = -56.9 kcal/mol at T=298 K, it follows that the reverse reaction is very slow. As a result, bare gallium sites are unlikely to exist under reaction conditions in the presence of N2O. Considering the known tendency of MP2 method to overestimate barriers, it is worthwhile noting that at MP4(SDTQ)//MP2 level the activation barrier (+21.0 kcal/mol) is lower by 1.8 kcal/mol than the activation energy (+22.8 kcal/mol) at MP2 level (Table 1). This activation barrier with the corrections for zero-point vibrational energy ( EZPVE) and for thermal energies ( H), on the basis of the MP2 geometries, decreases up to 13.9 kcal/mol. 2. Energetics of Nitrous Oxide Adsorption and Decomposition on 3T-Ga=O It has been found that for the (3T-Ga=O O=N=N) complex the binding energy Eads is equal to 9.11 kcal/mol. This value with the BSSE correction Ebsse decreases up to 1.80 kcal/mol. An activation barrier at MP2 level, E# = +26.48 kcal/mol, exists for reaction 4 at T=298 K (Table 1). It is also important to note that the activation barrier for the elementary step of the first N2O decomposition on 3T-Ga is lower by 10.81 kcal/mol than the activation barrier of the second N2O decomposition on 3T-Ga=O. The imaginary frequency associated with the -1 second transition state TS2 mode is –677i cm along the r(O-N) reaction coordinate that connects reactants to products (3T-GaO2). The normal coordinate vectors of the vibrational -1 modes, corresponding to the imaginary frequencies of transition states TS1 and TS2 at 447i cm and 677i cm-1, respectively, show that, in both cases, the dominant motions involve the rupture of O-N bond. Taking into account that the enthalpy of reaction is HR = -21.09 kcal/mol at T=298 K, it follows that the reverse reaction is very slow. It is worthwhile noting that at MP4(SDTQ)//MP2 level the activation barrier (+23.8 kcal/mol) is lower by 13.5 kcal/mol than the activation energy (+37.3 kcal/mol) at MP2 level (Table 1). The use of correction for zero- point vibrational energy ( EZPVE) and for thermal energies ( H), on the basis of the MP2 geometries, gives significantly lower magnitude for the activation barrier (by 10.8 kcal/mol) in comparison with MP4(SDTQ) calculation without these corrections. 3. Energetics of Nitrous Oxide Adsorption and Decomposition on 3T-GaO2 It has been found that for the (3T-GaO2 O=N=N) complex the binding energy Eads is equal to 8.74 kcal/mol. This value with the BSSE correction Ebsse decreases up to 1.71 kcal/mol. An activation barrier at MP2 level, E# = +43.67 kcal/mol, exist for reaction 6 at T=298 K (Table 1). It is also important to note that the activation barrier for the elementary step of the N2O decomposition on 3T-GaO2 is 17.19 kcal/mol higher than the activation barrier of the N2O decomposition on 3T-Ga=O. It is interesting to remark that the activation free energy associated # with TS3, 44.35 kcal/mol, is 0.68 kcal/mol higher than the activation energy E (Table 1). The specific negative activation entropy for oxidation reaction 6 indicates that the structure of the corresponding transition state TS3 is more ordered in comparison to transition states TS1 and TS2 for oxidation reactions 2 and 4, respectively. This agrees with calculated vibration contributions to entropies of the reactant (49.67 cal/mol.K) and the TS3 (47.27 cal/mol.K) for the reaction 6. -1 The imaginary frequency associated with the third transition state TS3 mode is -812i cm along 160 Conference on Current Trends in Computational Chemistry 2008 the r(O-N) reaction coordinate that connects reactants to products (3T-GaO3). The normal coordinate vectors of the vibrational modes, corresponding to the imaginary frequencies of -1 -1 -1 transition states TS1, TS2, and TS3 at 447i cm , 677i cm and 812i cm , respectively, show that, in all cases, the dominant motions involve the rupture of O-N bond. Taking into account that the enthalpy of reaction is HR = -16.88 kcal/mol at T=298 K, it follows that the reverse reaction is very slow. It is worthwhile noting that at MP4(SDTQ)//MP2 level the activation barrier (+37.1 kcal/mol) is lower by 9.3 kcal/mol than the activation energy (+46.4 kcal/mol) at MP2 level (Table 1). This activation barrier with the corrections for zero-point vibrational energy ( EZPVE) and for thermal energies ( H), on the basis of the MP2 geometries, decreases up to 34.4 kcal/mol. - + - + 4. Energetics of O2 desorption from 3T [OGaO2] and 3T [GaO3] - + The calculated energy of reaction for desorption of singlet O2 from the 3T [Ga(O)3] cluster at MP2 level is 33.4 kcal/mol. When one takes into account the entropy gained upon the desorption of singlet O2, the contribution of entropy to the free energy of desorption is TΔS =12.3 kcal/mol at 298 K. The calculated energy of the singlet oxygen desorption from 3T- + [OGaO2] cluster ΔH (298 K)=+43.57 kcal/mol and ΔG(298 K)=30.13 kcal/mol is significantly - + higher than the barriers of the singlet molecular oxygen desorption from 3T [Ga(O)3] cluster. Table 1. Computed reaction enthalpies HR, reaction free energies GR, at 298 K, activation # energies ( Ea , E , at 298 K), and activation free energies Ga , at 298 K, (in kcal/mol), for - + - + - + N2O decomposition on 3T [Ga] , 3T [GaO] , and 3T [GaO2] clusters at MP2 level. Energies Reaction 2 Reaction 4 Reaction 6 Ea (MP2) 22.78 37.27 46.38 E# 15.67 26.48 43.67 Ga 14.05 21.21 44.35 Ea (MP4) 21.02 23.78 37.09 HR -56.88 -21.09 -16.88 GR -63.58 -27.38 -13.88 1. Solkan, V. N.; Zhidomirov, G. M.; Kazansky, V. B. Int. J. Quantum Chem. 2007, Vol. 107, Iss. 13. pp 2417-2425. Conference on Current Trends in Computational Chemistry 2008 161 DFT Study on Interaction of Acylation Reagents with 4- phenyl-1,3-dihydro-1,5-benzodiazepin-2-one L. Sviatenko,1,2 S. Okovytyy,2,3 A. Gaponov,3 L. Kasyan,3 I. Tarabara,3 J. Leszczynski2 1 Kirovograd State Pedagogical University, Kirovograd, 25006, Ukraine; 2 Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson State University, Jackson, Mississippi 39217 USA; 3Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine The interest to acylation products of benzodiazepinones is caused by their potential biological activity. The mechanisms for the acylation reactions of 4-phenyl-1,3-dihydro-1,5- benzodiazepin-2-one (1) with acetic anhydride, benzoic anhydride, trifluoroacetic anhydride and acetyl chloride were investigated at the B3LYP/6-31G* level of theory. Solvent effects were considered via polarizable continuum model. O H O H N N CH 3 O N N H2C (CH3CO)2O CH3COCl H N O 10 1 2 8 9 2 5 3 7 4 6 5 11 N 1 (CF CO) O (C6H5CO)2O 3 2 H N O O H N O O N N CF3 3 4 The obtained results are in line with experimental study which shows that the direction of acylation of 4-phenyl-1,3-dihydro-1,5-benzodiazepin-2-one depends on the structure of acylation reagent. The electrophilic attack occurs either on the atom of oxygen, or on the atom C3 and results in formation of mono-acyl substituted 1,5-benzodiazepines (2, 3, 4) or isomerization of initial benzodiazepin-2-one (1) in benzimidazol-2-one (5) takes place. The formation of N-acyl derivatives does not occur under abovementioned conditions of reactions. 162 Conference on Current Trends in Computational Chemistry 2008 Two-photon Absorption Predicted with Time-Dependent Density Functional Theory: Sum over States vs. Coupled Electronic Oscillator formalisms Sergio Tafura,b, Ivan A. Mikhailova, Artëm E. Masunova,c,b a Nanoscience Technology Center, bDepartment of Physics, cDepartment of Chemistry, dCREOL, College of Optics and Photonics, University of Central Florida, 12424 Research Pkwy Suite 400, Orlando 32816, USA E-mail: [email protected] Two-photon absorption (2PA) is an electronic excitation process involving the simultaneous absorption of two photons. 2PA probability is quadratically dependent on the intensity of incident light, so it may be localized in space with a tightly focused laser beam. There are a wide range of 2PA applications, such as lithographic micro-fabrication, three dimensional data storage, photonic devices, quantum information technology, optical limiting, two-photon pumped lasing in organic chromophores and quantum dots, in-vivo imaging, and cell-selective photo-dynamic therapy. Most applications require chromophores with large 2PA cross-sections to minimize laser intensity requirements and prevent overheating of targets. To design more efficient 2PA chromophores, it is important to understand their structure/activity relationships. Computer modeling of 2PA spectra facilitates understanding of these relationships and represents a rational approach in chromophore design. Time-Dependent Density Functional Theory (TD-DFT) was successfully used in many cases to describe the excited states in large conjugated molecules. In its linear response formalism it results in non-Hermitian eigenvalue problem: ⎛ A B ⎞⎡X ⎤ ⎡X ⎤ ⎜ ⎟⎢ ⎥ = Ω⎢ ⎥ , (1) ⎝− B − A⎠⎣Y ⎦ ⎣Y ⎦ where matrices A, B stand for excitation, deexcitation operators correspondingly, Ω are the excitation energies, and the transition density matrix is block-diagonal with occupied-vacant X and vacant-occupied Y blocks being nonzero. We recently combined TD-DFT with the Coupled Electronic Oscillator (CEO) formalism [1] to simulate 2PA electronic spectra in large conjugated molecules [2, 3]. These 2PA predictions were shown to achieve superior accuracy, when compared to semiempirical wavefunction theory methods. The CEO-DFT method is developed to the third order. The 1PA and 2PA cross sections are obtained as imaginary part of optical polarizability α and second hyperpolarizability γ: 4π ω 4π 2 ω 2 σ = h ℑ α()− ω;ω , σ = h L4 ℑ γ ()− ω;ω,ω,−ω , (2) 1PA ηc 2PA η 2c 2 where ω is photon energy, η is a dielectric constant, L – a scaling factor, stands for orientation averaging. An alternative, more traditional approach to prediction of 2PA spectra makes use of Sum over States (SOS) formalism. In the SOS, the orientationally averaged 2PA cross-section at resonance ω is given by [4]: 8π 3ω 2 3 1 N ⎛ μ i μ j + μ j μ i ⎞ σ = g()2ω M M * + 2M M * , M = ⎜ fk kg fk kg ⎟ . (3) 2PA 2 ∑()ii jj ij ij ij ∑⎜ ⎟ 15c i, j 2h k ⎝ ωkg − ω − i Γ h ⎠ Conference on Current Trends in Computational Chemistry 2008 163 Here g(2ω) is a Lorentzian lineshape with an empirical linewidth Γ; Mij are the two-photon i transition matrix elements; μnm are spatial components of state-to-state transition dipoles; spatial indices i,j = x, y, z; index k runs over all states up to state N; and hωkg stands for energy difference between the states. The SOS approach opens new venues for interpretation of 2PA properties in terms of molecular electronic structure and can be used for rational design of 2PA i chromophores. However, it requires permanent and state-to-state transition dipole moments μnm , which are not available in linear response TD-DFT. These dipole moments can also be used to identify the essential states governing the 2PA process. Figure 1. Structural formulas (top row), 1PA profiles (row 2), 2PA profiles (row 3), and isosurfaces for natural transition orbitals (bottom row) for studied conjugated chromophores. Red dots mark the experimental profiles, green and blue solid lines correspond to theoretical predictions with SOS and CEO formalisms respectively. The 2PA curves for CEO are slightly lower, than ones for ATDA. The 1PA represents a linear response and is the same for the both formalisms. In order to predict these dipole moments, we introduced a posteriori Tamm-Dancoff approximation (ATDA) [5]. In this approximation, the deexcitation block of the transition density Y is annihilated after solving the full TD-DFT equation (1). As a result, Coulomb- exchange-correlation coupling terms in CEO expressions for polarizabilities vanish, and familiar single configuration interactions formulas can be used for the permanent and transition dipoles. The doubly excited states are added according to the CEO formalism. Thus excitation energies in the ATDA and CEO methods coincide by definition. 164 Conference on Current Trends in Computational Chemistry 2008 In this contribution we calculate permanent and state-to-state transition dipole moments nm using ATDA and employ them to identify the essential states governing the 2PA process. We also validate ATDA by using these approximate nm to predict the resonant 2PA cross- sections with the SOS model and compare them to CEO results as well as experimental values. The conjugated chromophores selected as the subjects of this study are presented on Fig.1. These compounds were experimentally synthesized and characterized by Belfield et al. [6]. Theoretical models of these were derived by truncation of the aliphatic chains and replacing them with to methyl groups in the original experimental structures. We present 2PA profiles obtained with both SOS and CEO formalisms on Fig.1. To analyze the electronic structure of the excited states, we use the natural transition orbitals, which diagonalize the transition density matrix and give the best representation of the electronic excitation in single-particle terms [7]. SOS and CEO results are in quantitative agreement with each other and also agree well with experimental ones. ATDA/SOS approach takes much less computational resources than CEO or response methods thus opening new possibilities for interpretation and predictions of 2PA properties in terms of molecular electronic structure and can be used for rational design of 2PA chromophores. This validates the use of TD-DFT as a part of rational design strategies directed toward new and improved two-photon absorbing materials. References [1] S. Tretiak, S. Mukamel, Chemical Reviews 2002, 102, 3171. [2] A. M. Masunov, S. Tretiak, Journal of Physical Chemistry B 2004, 108, 899. [3] E. A. Badaeva, T. V. Timofeeva, A. M. Masunov, S. Tretiak, Journal of Physical Chemistry A 2005, 109, 7276. [4] K. Ohta, K. Kamada, Journal of Chemical Physics 2006, 124. [5] I. Mikhailov, S. Tafur, A. Masunov, Phys. Rev. A 2008, 77, 012510. [6] K. D. Belfield, M. V. Bondar, J. M. Hales, A. R. Morales, O. V. Przhonska, K. J. Schafer, Journal of Fluorescence 2005, 15, 3. [7] R. L. Martin, Journal of Chemical Physics 2003, 118, 4775. Conference on Current Trends in Computational Chemistry 2008 165 Ab Initio Calculations of Guanine-Aspartic Acid Interactions Patrina Thompson-Harris(a) , Bridgit O. Crews(b) , Mattanjah S. de Vries(b) , Glake Hill(a)* aDepartment of Biochemistry and Chemistry, Jackson State University, MS, and bDepartment of Chemistry and Biochemistry, UC of Santa Barbara, CA Hydrogen-bonded clusters of Guanine and Aspartic Acid are being studied by the hartree- fock (HF) theory and the density functional theory (DFT) at the B3LYP level with applications of different basis sets. The Guanine-Aspartic Acid clusters were evaluated independently by performing optimizations, frequency, and single point energy calculations. In the spectral region of 32,500 cm-1 to 35,500 cm-1, five isomers of Guanine-Aspartic Acid clusters are being observed and are assigned their specific structures based on the theoretical IR spectra and HF and DFT calculations. Frequency calculations are scaled according to what basis set is being utilized to correspond with experimental data produced. This research represents the first set of ab initio calculations of the isolated, microscopic interactions of an amino acid and a nucleobase, the building blocks of RNA and proteins. Calculations and results will be discussed. 166 Conference on Current Trends in Computational Chemistry 2008 The Time Dynamics of Spherical Nanoparticles Aggregation Oleg G. Tovmachenko, Paresh C. Ray Chemistry Department, Jackson State University The time dynamics of noble metal nanoparticles aggregation has been studied in presence the Rhodamine 6G (Rh6G) molecules. The specific difference of this research concludes in using the Rh6G molecules both as the Surface enhanced Raman scattering (SERS) tags and the chemical agents to initiate the aggregation of nanoparticles. This is very interesting contrary to well known fact that Rh6G molecules don’t adsorb to gold surface. Comparison aggregation processes for gold and silver nanoparticles shows that the aggregation rate dependence for silver and gold nanoparticles aggregation is quite different and the gold nanoaggregates are extremely stable. One goal of this work is to optimize the noble metal nanoparticles aggregation process to provide the feasibility of using SERS for detection of the HIV, anthrax DNA, using low-cost and portable Raman spectrometers. Typically, these spectrometers arranged with an NIR diode laser as the excitation source due to reason that NIR excitation reduces the native fluorescence background from microorganisms. One of most popular diode laser excitation wavelength is 785 nm. Conference on Current Trends in Computational Chemistry 2008 167 A Theoretical and Matrix-Isolation Infrared Spectroscopic Study of Mixed MDyX4 (M = Alkali Metals, X = Halogens) Vapor Complexes Zoltán Varga,a Attila Kovács,a Cornelis Petrus Groen,b Magdolna Hargittaia aMaterials Structure and Modeling Research Group of the Hungarian Academy of Sciences,Budapest University of Technology and Economics H-1111 Budapest, Szt. Gellért tér 4, Hungary; bUrenco Nederland B. V., P.O. Box 158, 7600 AD Almelo, The Netherland The formation of MLnX4 type complexes (M = alkali metal, Ln = lanthanide, X = halogen) from the parent alkali and lanthanide(III) halides in high temperature vapors has great importance in high-intensity metal halide lamps. These complexes are responsible for the vapor transport of the lanthanide elements from the cooler regions to the emitting arc.1 The thermodynamics of this process, however, is not yet fully understood lacking reliable molecular data on the species involved and on the energetics of the possible reactions at high temperature. 2,3 Previously we performed systematic studies on LiLnX4 (Ln = La, Ce, Dy; X = F, Cl, Br, I) 4 5,6 and MLaX4 complexes (M = Na, K, Cs; X = F, Cl, Br, I) as well as on NaDyBr4. These studies determined the structural characteristics of these complexes: from the possible monodentate, bidentate, and tridentate coordination of the alkali metal, the latter two structures (Figure 1) have sufficient (and similar) stability in real systems. We have elucidated also a few trends in the structural and vibrational properties within the investigated set of molecules. Figure 1. Relevant structures of MLnX4 complexes We report here our new results on the structure, energetic and vibrational properties of MDyX4 (M = Li, Na, K, Cs; X = F, Cl, Br, I) mixed alkali metal/dysprosium trihalide complexes obtained by a joint theoretical and spectroscopic study. We have investigated the relative stabilities of the relevant bidentate and tridentate structures by DFT calculations (MPW1PW91 in conjunction with relativistic effective core potentials and cc-pVTZ valence basis sets). The results indicate that, although at room temperature the tridentate form is the most stable; the stability of the bidentate form increases with temperature, due to the entropy effect (Figure 2). 168 Conference on Current Trends in Computational Chemistry 2008 Etri - Ebi (0K, kJ/mol) ΔGtri – ΔGbi (1000 K, (kJ/mol) 35 40 30 25 35 20 30 15 F F 25Cl 10 Cl Br Br 5 20 I I 0 15 -5 10 -10 -15 5 -20 0 Li Na KRbCs Li NaKRb Cs Figure 2. Energy differences of the two relevant structures (tri = tridentate and bi = bidentate). The survey of various dissociation processes revealed the preference of the dissociation to neutral MX and DyX3 fragments over ionic and radical dissociation products (Figure 3). Cationic complexes are considerably less stable at 1000 K than the neutral complexes, and they prefer + − dissociation to M + DyX4 fragments. 1000K 1400 ΔG + (kJ/mol) LiF+DyF3 + 1200 LiF +DyF3 Li++DyF · + 1000 + 4 CsI+DyI3 LiDyF4 + 800 CsI +DyI3 · · Li+DyF4 + · Cs +DyI4 600 - + -1e CsDyI4 + - Li +DyF4 · · 400 Cs +DyI4 + - -1e- 200 Cs +DyI4 CsI+DyI3 0 LiF+DyF3 LiDyF4 CsDyI4 -200 Figure 3. Comparison of various dissociation processes. The vapor species existing over mixtures of CsBr + DyBr3 and CsI + DyI3 in the temperature range 900 – 1000 K have been isolated in krypton and xenon matrices and were investigated by infrared spectroscopy. Beside the characteristic vibrational frequencies of the monomeric CsX and DyX3 and the dimer Cs2X2 species, signals have been observed confirming the formation of mixed complexes of stoichiometry CsDyX4 (Figure 4). From the two possible structures, the bidentate form was the major species in the matrix (bands indicated by red Conference on Current Trends in Computational Chemistry 2008 169 arrows). A weak additional band found in the Dy–X stretching region of the spectra (blue arrow) suggests a minor amount of the tridentate form in the matrix. CsDyBr4 CsBr A DyBr3 Cs2Br2 50 75 100 125 150 175 200 225 -1 Wavenumber (cm ) Figure 4. FT-IR spectrum of matrix(Xe)-isolated CsDyBr4 Acknowledgement: This research has been supported by the Hungarian Scientific Research Foundation (OTKA, No. K 60365). References (1) Hilpert, K.; Niemann, U. Thermochim. Acta 1997, 299, 49. (2) Groen, P.; Oskam, A.; Kovács, A. J. Mol. Struct. (THEOCHEM) 2000, 531, 23. (3) Groen, P.; Oskam, A.; Kovács, A. Inorg. Chem. 2000, 39, 6001. (4) Groen, P.; Oskam, A.; Kovács, A. Inorganic Chemistry 2003, 42, 851. (5) Varga, Z.; Hargittai, M. Struct. Chem. 2006, 17, 225. (6) Liebman, J. F.; Varga, Z.; Hargittai, M. Struct. Chem. 2007, 18, 269. 170 Conference on Current Trends in Computational Chemistry 2008 Multimillion to Billion Atom Simulations of NanoSystems Under Extreme Conditions Priya Vashishta Collaboratory for Advanced Computing and Simulations (CACS), Department of Physics & Astronomy, Chemical Engineering & Materials Science, and Department of Computer Science University of Southern California, Los Angeles, CA 90089-0242, USA, Email: [email protected] Advanced materials and devices with nanometer grain/feature sizes are being developed to achieve higher strength and toughness in ceramic materials and greater speeds in electronic devices. Below 100 nm, however, continuum description of materials and devices must be supplemented by atomistic descriptions. Current state of the art atomistic simulations involve 10 million – 1 billion atoms. MD simulations are performed to study critical issues in the area of structural and dynamical correlations, and reactive processes in nanostructured materials under extreme conditions. We report the results of MD simulations of: (1) CdSe nanorods embedded in a liquid undergoing forward and reverse structural phase transformation under hydrostatic pressure; (2) initiation, growth and healing of wing cracks in confined silica glass under dynamic compression where frictional sliding of pre-crack surfaces nucleates nanovoids, which evolve into nanocrack columns at the pre-crack tip; (3) hypervelocity projectile impact damage in aluminum nitride and strong interplay between shock-induced structural phase transformation, plastic deformation and brittle cracks; (4) interaction of nanovoids in silica glass under hydrostatic tension resulting in the nucleation of nanocavities in intervoid ligaments as a result of the expansion of Si-O rings due to a bond-switching mechanism; (5) initiation of chemical reactions at shock fronts prior to detonation and dynamic transition in the shock structure of an energetic material (RDX); and (6) exploding nano particles - explosive burning of aluminium nanoparticles. Conference on Current Trends in Computational Chemistry 2008 171 Stacking Influences on the Spectra of the Monomer of PFBT: A Theoretical Study Jing Wang, Jiande Gu, and Jerzy Leszczynski Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217 U. S. A.; Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203 P. R. China Conjugated polymers (CPs) contain one π-conjugated backbone and functional groups that ionize in high dielectric media. These materials combine the semiconducting and photon harvesting properties of electronically delocalized polymers with the charge-mediated behavior of polyelectrolytes. CPs can be used as highly responsive optical sensors for chemical and biological targets. One of the typical CPs, poly[9,9´-bis-(6´-N,N,N-trimethylammonium)hexyl] fluorene-alt-4,7-(2,1,3-benzothiadiazole)] (PFBT), has been applied in biosensors which incorporated into DNA chips and microarrays for the strand-specific DNA detections., The density functional theory (DFT) and the time-dependent density functional theory (TDDFT) approach were employed to simulate the absorption and emission spectra of the studied species in the present study. The stacking influences on the spectra of the monomer unit F(BT)F caused by the units fluorine (F) and 2,1,3-benzothiadiazole (BT) have been explored, respectively. 172 Conference on Current Trends in Computational Chemistry 2008 Computational Study of Interfacial Reaction Dynamics and Basicity Collin D. Wick Department of Chemistry, Louisiana Tech University, Ruston, LA, 71270 Molecular dynamics simulations with many-body potentials were carried out to study the propensity for the hydroxide anion for the air-water interface using the combined classical- quantum mechanical MS-EVB potential. In addition, the rate constant for NaCl dissociation at the interface, and how it compares to the bulk was calculated using the transition path sampling method. While the hydronium ion is fairly well accepted to have a propensity for the air-water interface, there is significant disagreement associated with the hydroxide anion. The MS-EVB potential allows the hydroxide anion to be treated in traditional molecular dynamics simulations, but explicitly accounts for proton sharing of water molecules with the hydroxide anion. For the hydroxide anion, reasonable agreement with experiment was found for both radial distribution functions and hydroxide anion diffusion. Also, while understanding more complex reactions than NaCl dissociation is desirable, this simple model system will bring initial insight into a challenging process of understanding interfacial reactions. Since many atmospherically relevant reactions are conjectured to occur at the surface of aqueous droplets, the understanding interfacial dynamics and structure will benefit the atmospheric field. The results showed that the NaCl dissociation was considerably slower at the air-water interface than in the bulk. This was consistent with the free energy profile of NaCl dissociation at the air-water interface, which showed a higher free energy peak than in the water bulk. Conference on Current Trends in Computational Chemistry 2008 173 Contribution of Nonpolar Interactions to Molecular Recognition and Binding of Type I Antifreeze Proteins at the Ice-Water Interface Andrzej Wierzbicki and E. Alan Salter Department of Chemistry, University of South Alabama, Mobile, Alabama 36688 Molecular dynamics simulations and molecular modeling are used to study the various molecular interactions, both hydrophobic and hydrophilic, that influence the recognition and binding of Antifreeze Proteins (AFPs) at water/ice interfaces. Based on our computational studies, we have designed and experimentally tested nine ice-binding AFP analogues to investigate the importance of nonpolar functional groups in the surface-orientation-dependent adsorption of Type I antifreeze proteins. Nonpolar functional groups of winter flounder (WF) AFP are chiefly responsible for its shape: the methyl groups of the threonine motif, which bulge from the helix, the leucines of the prominent ridges of the TANL side, and the smooth alanine- rich TAA side. Thus, nonpolar groups play a crucial role in the recognition and adsorption of the Type I AFPs to well-defined sites on the ice surface. We propose a new model for the binding of WF AFP to the {201} surface of ice, in a groove formed between {2-10} and {011} facets of ice. 174 Conference on Current Trends in Computational Chemistry 2008 Theoretical Study on the Magnetism in Finite Size Single Wall Carbon Nanotube Jianhua Wua and Frank Hagelbergb a CCMSI, Department of Physics, Atmospheric Sciences, and Geoscience, Jackson State University, Jackson, MS 39217, USA;b Department of Physics, Astronomy, and Geology, East Tennessee State University; Johnson City, TN 37614, USA Finite sized zigzag SWNTs of the (10,0) type have been investigated by DFT with respect to their geometric, energetic, electronic, and magnetic properties, with emphasis on the dependence of these properties on the mode of nanotube termination. Three termination prototypes were considered: Hydrogenation, truncation with edge reconstruction, and capping by fullerene hemispheres (see Fig.1). The evolution of the magnetic features of these types with increasing SWNT length was studied for systems varying in length from 2 to 40 layers. Further, we inspected the case of asymmetric termination by including (10,0) systems with a hydrogenated and a truncated end. (a) (b) (c) (d) Figure1. The equilibrium geometries of a (10,0) SWNT with (a) H-termination (C200H20), ( b) truncation with reconstructed edge layers (C200+20), (c) capping with fullerene hemispheres (C200+40), and (d) asymmetric termination with one end hydrogenated and the other one truncated (C200H10). Green symbols represent H, and grey symbols C atoms of intermediate layers, while light blue symbols indicate C atoms in the terminating decagons (b) or fullerene hemispheres (c). Magnetic ground states were found for all species investigated. The hydrogenated as well as the truncated units exhibit AFM ordering throughout, involving antiparallel magnetic moments which are localized at the tube edges. This configuration is associated with the presence of unpaired electronic edge states and thus with the incomplete saturation dangling C atom bonds by a single layer of H atoms or by C atom reconstruction following truncation. In contrast to the two other prototypes discussed here, the capped SWNTs display a delocalized magnetic density distribution along the tube axis. Further, no unanimous dominance of AFM ordering is recorded Conference on Current Trends in Computational Chemistry 2008 175 in this case. On the contrary, capped (10,0) were found to exhibit FM ground states in the asymptotic length limit. The energy separation between the FM and the AFM phase, as well as between the magnetic and the non-magnetic solution turned out to be markedly lower than in the cases of hydrogenation or truncation. The two latter models can be understood in analogy to a composite involving a non-magnetic metal surrounded by two layers with itinerant magnetism. In both arrangements, the respective middle segment mediates the magnetic interaction between system boundaries, while the magnetization induced in this region is strongly damped. For SWNT termination with fullerene hemispheres, however, this analogy breaks down. Here the magnetization penetrates into the intermediate regime, extending far beyond the ends of the tube. The near – degeneracy of the FM and AFM alternatives in the capped SWNTs studied in this work might make these systems suitable for use as magnetoresistive elements. 176 Conference on Current Trends in Computational Chemistry 2008 Phospholipid Molecular Recognition at the Monomer Boundaries of Copolymer Surfaces; Spectroscopic and Ab Initio Studies Min Yu,1 Marek W. Urban,1*Yinghong Sheng,2 and Jerzy Leszczynski2* 1 School of Polymers and High Performance Materials, The University of Southern Mississippi, Hattiesburg, MS 39406, 2 The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217 Lipid structural features and their interactions with proteins provide a useful vehicle for further advances in membrane proteins research. To mimic one of potential lipid interactions with macromolecules we synthesized poly(methyl methacrylate/n-butyl acrylate) (p-MMA/nBA) colloidal particles that were stabilized by phospholipid (PL). Upon particle coalescence, PL stratification resulted in the formation of surface localized ionic clusters (SLICs). These entities are capable of recognizing MMA/nBA monomer interfaces along the p-MMA/nBA copolymer backbone and form crystalline SLICs near the monomer interface. Utilizing attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and selected area electron diffraction (SAD) combined with ab initio calculations, we identified the origin of SLICs as well as their structural features formed on the surface of p-MMA/nBA copolymer films stabilized by 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) PL. Specific entities responsible for SLIC formation illustrated in Figure 1 are selective non-covalent bonds of anionic phosphate and cationic quaternary ammonium segments of DLPC that interact with two neighboring carbonyl groups of nBA and MMA monomers of the p-MMA/nBA polymer backbone. Remarkable agreements between the experimental data and theoretical predictions were obtained. To the best of our knowledge this is the first example of molecular recognition facilitated by coalescence of copolymer colloidal particles and the ability of PLs to form SLICs at the boundaries of the neighboring MMA and nBA monomer units of the p-MMA/nBA chain. The dominating non- covalent bonds responsible for the molecular recognition is a combination of H-bonding and electrostatic interactions. SAD O O O O 3 O O .9 0 P Å O O N 6.16Å nBA1 nBA2 O O O O O O O O Crystal lattice 4.0 Å MMA1 MMA2 6.2 Å A B C D Figure 1. SLICs structural features resulting from the interactions between p-MMA/nBA copolymer and DLPC determined by experimental and computational methods: A - ab initio calculated SLICs; B - 3D representation of calculated SLICs; C - selected area diffraction image of SLICs (lattice dimensions: 4.0 x 6.2 Å); D - ab initio calculated crystal lattice of SLIC (lattice dimensions: 3.90 x 6.16 Å). Conference on Current Trends in Computational Chemistry 2008 177 TGA SAM: a Potential Switch Jian-Ge Zhou and Quinton L. Williams Department of Physics, Atmospheric Sciences, and Geoscience, Jackson State University, Jackson, MS 39217, USA We show how TGA molecules form a self-assembled monolayer (SAM) on the Au(111) surface. The formation mechanism of gauche and trans conformers of TGA on the Au(111) [1] is discovered. The calculated Raman spectrum of TGA on the gold surface matches with the experimental data [2]. Our work is the first step toward the finding of the new SAM switch. References [1] J.-G. Zhou and Q. L. Williams, to appear. [2] A. Krolikowska et. al., Sur. Sci. 532, 227 (2003). 178 Conference on Current Trends in Computational Chemistry 2008 List of Participants Conference on Current Trends in Computational Chemistry 2008 List of Participants Conference on Current Trends in Computational Chemistry 2008 181 Damilola Adepegba Maria Barysz University of Maryland Nicolaus Copernicus University Eastern Shore Torun, 87-100 Poland 12609 Nichols Promise Drive Tel: +48 56 611-47-61 Bowie, MD 20720 U.S.A. Fax: +48 56 654 24 Tel: 240-464-4553 Email: [email protected] Email: [email protected] Shonda Allen Hill Desiree Bates Jackson State University University of Mississippi Department of Chemistry Department of Chemistry and 1325 Lynch St. Biochemistry Jackson, MS 39217 U.S.A. 107 Coulter Hall Tel: 16019793723 University, MS 38677-1848 U.S.A. Fax: 16019793723 Tel: 662 915-7301 E-mail: [email protected] Fax: 662 915-7301 Email: [email protected] Anatoliy Artemenko Tony Bednar A.V. Bogatsky Physical-Chemical Environmental Laboratory Institute National US Army Engineer Research and Academy of Sciences Development Center 86 Lustdorskaya doroga, 3909 Halls Ferry Road Odessa, 65080 Ukraine Vicksburg, MS 39180 Tel: +380487225127 Email: [email protected] Vladimir Azriel Manikanthan Bhavaraju Institute of Energy Problems Mississippi State University of Chemical Physics Starkville, MS 39762 U.S.A. Moscow, 119334 Russia Tel: 8457311755 Tel: +7(495)1374104 Email: [email protected] E-mail: [email protected] Del Bagwell Pierre Bonifassi US Army ERDC, Jackson State University Information Technology Laboratory Department of Chemistry 3909 Halls Ferry Road 1325 J.R. Lynch Street Vicksburg, MS 39180-9981 P.O. Box 17910 Tel: 601-634-2860 Jackson, MS 39217 U.S.A. Fax: 601-634-2236 Tel: 601-842-6754 E:mail: [email protected] E-mail: [email protected] Jon Baker Jaroslav Burda Parallel Quantum Solutions Department of Chemical Physics and 2013 Green Acres Rd Optics, Faculty of Mathematics and Suite A Physics,Charles University Fayetteville, AR 72703 U.S.A. Ke Karlovu 3 Tel: 479-521-5118 Charles University Fax: 479-521-5167 Prague, 12116 Czech Republic E-mail: baker@pqs-chem.com Tel: +420221911246 E-mail: [email protected] Anu Bamgbelu Adegoke Bei Cao Jackson State University University of Mississippi Department of Chemistry Department of Chemistry and 1325 J.R. Lynch Street Biochemistry P.O. Box 17910 107 Coulter Hall Jackson, MS 39217 U.S.A. University, MS 38677 U.S.A. Tel: 601 979 3723 Tel: 662-915-7301 E-mail: [email protected] Fax: 662-915-7300 Email: [email protected] 182 Conference on Current Trends in Computational Chemistry 2008 List of Participants Erica Chong Dalephine Davis Mississippi College Jackson State University 200 South Capitol Street Department of Chemistry Clinton, MS 39058 U.S.A. 1400 JR Lynch St. Tel: 601-925-3852 Jackson, MS 39217 U.S.A. Fax: 601-925-3933 Tel: (601)979-1525 Email: [email protected] Email: [email protected] Tim Clark Deborah F. Dent University of Erlangen-Nuremberg Deputy Director, ITL Erlangen, 91052 Germany US Army Corps of Engineer Research Tel: +49(0)-9131-85 22948 and Development Center Fax: +49(0)-9131-85 26565 ERDC Executive Office Email: [email protected] 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199 Tel: 601-634-3455 Fax: 601-634-2638 David Close Tandabany Dinadayalane East Tenn. St. Univ. Jackson State University,CCMSI Physics Dept. Department of Chemistry Box 70652 1400 J.R. 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P.O. Box 17910 Tel: 01133243868377 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979-1797 E-mail: [email protected] Ernest Davidson Velvelyn B. Foster Univ of Washington Vice President for Academic 504 Copperline Drive Affairs and Student Life Chapel Hill, NC 27516 U.S.A. Jackson State University Tel: 9199671992 P.O. Box 17199 Email: [email protected] Jackson, Mississippi 39217 Tel: 601 979-2244 Fax: 601 979-8246 List of Participants Conference on Current Trends in Computational Chemistry 2008 183 Fillmore Freeman Mark G. Hardy Department of Chemistry College of Science, Engineering, University of California, and Technology, 1113Natural SciencesII, Jackson State University Irvine, CA 92697-2025 U.S.A. Jackson, MS 39217 Tel: 949-824-6501 Tel: 601-979-3449 Fax: 949-824-8571 Email: [email protected] E-mail: [email protected] Al'ona Furmanchuk Ayorinde Hassan Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 J.R. 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Tel: 601-979-1134 Tel: 6019793979 Fax: 601-979-3723 Fax: 6019797823 E-mail: [email protected] E-mail: [email protected] Melva James Carlos Kubli-Garfias Massachusetts Institute of Technology Texas A&M University 70 Pacific Street College Station, TX 77843-3122 Cambridge, MA U.S.A. Cambridge, MA 02139 USA Tel: 979-862-1329 Tel: (617) 452-4252 Email: c0k2008.chemail.tamu.edu Email: [email protected] Jyothsna Kanipakam Vitalina Kukueva Jackson State University Fire Safety Institute Jackson, MS 39217 USA Onoprienko str. 8 Tel: 601-979-0253 Cherkassy, 18034 Ukraine Fax: 601-979-7823 Tel: +380472362233 Email: [email protected] Fax: +380472 550971 E-mail: [email protected] List of Participants Conference on Current Trends in Computational Chemistry 2008 185 Gulnara Kuramshina Meng-Sheng Liao Department of Physical Chemistry, Department of Chemistry Faculty of Chemistry Jackson State University Moscow State University 1400 J. R. Lynch Street (M.V.Lomonosov) Jackson, MS 39217 U.S.A. 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Mosher University of Central Florida Director, Information Technology 12424 Research pkwy, suite 400, Laboratory, Engineer Research and NanoScience Technology Center Development Center Orlando, FL 32826 U.S.A. 3909 Halls Ferry Road Tel: 1-407-882-2840 Vicksburg, MS 39180-6199 Fax: 1-407-882-1578 Tel: 601-634-4581 Email: [email protected] Harley R. McAlexander Katherine Munroe Department of Chemistry and Mississippi College Biochemistry 200 South Capitol Street Mississippi College Clinton, MS 39058 USA P.O. Box 3046 Tel: 601-925-3852 Clinton, MS 39058 USA Fax: 601-925-3933 Tel: 601-925-3852 Email: [email protected] Fax: 601-925-3933 E-mail: [email protected] Vincent Meunier Jane Murray Oak Ridge National Laboratory Department of Chemistry Bethel Valley Road University of New Orleans and Oak Ridge, TN 37922 U.S.A. Clevland State University Tel: 8655747632 New Orleans, LA 70148 U.S.A. Fax: 8655740680 Tel: 202-351-1554 Email: [email protected] Fax: 440-331-1785 E-mail: [email protected] Andrea Michalkova Jamshid Najafpour Jackson State University Department of Chemistry, Department of Chemistry Faculty of science, 1325 J.R. Lynch Street Islamic Azad University P.O. Box 17910 Shahr-e-Rey Branch, Narmak, Golestan Jackson, MS 39217 U.S.A. Tehran, Tehran 18735 334 Iran Tel: 601-979-1041 Tel: +98-21-55277800 E-mail: [email protected] Fax: +98-21-22296122 E-mail: [email protected] Brandon Mitchell Brian Napolion Mississippi College Jackson State University 200 South Capitol Street Department of Chemistry Clinton, MS 39058 USA Jackson, MS 39206 U.S.A. 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Clinton, MS 39058 USA Tel: 601-979-2922 Tel: 601-925-3852 Fax: 601-979-3674 Fax: 601-925-3933 E-mail: [email protected] Email: [email protected] Brandice Nowell Biswarup Pathak Mississippi State University Jackson State University Mississippi State, MS 39762 USA 1400 Valley Street, Palisades, Tel: 662-325-0640 apartment 222 C Email: [email protected] Jackson, MS 39204USA Tel: 6019791219 Email: [email protected] Felix Okojie Yuliya Paukku Vice President for Research Jackson State University and Strategic Initiatives Department of Chemistry Jackson State University 1325 J.R. Lynch Street Jackson, MS 39217 USA P.O. Box 17910 Tel: 601-979-2931 Jackson, MS 39217 U.S.A. Fax: 601-979-3664 Tel: (601)979-3723 Email: [email protected] E-mail: [email protected] Sergiy Okovytyy James Perkins Dneporpetrovsk National University Director of Research, Industrial & 72 gagarina Av Community Relations Dnepropetrovsk, 49050 Ukraine Jackson State University Tel: +(38056)5919276 College of Science, Engineering & E-mail: [email protected] Technology (CSET) Vicksburg, MS 39180 USA Tel: 601-634- 3111 E-mail: [email protected] Valentin Oshchapovsky Tetyana Petrova Lviv State University of Life Safety Jackson State University 35 Kleparivska Str. Department of Chemistry Lvov, 79007 Ukraine 1325 J.R. Lynch Street Tel: (38-032)-233-02-02 P.O. Box 17910 Fax: (38-032)-233-00-88 Jackson, MS 39217 U.S.A. E-mail: [email protected] Tel: (601) 979-3979 Fax: (601) 979-7823 Email: [email protected] 188 Conference on Current Trends in Computational Chemistry 2008 List of Participants Peter Politzer Mohammad Mo Qasim University of New Orleans USACE ERDC Environmental Lab Department of Chemistry 3909 Halls Ferry Road New Orleans, LA 70148 USA Vicksburg, MSWarren 39180 U.S.A. Tel: 202-351-1555 Tel: (601) 634 3422 Fax: 440-331-1785 Fax: (601) 634 2742 E-mail: [email protected] E-mail: [email protected] Morgan Ponder Nurmurod Ramazonov Samford University Institute of the Chemistry of Department of Chemistry plant substances Birmingham, AL 35229-2236 U.S.A. Kh. 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Price Teri Robinson Research Agronomist University of California, US Army Corps of Engineer Research Santa Barbara and Development Center Department of Chemistry and Biology ERDC Executive Office Santa Barbara, CA 93106-9510 U.S.A. 3909 Halls Ferry Road Tel: 805-893-4913 Vicksburg, MS 39180-6199 Fax: 805-893-4720 Email: [email protected] E-mail: [email protected] Peter Pulay Dorris Robinson-Gardner Parallel Quantum Solutions Dean, Division of Graduate Studies 2013 Green Acres Road, Suite A Jackson State University Fayetteville, AR 72703 U.S.A. Jackson, MS 39217 Tel: (479) 521-5118 Tel: 601-979-2455 Fax: (479) 521-5167 E-mail:[email protected] Email: [email protected] List of Participants Conference on Current Trends in Computational Chemistry 2008 189 Joshua Rodgers Dulal Senapati Mississippi State University Jackson State University Mississippi State, MS 39762 US Department of Chemistry Tel: (662)325-7602 Jackson, MSU.S.A. Email: [email protected] Szczepan Roszak Indu Shukla Wroclaw University of Technology Jackson State University Wroclaw, 30-579 Poland Department of Chemistry Tel: 48-71-3204310 1325 J.R. Lynch Street Fax: 48-71-3203364 P.O. Box 17910 E-mail: [email protected] Jackson, MS 39217 U.S.A. Tel: 601-979-3723 Fax: 601-979-7823 E-mail: [email protected] Karim Salazar Manoj Shukla Texas A & M University Jackson State University Jack E. Brown Department of Chemistry 3122 TAMU 1325 J.R. Lynch Street College Station, TX 77843 U.S.A. P.O. Box 17910 Tel: 979-86-21343 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979-1136 Fax: 601-979-7823 E-mail: [email protected] Julia Saloni Volha Shukruto Jackson State University IVIC, Centro de Quimica Department of Chemistry Carr. Panamericana, km. 11 1400 J.R. Lynch Street Apartado 21827 P.O. Box 17910 Caracas, Miranda1020-A Venezuela Jackson, MS 39217 U.S.A. Tel: +58-212-504-1906 Tel: 601-979-1797 Fax: +58-212-504-1350 Fax: 601-979-7823 Email: [email protected] E-mail: [email protected] Alden Sanders Tomekia Simeon Jackson State University Jackson State University 1400 J.R. Lynch St. Department of Chemistry Jackson, MS 39217 4535 Parisian Dr. United States Jackson, MS 39206 U.S.A. Tel: (601)384-7047 Tel: 601-918-5983 Email: [email protected] E-mail: [email protected] G. Narahari Sastry Vitaly Solkan Indian Institute of Chemical Technology N. D. Zelinsky Institute of Molecular Modeling Group Organic Chemistry Hyderabad, Andhra Pradesh 500 607 47 Leninskii Prospect India Moscow, 119991 Russia Tel: ++91-40-27193016 Tel: +7(495)1356425 Fax: ++91-40-27160512 Fax: +7(495)1355328 Email: [email protected] E-mail: [email protected] Jorge Seminario Shelton Swanier Texas A&M University Director of The Office of College Station, TX 77843 U.S.A. Strategic Initiatives Tel: 979-845-3301 College of Science, Engineering Email: [email protected] and Technology Jackson State University Jackson, MS 39217 Tel: 601-979-2312 Email: [email protected] 190 Conference on Current Trends in Computational Chemistry 2008 List of Participants Paul B. Tchounwou John Watts Interim Associate Dean Jackson State University College of Science, Engineering Department of Chemistry and Technology 1325 J.R. Lynch Street Jackson State University P.O. Box 17910 1325 Lynch St Jackson, MS 39217 U.S.A. Jackson, MS 39217 Tel: 601 979 3488 601-979-2153 Fax: 601 979 3674 E-mail: [email protected] E-mail: [email protected] Willie Thompson Robert W. Whalin Jackson State University Associate Dean, College of Science, 1124 Hallmark Dr. Engineering & Technology Jackson, MS 39206 U.S.A. Jackson State University Tel: (601) 981-5076 Jackson, MS 39217 U.S.A. E-mail: [email protected] Tel: 601-979-4043 E-mail: [email protected] Patrina Thompson-Harris Collin Wick Jackson State University Louisiana Tech University Jackson, MS 39194 USA P.O. Box 10348 Tel: 601-606-5824 Ruston, LA 71270 U.S.A. Email: [email protected] Tel: 318-257-2345 Fax: 318-257-3823 Email: [email protected] Oleg Tovmachenko Andrzej Wierzbicki Department of Chemistry University of South Alabama Jackson State University Department of Chemistry 1400 Valley Street, Apt. 223 A Mobile, AL 36688 U.S.A. Jackson, MS 39204 U.S.A. Tel: 251-4607436 Tel: 6016682383 Fax: 251-4607359 E-mail: [email protected] E-mail: [email protected] Marek W. Urban Jianhua Wu The University of Southern MS Jackson State University 118 College Drive, #10076 Department of Physics Hattiesburg, MS 39406 USA Jackson, MS 39217 USA Tel: 601-266-6868 Tel: 6019793640 Email: [email protected] Fax: 6019793630 Email: [email protected] Priya Vashishta Hongtao Yu University of Southern California Jackson State University Los Angeles, CA 90089 USA Department of Chemistry Tel: (213) 821-2663 1325 Lynch St. Fax: (213) 821-2664 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: (601)979-2174 Fax: (601)979-3674 Email: [email protected] Jing Wang Min Yu Jackson State University The University of Southern Mississippi Department of Chemistry P. O. Box 10076 1400 J.R. Lynch Street Hattiesburg, MS 39406 USA P.O. Box 17910 Tel: 6012666724 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979-1159 Fax: 601-979-7823 E-mail: [email protected] List of Participants Conference on Current Trends in Computational Chemistry 2008 191 Jian-Ge Zhou Jackson State University Department of Physics 1400 Lynch Street Jackson, MS 39217 U.S.A. Tel: 601-979-3758 Fax: 601-979-3630 E-mail: [email protected] Author Index Conference on Current Trends in Computational Chemistry 2008 193 Author Index Adepegba, D. A...... 49 Guha, R...... 53 Ahuj, R...... 87 Gutiérrez-Oliva, S...... 114 Altilio, D...... 53 Gwaltney, S. R...... 28,140,141 Artemenko, A...... 82,90,127 Habenicht, B. F...... 89 Azriel, V. M...... 19 Habib, T...... 130 Balasubramanian, K...... 152 Hagelberg, F...... 62,174 Bamgbelu, A...... 20 Hargittai, M...... 64,167 Baran, J...... 87 Harkless, J. A.W...... 66 Barysz, M...... 21 Hassan, A...... 67 Bates, D. M...... 23 Hill, F...... 82,109 Belfield, K. D...... 73 Hill, G...... 145,165 Berhanu, W...... 24 Hirata, S...... 69 Bhavaraju, M...... 28 Huang, M. J...... 32,36,102 Bishop, G. R...... 111 Huff, E. M...... 70 Bolshakov, V...... 29,31 Huwe, P. J...... 71 Bonifassi, P...... 32,36 Inerbaev, T...... 53 Brasfield, S...... 130 Iqbal, P...... 73 Bui, V. T...... 51 Isayev, O...... 77 Burda, J. V...... 114 Jarrosson, T...... 142 Burns, J. C...... 113 Kamiya, M...... 69 Cao, B...... 38 Kanipakam, J...... 78 Cenas, N...... 77 Kapat, J...... 53 Chong, E...... 39 Karamanis, P ...... 32,36 Clark, T...... 40 Karasiev, V. V...... 80 Cochran, A...... 125 Kasyan, L. I...... 122,161 Coghlan, C. B...... 104 Kholod, Y...... 82 Collier, W...... 121,140 Kilin, D. S...... 80 Crews, B. O...... 165 Kochikov, I.V...... 83 Daoudi, Y...... 36 Kohn, W...... 86 Darbha, G. K...... 119 Kołodziejczyk, W...... 87,88,145 Daul, C. A...... 142 Koprivanac, N...... 99 Davidson, E. R...... 41 Korkin, A...... 80 Davis, D...... 42 Kosenkov, D...... 89 de Vries, M. S...... 165 Kovács, A...... 167 Deng, Y...... 130 Kovdienko, N.A...... 90,127 Denslow, N...... 130 Kubli-Garfias, C...... 93,143 Deriabina, A...... 52 Kumar, T.K.S...... 70 Diaconescu, B...... 62 Kuramshina, G.M...... 83,95 Dinadayalane , T. C...... 43,67,78 Kušić, H...... 99 Ding, Y...... 45,46 Kuz’min, V.E...... 82,90,127 Dixon, D. D...... 134 Larsso, J. A...... 87 Doyle, F., III ...... 130 Larsso, P...... 87 Dubey, M...... 151 Lee, T. B...... 100 Fang, D.-C...... 46 Lesczynska, D...... 99 Ferreira, D...... 45,46 Lester, W. A. Jr...... 101 Ford-Green, J...... 47,48 Leszczynski, J...... 20,29,31,32,36,43,47,48, Freeman, F...... 49,51 52,67,77,78,82,88,89,99,109,122,126,127, Furmanchuk, A...... 52 128,131,132,146,151,152,158,161,171,176 Ganopadhyay, S...... 53 Li, S.-L...... 46 Gaponov, A...... 161 Li, X.-C...... 45,46 Garcia-Reyero, N...... 130 Li, Y...... 130 Gill, Gurvinder ...... 42,120 Liao, M.-S...... 32,36,102 Goel, S...... 57 Lin, N...... 103 Gonzalez, E...... 52 Liskin, D. V...... 71 Gorb, L...... 47,52,77,82,89,109,132 Liu, R.-Z...... 46 Griffin, J...... 61,119,150 Lofton, C. D...... 104 Groen, C. P...... 167 Magers, A. K...... 105,106 Gryn’ova, G.V...... 122 Magers, D. B...... 105,106,112 Gu, J...... 171 Magers, D. H...... 39,71,103,104,105, Guan, X...... 130 107,111,112,113,125 194 Conference on Current Trends in Computational Chemistry 2008 Author Index Majumdar, D...... 48,88,126 Senyavin, V.M...... 83 Martinez, A...... 52 Sharapov, D.A...... 95 Martinovic, D...... 130 Sharapova, S.A...... 95 Masunov, A. E...... 24,53,57,73,162 Sheng, Y...... 176 McAlexander, H. R...... 107,112 Shiozaki, T...... 69 McKee, M. L...... 100 Shoemaker, J...... 130 Mesit, J...... 53 Shukla, I...... 20 Meunier, V...... 108 Shukla, M. K...... 151 Michalkova, A...... 109,128,131,146 Simeon, T...... 152 Mikhailov, I. A...... 24,73,162 Singh, A. K...... 119,150 Mitchell, B...... 111 Sleiti, A...... 53 Mobley, E...... 112 Smith, S. V...... 42 Munroe, K...... 113 Solkan, V...... 154,156,158 Muratov, E...... 82,90,127 Sood, A...... 39 Murray, J. S...... 114 Sviatenko, L...... 161 Najafpour, J...... 115 Tafur, S...... 162 Neely, A...... 119 Tarabara, I.N...... 31,132,161 Nenchev, G...... 62 Thompson-Harris, P...... 165 Nikmaram, F. R...... 115 Tius, M. A...... 134 Noe, E. A...... 42,120 Tkachenko, I.V...... 31 Novikova, N.S...... 90 Tokar, A.V...... 122 Novohatskaya, H...... 90 Toro-Labbé, A...... 114 Nowell, B...... 121 Tovmachenko, O. G...... 166 Ognichenko, L.N...... 90 Tschumper, G. S...... 23,38 Okovytyy, S.I...... 29,31,122,132,161 Urban, M.W...... 176 Orlovskaya, N...... 53 Valeev, E. F...... 69 Oshchapovsky, V. V...... 123 Valente, E. J...... 71 Ouamerali, O...... 142 Varga, Z...... 167 Pachter, R...... 124 Vashishta, P...... 170 Pan, Y...... 125 Villeneuve, D. L ...... 130 Pathak, B...... 126 Voronkov, E.O...... 29,31 Paukku, Y...... 127,128 Wang, J...... 20,171 Pawar, D. M...... 42,120 Watts, J.D...... 32,36,102 Pentin, Y.A...... 95 Wick, C. D...... 172 Perkins, E. J ...... 47,130 Wierzbicki, A...... 173 Petrova, T...... 131,132 Williams, Q. L...... 177 Peykani, M.K...... 115 Wu, J...... 174 Pittman, C. U. Jr...... 121,140 Yu, M...... 176 Pohl, K...... 62 Zakar, E...... 151 Politzer, P...... 114 Zhou, J.-G...... 177 Poltev, V. I...... 52 Pratt, L. M...... 134 Prezhdo, O. V...... 89,135 Pulay, P...... 70 Qasim, M...... 47,77,82,109 Rai, U. S...... 61,119 Rangel, N. L...... 136 Rasulev, B...... 99 Rattananakin, P...... 121,140 Ray, P.C...... 32,36,61,119,150,166 Rodgers, J. M...... 141 Rossikhin, V.V...... 29,31 Roszak, S...... 88,145 Rusin, L. Yu...... 19 Saal, A...... 142 Salazar-Salinas, K...... 93,143 Saloni, J...... 145 Salter, E. A...... 173 Sanders, B...... 146 Sastry, G. N...... 148 Schulte, A...... 24 Seminario, J. M...... 93,136,143,149 Senapati, D...... 150