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GUIDE to the Zarelabmay 2008 Department of Chemistry, Stanford University Welcome to the ZARELAB

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GUIDE to the Zarelabmay 2008 Department of Chemistry, Stanford University Welcome to the ZARELAB GUIDE TO THE ZARELABMay 2008 Department of Chemistry, Stanford University Welcome to the ZARELAB. This booklet has been prepared to make your visit with us more rewarding by presenting a survey of our recent research activities. Each section was written by those members pursuing the work described therein. Please feel free to ask my lab manager, Dick Zare and the rocket test. Dr. David Leahy, or any other members of my group to discuss any project. INSIDE THIS GUIDE On page 19 is a list of all members of the Table of Contents 2 Zare group as of May 15, 2007 and Research Activities 3 information on how to contact them. On Reaction Dynamics pages 20 and 21 are floor plans of offices Absorption Spectroscopy and labs in Mudd. On page 22 is the Mass Spectroscopy Capillary Electrophoresis floor plan of the East wing at the Clark Microfluidics and SPR Imaging Center, which is across the street from Biosensors Mudd. The last pages show maps of the Single-Molecule Fluorescence Stanford campus and its vicinity. Supercritical Fluids Selected Recent Publications 17 Do enjoy your visit! Group Members 19 Floor Plans of Offices and Labs 20 Maps of Stanford Campus & Vicinity 23 TABLE OF CONTENTS Reaction Dynamics 3 H + H2 Reaction Dynamics Noah Goldberg, Jianyang Zhang, Dan Miller, Nate Bartlett Absorption Spectroscopy 4 Rayleigh Scattering Measurements Using Cavity-Ring Down Spectroscopy Doug Kuramoto 5 Cavity-Ring down Spectroscopy as Applied to Complex Organic Molecules Christa Haase Mass Spectroscopy 6 Two-step Laser Mass Spectrometry of Terrestrial and Extraterrestrial Materials Maegan Spencer, Matthew Hammond, Amy Morrow 7 Hadamard Transform Time-of-Flight Mass Spectrometry Ignacio Zuleta, Oh Kyu Yoon, Matthew Robbins, Griffin Barbula 8 The Development of New Methodologies for the Selective Binding of Phosphopeptides and The Discovery of Potential Biomarkers Songyun Xu, Harvey Cohen Capillary Electrophoresis 9 Photopolymerized Sol-Gel as Chromatographic Media and Chemical Reactors Maria T. Dulay Microfluidics 10 Microfluidic Device for Coupling Capillary Electrophoresis With Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Yiqi Luo 11 Microfluidic Device Coupled with Surface Plasmon Resonance Imaging Yiqi Luo, Logan Leslie, Wing Li 12 Method for Fabricating Three-Dimensional Polydimethylsiloxane Microfluidic Devices Yiqi Luo Biosensors 13 Designing a Capillary Flow System for Impedance Spectroscopy of Individual Cells David Altman Single-Molecule Fluorescence 14 Single Molecule Fluorescence Spectroscopy Spectroscopy Samuel Kim 15 Single-cell Analysis on a Microfluidic Platform Bor-han Chueh, Eric Hall, Samuel Kim Supercritical Fluids 16 Nanoparticle Formation Using Supercritical Fluids Technology Gunilla B.J. Andrews Selected Publications 17 Zare Group Member 19 Office/Lab Floor Plans 20 Maps of Stanford & Vicinity 23 2 H + H2 REACTION DYNAMICS Noah Goldberg, Jianyang Zhang, Dan Miller, Nate Bartlett The simplest of all bimolecular reactions, the H + H2 reaction has been studied since the dawn of modern quantum mechanics. The Zarelab has contributed much to these studies over the last twenty years and was among the first labs to provide experimental results sufficiently refined to compare with accurate quantum mechanical calculations. Using the photoloc technique (photoinitiated reaction analyzed with the law of cosines), we continue this tradition by providing state-to-state differential cross sections (DCSs) for both the reactively and inelastically scattered products. We co-expand a mixture of HBr and D2 through a single nozzle into the extraction region of a Wiley- McLaren time-of-flight mass spectrometer. There, the HBr is photolyzed by a tunable, polarized laser, producing fast H atoms with a well-defined speed and spatial distribution. After waiting approximately 20 ns to allow the buildup of products from single collisions between H atoms and D2 molecules, the HD(v',j') or D2(v',j') products of interest are ionized via (2+1) resonance-enhanced multiphoton ionization (REMPI) using a second laser. These ions are accelerated toward a time and position sensitive detector, and the data are analyzed to obtain the three-dimensional velocities [Vx, Vy, Vz] of individual product molecules. For the reactive channel, we have measured HD(v'=1, j') scattering angle distributions for collision energies in the range 1.48 – 1.94 eV. These experiments agree nearly perfectly with fully converged quantum mechanical calculations. Products with low rotational excitation are predominantly back scattered, and as j' increases the distribution shifts toward side scattering. For most product quantum states the DCS depends very weakly on the collision energy. These observations are consistent with the expectation that most reactive collisions involve a direct recoil mechanism. For HD(v'=1, j'=2) we observe a second peak which grows as the collision energy increases. This peak is believed to originate from one or more indirect mechanisms involving scattering from the conical intersection. Nonreactive collisions can transfer large amounts of energy into D2 vibration. The standard wisdom has been that this process occurs via hard collisions at low impact parameters, resulting in backward scattering of the products. We have studied D2(v'=1–4, j') products over the collision energy range 1.58 – 1.94 eV. Surprisingly, the products are dominantly scattered in the forward direction! In most cases the DCS is essentially independent of the product vibrational state even though the differences in internal energy are large: each quantum of vibration is roughly equal in energy to the reaction barrier on the minimum energy path. By comparing our experimental results with quasi-classical trajectory calculations, we have explained this behavior with a new tug-of-war mechanism in which attractive forces dominate the inelastic scattering process. The incoming H atom pulls on the nearest D atom but fails to capture it and form the HD product; instead, the H atom departs and the stretched D-D molecule snaps back together with increased vibrational energy. 3 RAYLEIGH SCATTERING MEASRUMENTS USING CAVITY RING-DOWN SPECTROSCOPY Doug Kuramoto Cavity ring-down spectroscopy (CRDS) is an ultrasensitive absorption technique that is capable of measuring absorption changes of 10-10 cm-1. In the simplest form of CRDS, two highly reflective mirrors face one another to form an optical cavity. A laser pulse enters the cavity through the back of one mirror and oscillates back and forth inside the cavity, leaking out a small amount of light. The rate constant for the exponential decay of the light intensity depends upon all losses of light within the optical cavity. These losses include mirror transmissions, absorption by the chemical sample, and reflection and scattering caused by the sample. In most CRDS experiments, the absorbance of the sample is determined to measure a trace amount of a species or to resolve a weak absorption peak that is below the detection limit of traditional absorption techniques. We are interested in using CRDS to look at losses caused by the sample other than absorption, more specifically losses caused by Rayleigh scattering. Much of the theory of Rayleigh scattering was developed over 100 years ago. It has been difficult, however, to make direct measurements in the laboratory owing to the small cross section. The extended path length of CRDS makes it possible to measure the total loss caused by atoms or molecules in the gas phase within the cavity. By operating in regions where there are no absorption peaks, the total loss observed is caused primarily by Rayleigh scattering from which the Rayleigh scattering cross section can be determined. Our recent focus has been on the development of a three-mirror cavity in the ring configuration (Figure 1). Although this configuration adds more complexity to the setup, we hope to use this design to our benefit. One advantage of this configuration is it provides a small amount of optical feedback to the laser that can used to affect the properties of the laser. Once this instrument is set up, measurements of the Rayleigh scattering cross section of molecules in the gas phase should be possible. Figure 1. Three-Mirror Cavity Ring-Down Spectroscopy Cavity 4 CAVITY RING-DOWN SPECTROSCOPY (CRDS) AS APPLIED TO COMPLEX ORGANIC MOLECULES Christa Haase It is important to be able to analyze complex organic mixtures, and in particular their isotope ratios, for many applications. These range from environmental chemistry (for example, the study of volatile organic compounds) to medicinal chemistry (for example, in the application of non-radioactive, stable isotope labeled tracers). For a number of these applications, Gas Chromatography-Combustion-Isotope Ratio Mass Spectrometry (GC-C-IRMS) is the method of choice. The basic principle behind this method is to use a gas chromatograph to separate an organic mixture into its various components. These are catalytically decomposed into carbon dioxide and water. After removing the 13 12 water, the isotope ratio of the carbon dioxide ( CO2 to CO2) is measured. The advantage of using such a simple molecule for isotope ratio measurements is that it allows increased sensitivity. However, GC-C-IRMS instruments are expensive and complex, in part because of the necessity to remove solvents, water (which is created during the combustion process) and other gases because they lead to interferences in the mass spectra. Therefore, it is important to find less expensive (and possibly
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