DENSITY FUNCTIONAL THEORY OF THE SI(100) SURFACE
Tran Phung, Janice A. Steckel, and Kenneth D. Jordan, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA. 15260

The interaction of hydrogen with Si surfaces is of great importance both in the passivation of the surface and growth through chemical vapor deposition. A slab-model, using density functional theory with the Perdew- Wong (PW91) exchange-correlation functional was used to optimize the geometries for the bare Si(100)-2x1 surface and the surface with two H atoms absorbed at a dimer site. The Nudge Elastic Band (NEB) was used to locate the transition state for H₂ desorption.[1,2] These results were used to build cluster models for the three species. The cluster models contained four surface Si dimers and seven silicon layers. The dangling substrate silicon bonds were terminated with hydrogen atoms. The cluster models were used to carry out Becke3-LYP calculations using flexible basis sets.[3-6] To save computational time, the absorbing H atoms and the top two Si layers were described with a 6-311G(d,p) basis set, while the bottom five layers were described with the 3-21G basis set. The calculated energies were used to obtain improved estimates of the reaction and activation energies.

References
1 H. Jónsson, G. Mills, K. W. Jacobsen, World Scientific, 385 (1998).
2 G. Mills, H. Jónsson and G. K. Schenter, Surface Science 324, 305 (1995). 3 A. D. Becke, Phys. Rev. A 38, 3098 (1988).
4 A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
5 C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988).
6 S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980).
 

VIRTUAL MASS SPECTROMETRY LABORATORY.
Bryan R. Meyer, Joseph J. Grabowski, and Mark E. Bier, Departments of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 and Carnegie Mellon University, Pittsburgh, PA 15213.

The limited availability of modern instrumentation in undergraduate laboratories can be a hindrance to the education of students. Briefly covered in undergraduate chemistry courses and rarely in other science subjects, mass spectrometry (MS) is one instrumental approach that can be applied today to sciences such as biology, biochemistry, environmental studies, geology, and physics, as well as chemistry. As the usage of MS is expanding, there is a need for students to be able to collect and analyze mass spectral data for problems in the field of their choice. The purpose of the Virtual Mass Spectrometry Laboratory (VMSL) is to solve the issue of limited access for students to mass spectrometers and to create an interdisciplinary pathway between the sciences by utilizing a case study approach. This is achieved by simulating several types of mass spectrometers on the World Wide Web. In this segment of the ongoing project, an electron ionization (EI) mass spectrometer was simulated for use with a case study regarding the early history of general anesthetics. The student is presented with a situation in which a vial of liquid has been found in a Civil War-era medicine kit. After reading a detailed background and manipulating structural images of several general anesthetics, the student will use the VMSL to collect the mass spectral data for the unknown liquid and then will interpret that data to determine what chemical the vial contains. Without proper preparation, as in any laboratory experiment, the student is unlikely to know the correct MS technique necessary to solve the problem presented. It is therefore important that the VMSL be so configured that improperly designed or executed experiments can fail as in the real world. The web address of the VMSL is http://mass-spec.chem.cmu.edu/vmspec

SECOND HARMONIC GENERATION (SHG) IS A POWERFUL PROBE OF CRYSTAL STRUCTURE AND MOLECULAR ORIENTATION AT INTERFACES.
Christopher Lea and Eric Borguet, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

The knowledge of these properties is important in understanding the electrochemical properties of interfaces and the reactions and interaction that between two different media. SHG depends upon two main factors, the nonlinear optical susceptibility tensor and the Fresnel factors for the system being probed. The Fresnel factors are functions of the angle of incidence and the linear optical properties of the bulk materials that constitute the interface. We have calculated the Fresnel factors and used them to predict the SHG intensity for several different experimental geometries (angle of incidence and polarization). The ultimate goal is to optimize the experimental conditions that enable the most accurate determination of the average molecular orientation of self-assembled molecular films and crystalline structure of electrode interfaces.
 

THEORETICAL STUDY OF THE REACTION PATHWAY FOR THE PROTONATION OF METHANE.
Jeffrey M. Tran and Peter E. Siska, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260

Our project concerns the reaction pathway in which a nucleophile is added into methane. It has been proposed that a nearby nucleophile can lower the barriers to deformation in methane, allowing the nucleophile to act on electrons on the central carbon rather than through bond insertion. We are attempting to relate this mechanism to charge distribution and charge transfer, and have been studying the specific system of a proton attacking neutral methane.
 

MODELING OF WATER ON THE NACL(100) SURFACE.
Joe Dukes and Kenneth D. Jordan, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

There is considerable interest in the properties of water on salt surfaces. Although experiments provide information of the positions of the O atoms, the locations of the H atoms, and, thus the orientaitons of the water molecules, have not been established. This study uses density functional methods together with slab models to study the structure and binding energies of water on the NaCl(100) surface. Both full coverage and partial coverage of the surface is considered. The results produced agree well with experiment and studies performed using other periodic Hartree Fock with correlation corrections.
 

WAVEFORM ANALYSIS IN PHOTOACOUSTIC CALORIMETRY.
Alexander Bayden and Joseph J. Grabowski, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

A photon can interact with a molecule by promoting it to an excited state, which is only metastable. The molecule can transform its high potential energy into three different forms. It can undergo a reaction with the result that part of the energy is stored as chemical energy. Alternatively, a photon can be emitted, taking some of the excess energy with it. Finally, some of the energy may leave the molecule causing a temperature rise in the local environment. This last pathway, non-radiative relaxation, can be measured by a relatively new spectroscopic technique called photoacoustic calorimetry.

Photoacoustic calorimetry involves shooting a laser pulse through solution and picking up the resulting acoustic wave with a microphone. Often the decay of the exited state to the ground state happens in several steps, with each step having a unique time constant and heat release yield. The deconvolution of the observed heat signature into the constituent parts, requires a robust and user-friendly computer program, which I am writing. In the future this program will be used for energy analysis of C₆₀.

MODELING ION CURRENT THROUGH 3D BIOLOGICAL ION CHANNELS.
Carnie Abajian, Alfredo E. Cárdenas and Rob D. Coalson, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.
Channel proteins embedded in lipid bilayers (e.g., cell membranes) provide gates for ions like Na⁺, Cl^-, K⁺, and Ca²⁺ to enter and exit a cell. These channels aid the cell by maintaining desired internal concentrations and by mediating functions such as energy storage and signal transduction. Kurnikova et al. have developed a lattice relaxation algorithm to solve the Poisson- Nernst-Plank (PNP) equations for ion transport through arbitrary three- dimensional volumes. This allows for the calculation of the current through a three-dimensional ion channel, nearly replicating experimental results. Several issues, however, are not addressed by the PNP model. Ion size and, in general, ion-ion correlation effects are neglected. A Brownian Dynamics algorithm is being developed to address these issues and to provide a means for modeling coulombic and non-coulombic ion pair interactions and saturation of conduction with increasing reservoir concentration.

Views of Phospholamban:

Phospholamban is an ion channel protein which controls Ca²⁺ transport through the cardiac sarcoplasmic reticulum. Phospholamban's transmembrane domain is a parallel five-helix bundle. Each subunit is composed of 52 residues.
 

THE LENNARD-JONES{38} CLUSTER: A STUDY IN GLOBAL OPTIMIZATION.
William W. Kennerly, Arnold Tharrington and Kenneth D. Jordan, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

The Lennard-Jones 38 cluster (LJ₃₈, an isolated aggregate of 38 point particles under the influence of the two-body LJ potential) has attracted considerable attention. The potential energy surface of this cluster has multiple "funnels" that drain into different low-lying energy minima, with the second lowest energy structure being located more often than the global minimum by many optimization methods.[1] Accordingly, this serves as an important test case for global optimization methods.[1,2] Our current work utilizes MC simulations combined with a jump-walking algorithm [3] to try and locate this global minimum and to characterize the thermodynamics of the cluster.

MC simulations consist of a series of moves in which a random atom is selected and an attempted move is made to another randomly selected position. The energy of the cluster is then calculated. If it is lower than before, the move is accepted, and the simulation continues. If it is higher, the move may be accepted, with a probability that decays exponentially as the energy difference increases. (This is known as Metropolis sampling.)

The jump-walk algorithm helps to prevent trapping in local minima. This process involves running a regular MC simulation at one temperature, and then another at a lower temperature. However, at random intervals the lower temperature run selects a configuration previously sampled in the higher temperature run, using the same Metropolis type criterion for accepting the transition. If the move is accepted, then the ``jump'' is accepted and the cluster ``walks'' to this new configuration. Clusters at higher temperatures have higher energy configurations available, and this helps prevent trapping in a local minimum. This, in turn, increases the likelihood to find the global minimum geometry when quenching configurations from a low temperature MC/jump- walk.

The MC simulations also provide information on the melting behavior of these small clusters. We are familiar with melting points for bulk (macroscopic) samples. In fact, it is known that arbitrarily close to the melting point of a bulk sample, the heat capacity (C_V) is arbitrarily large. Clusters exhibit this sort of behavior, but the C_V vs. T curves show a finite maximum value. This may be taken as indicative of a phase change at the corresponding temperature.

References
1 J. P. K. Doye, D. J. Wales, M. A. Miller, J. Chem. Phys. 109, 8143 (1998). 2 D. B. Faken, A. F. Voter, D. L. Freeman, J. D. Doll, J. Phys. Chem. (in press).
3 D. D. Frantz, J. Chem. Phys. 102, 3437 (1995).

STRUCTURE AND DYNAMICAL BEHAVIOR OF DIPHENYLACETYLENE IN ITS GROUND AND ELECTRONICALLY EXCITED STATES.
Grace Chou and David W. Pratt, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

Diphenylacetylene (tolane) is a highly symmetric molecule that is believed to have a center of inversion in both its ground and electronically excited states. The molecule also exhibits large amplitude torsional motion about the linkage between the two phenyl rings. The goal of this project is to study the structure and dynamical behavior of diphenylacetylene in both the ground and electronically excited states via laser induced fluorescence excitation spectroscopy at both vibrational and rotational resolutions. The rationally resolved experiment is extremely sensitive to changes in electron density, hence it is a useful tool in studying the p conjugation between the CºC and the two phenyl rings. This conjugation gives rise to the torsional barrier in tolane. A variety of ab initio calculations (HF, DFT, CIS) has been performed to model not only the molecular geometry, but also the shape of the potential energy surface governing the relative motion of the phenyl rings. A combination of experiments and calculations has been used to determine the specific electronic energy levels probed in the fluorescence excitation spectra.

FLUOROUS TECHNIQUES IN ORGANIC SYNTHESIS.
Jeffrey D. Rimer and Dennis P. Curran, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

In organic synthesis, the goal of strategy level separation is to devise a reaction that can be purified simply by workup. There are four common phases in organic reactions - gas, water, organic liquid, and solid phases - which can be separated by evaporation, extraction, or filtration. However, there exists an additional phase known as a "fluorous" phase that is orthogonal to the other common phases, thereby allowing fluorous compounds to be isolated from organic and aqueous products.

Fluorous synthesis involves the use of fluorous reagents, which are organic compounds with high fluorine contents. One or more components are tagged ("labeled") with a highly fluorinated domain. Tagged substrates are designed so that the fluorous tag can be removed at some later stage. Components that do not become part of the final product, such as catalysts or reagents, can be tagged permanently and can be recovered for reuse at the end of a reaction.

In the early stages of fluorous synthesis, liquid-liquid extraction between perfluorinated solvents and organic solvents was the most common form of separation. Recently, fluorous, reverse-phase silica gels are being applied to various chromotographic separations. For instance, the Curran group is currently using HPLC techniques to test fluorous solid phase extraction (FSPE).

The goal of this particular research project is to use fluorous tin hydrides to selectively reduce acid chlorides to aldehydes. The underlying objective is to assay whether or not fluorous tin hydrides can be used in place of organotin hydrides. The use of fluorous reagents in this reaction has several advantages over conventional methods, such as: the ability to isolate the product during the workup, to achieve better isolated yields, and to recover expensive reagents for reuse.

Fluorous synthesis is an expanding field in chemistry that is gaining more attention for its use and development in organic and combinatorial synthesis. The application of fluorous techniques offers a distinct advantage in strategy level separation. There is much more to be discovered in fluorous synthesis.
 

Tuesday August 3, 1999 9:30 AM Chevron Science Center - Room 132

COMPUTATIONAL STUDIES OF THE GEOMETRY AND NO STRETCHING FREQUENCY OF CH₃SNO AND CYSTEINE-BOUND NO.
John R. Fredericks and Gilbert Walker, University of Pittsburgh, Department of Chemistry, Pittsburgh, PA 15260.

Geometries were optimized and vibrational frequencies were calculated for cis methyl thionitrite, CH₃SNO, trans CH₃SNO, cis cysteine-bound NO (Cys-NO) and trans Cys-NO using Hartree-Fock (HF), second-order Moller-Plesset (MP2) and density functional (DFT) methods with various basis sets (6-31G*,6-31G**, 6-31+G*, cc-pVDZ). The most accurate results, based on the NO stretch frequency, were obtained at the B3LYP/6-31G* level of theory. The calculated NO stretch frequency for cis CH₃SNO and trans CH₃SNO were within 1.6% and 3.4%, respectively, of the experimental value of 1560 cm^-1. Those for cis Cys-NO and trans Cys-NO were within 0.13% and 2.4%, respectively, of the experimental value of 1560 + 39 cm^-1. The frequencies were scaled using individual rather than overall scaling factors. The optimized geometry of CH₃SNO revealed C_s symmetry with a possible weak hydrogen bond of 2.18Å formed between the oxygen and hydrogen atoms in the HCSNO plane. In cis and trans Cys-NO, however, the carbon and hydrogen are no longer co-planar with the S, N, and O, and may indicate an attraction between the NO and the amine group of the cysteine moiety. A weak hydrogen bond (2.24 Å) is seen in the cis Cys-NO.

I also worked on a creating a web page designed for high school chemistry teachers and students. You can visit the page at: http://homepages.msn.com/LibraryLawn/chempage/home.html