Department of Chemistry
REU Abstracts

1:00 IMAGING SURFACE DYNAMICS AT THE MOLECULAR LEVEL: EXPERIMENTAL AND THEORETICAL STUDIES. William J. Lokar

1:20 CALCULATION OF ACTIVATION ENERGIES FOR HYDROGEN DIFFUSION ACROSS THE SILICON(100) SURFACE. Brandi Schmidt

1:40 GAS PHASE MOLECULAR STRUCTURES OF THE DIMERS OF 2- AND 3- AMINOPHENOL. Brian Blasiole

2:10 VIBRATIONALLY RESOLVED ELECTRONIC EXCITATION SPECTRA OF TRANS OCTATETRAENE IN THE GAS PHASE AND SOLUTIONS. R.V. Krems

2:30 A COMPUTATIONAL STUDY OF THE REACTION MECHANISM OF ATOMIC OXYGEN RADICAL ANION WITH METHANOL Lisa M. Reilly

2:50 ELECTROSTATIC CONTRIBUTIONS OF MgATP BINDING AND HYDROLYSIS IN BIOLOGICAL NITROGEN FIXATION. Adam K. Charnley

3:20 COMPUTER MODELING OF DENDRIMERS USING HYPERCHEM. Rebecca B. Botham

3:40 EXPERIMENTAL AND THEORETICAL STUDIES OF THE "INTRA-MOLECULAR SALT EFFECT": THE SYNTHESIS OF AN EASILY REMOVABLE ASYMMETRIC SALT AND ITS INFLUENCE UPON 1,3-DIPOLAR CYCLOADDITIONS. Melissa Arredondo

4:00 EXPLORING THE MECHANISM OF a,w-DIAMINOALKANE MEDIATED GLYCOPROTEIN SEPARATIONS BY CAPILLARY ELECTROPHORESIS. Michelle M. Muza

4:20 MAXIMIZATION OF DEPHOSPHORYLATION OF PUC19 AS A VECTOR PURIFICATION TECHNIQUE. Joshua Kern

IMAGING SURFACE DYNAMICS AT THE MOLECULAR LEVEL: EXPERIMENTAL AND THEORETICAL STUDIES. William J. Lokar, Eric Borguet, and Tao Ye, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260

An understanding of surface processes requires both atomic resolution and sub-picosecond time resolution. Currently STM and AFM offer the former, but not the latter. We propose a scheme using short perturbations to overcome these limitations. Theoretical studies of surface dynamics were conducted to determine suitable perturbations for minimal desorption and optimal diffusion based upon different temperature versus time perturbations. It was determined that a "window" of allowed energies of diffusion and desorption exists which allows for a change in surface coverage of only 0.1%, while minimizing diffusion in the absence of the perturbation. Molecular adsorbates on highly-ordered pyrolytic graphite (HOPG) provide prototypical systems to investigate these dynamics. Atomic imaging of HOPG surfaces was achieved using STM with mechanically cut Pt-Ir tips. Furthermore, molecular images of a number of adsorbed molecules on HOPG under phenyloctane were obtained.

1:20 CALCULATION OF ACTIVATION ENERGIES FOR HYDROGEN DIFFUSION ACROSS THE SILICON(100) SURFACE. Brandi Schmidt, Jan Steckel and Ken Jordan. Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260

The main goal of this research project was to calculate the activation energy for hydrogen atom diffusion on the silicon(100) surface. The activation energies were calculated for three different processes corresponding to different directions the hydrogen atom can diffuse on the surface. These are termed intra-dimer, intra-row, and inter-row. The geometries of the minima and the transition structures were generated from plane-wave slab-model density functional theory calculations. The clusters were then cut out of the slabs and the dangling bonds on the subsurface Si atoms terminated by H atoms. The Becke3LYP and Perdew-Wang exchange-correlation functionals were employed together with the 6-311G** basis set. The results obtained from the Perdew-Wang functional are very close to those obtained from the plane-wave slab-model calculations using the same functional. However, the Becke3LYP functional, which is believed to be more reliable for calculating activation energies, gives appreciably higher values.

1:40 GAS PHASE MOLECULAR STRUCTURES OF THE DIMERS OF 2- AND 3-AMINOPHENOL. Brian Blasiole and David W. Pratt, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260

Predicting crystal structures from the usual intermolecular functional group interactions, such as hydrogen bonding of the N- H•••Oand O-H•••N type and herringbone interactions, is many times not successful. In crystal packing, these interactions often interfere with one another, resulting in unusual molecular recognition patterns such as N-H••• p and C-H•••O. The goal of this research is to determine the preferred functional group interactions of 2- and 3-aminophenol dimers in the gas phase to gain some insight into the correspondence between their molecular and crystal structures. Computationally, semi-empirical AM-1 calculations of various dimer configurations were run on Spartan to find the lowest energy structures; subsequent ab intio calculations are planned. Experimentally, vibrationally resolved S₁? S₀ fluorescence excitation spectra of the isolated molecules have been recorded in a supersonic jet; subsequent rotationally resolved experiments on their dimer structures are also planned.

2:10 VIBRATIONALLY RESOLVED ELECTRONIC EXCITATION SPECTRA OF TRANS OCTATETRAENE IN THE GAS PHASE AND SOLUTIONS. R.V. Krems, A. E. Cárdenas, R.D. Coalson, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.

High resolution absorption spectra of ¹A_g -> 1 ¹B _u transition for trans octatetraene in the gas phase and chloroform solution have been simulated using a hybrid technique of Gaussian wavepacket dynamics and molecular dynamics methods. The spectra are similar to the highly resolved fluorescence excitation spectra obtained experimentally in an n-hexane matrix at 4.2 K [M.F. Granville, G.R. Holtom, and B.E. Kohler, J. Chem. Phys., 72, 1980, 4671.] and in solutions [M.F. Granville, B.E. Kohler, and J.B. Snow, J. Chem. Phys., 75, 1981, 3765.]. The calculated spectral shift in the presence of solvent is 3500 cm^-1 while the experimental value varies from 3000 to 3400 cm^-1. The broadened solution spectrum has only two vibronic peaks in its structure instead of four in the gas phase spectrum.

2:30 A COMPUTATIONAL STUDY OF THE REACTION MECHANISM OF ATOMIC OXYGEN RADICAL ANION WITH METHANOL. Lisa M. Reilly and Joseph J. Grabowski, Departments of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 and Mercyhurst College, Erie, PA 16546

In order to predict whether the atomic oxygen radical anion will generate a certain didehydro radical anion, we need a good appreciation of the mechanism by which it reacts. With this goal, the reaction of methanol with the atomic oxygen radical anion was studied using the density functional theory Becke3LYP with the 6-31+G* basis set. An initial study of the acidity of methanol using three levels of theory and nine basis was completed to verify the choice of methods. The results demonstrate that Becke3LYP is in close agreement with experimental data while MP2 and HF methods display larger differences. The atomic oxygen radical anion can react with methanol by four exothermic pathways and several interesting endothermic pathways; for each pathway two distinct ion-molecule complexes are of interest as are the transition states that connect them. Strategies to find and characterize several of the key complexes and intermediates will be discussed.

2:50 ELECTROSTATIC CONTRIBUTIONS OF MGATP BINDING AND HYDROLYSIS IN BIOLOGICAL NITROGEN FIXATION. Adam K. Charnley, Igor V. Kurnikov, and David N. Beratan, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260

Biological nitrogen fixation is a process in which atmospheric N₂ is converted to ammonia, NH₃, by the nitrogenase enzyme. It is believed that the electron transfers associated with this process are controlled by conformational changes in the Fe-protein of nitrogenase, as a result of MgATP binding and hydrolysis. Several X-ray structures are available for the component proteins of nitrogenase that demonstrate these conformational changes. Basic electrostatic calculations simulating MgATP binding and hydrolysis provide quantitative insight into these two events. Computer models of two Fe- proteins with MgATP bound in the catalytic sites were created from X-ray structures of the "free" and "stabilized" protein conformations. We devised and executed calculations to examine the electrostatic contribution to MgATP binding and hydrolysis in these systems by numerically solving the Poisson- Boltzman equation.

3:20 COMUTER MODELING OF DENDRIMERS USING HYPERCHEM. Rebecca B. Botham and Toby M. Chapman, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260

This computer modeling of dendrimers has two main focuses: the position of the terminal ends of the dendrimers and the atom distribution from the center outward. The atom density distribution is needed to increase our understanding of the physical nature of dendrimers. The terminal end distribution is crucial to understanding chemical reactivity and their availability to function as donors or acceptors. This will contribute to the understanding of why synthesis can not go on indefinitely. The goal of this problem is to try and understand differences between dendrimers whose monomers are symmetrical and those monomers lacking symmetry. The computer program used was Hyperchem version 5.0 on a PC.

3:40 EXPERIMENTAL AND THEORETICAL STUDIES OF THE "INTRA-MOLECULAR SALT EFFECT": THE SYNTHESIS OF AN EASILY REMOVABLE ASYMMETRIC SALT AND ITS INFLUENCE UPON 1,3-DIPOLAR CYCLOADDITIONS. Melissa Arredondo, John Stephens, Craig Wilcox. Department of Chemistry, University of Pittsburgh, Pittsburgh, PA. 15260

The presence of ions in the active site of an enzyme is thought to have a significant influence on enzymatic function through an "intra-molecular salt effect". The primary role of these charged components in the active site is considered to be structural [via salt-bridges and similar motifs] and/or catalytic [by stabilizing polar transition states]. Early investigations into "artificial" intra-molecular salts have demonstrated their efficacy as catalysts. In fact, recent studies suggest that these salts can influence the stereochemistry of certain reactions. Significant interest now resides in combining these features - catalysis and stereocontrol. Through the synthesis of an easily removable chiral auxiliary (2), which can possibly enhance the selectivity of a 1,3-dipolar cycloaddition, the "intra- molecular salt effect" will be further examined. In addition, semi-empirical and ab-initio calculations will be evaluated for the influence of an "intra- molecular salt" upon the course and rate of a reaction.

4:00 EXPLORING THE MECHANISM OF a,w -DIAMINOALKANE MEDIATED GLYCOPROTEIN SEPARATIONS BY CAPILLARY ELECTROPHORESIS. Michelle M. Muza and James P. Landers. Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260.

The separation and characterization of glycoproteins is applicable to all forms of biochemical research including the biomedical and clinical sciences. A high resolution separation of ovalbumin, a heterogeneous glycoprotein, has been achieved by Landers et al.[1992, Anal. Biochem., 205:115-124] through the use of Capillary Electrophoresis and a buffer system containing 100 mM borate and 1 mM 1,4 diaminobutane (DAB). However, the mechanism by which this additive (DAB) facilitated the separation of glycoforms is not clear. The present study is a characterization of the effect of 1,4 diaminobutane and related a,w-diaminoalkanes on the electroosmotic flow (EOF) in the capillary as well as the resolution of the glycoforms of ovalbumin, a model glycoprotein. The effect of concentration of additive and chain length of the alkane on EOF and resolution are addressed. Diaminoalkanes with a chain length of less than three carbons had minimal effect on EOF and did not result in high resolution of the ovalbumin separation. The effect on EOF in response to varying the concentration of the additives does not follow the predicted linear decrease. The universality of this system for the resolution of protein glycoforms was illustrated through the application to another glycoprotein of interest, human serum transferrin.

4:20 MAXIMIZATION OF DEPHOSPHORYLATION OF PUC19 AS A VECTOR PURIFICATION TECHNIQUE. Joshua Kern and Dr. Jumi Shin, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260.

The GCN4 protein is a highly characterized yeast transcriptional activator that employs the basic region/leucine zipper motif (bZIP) for sequence specific recognition of DNA. Synthesized protein dimers of the basic region of the GCN4 protein are used to select DNA from a random pool of 54 base pair duplex DNA. Selections are performed using both a column covalently bound with dimers of the GCN4 basic or a solution-based selection and gel mobility shift assay. After multiple rounds of selection and polymerase chain reaction, amplification, the selected duplexes are digested with Sac1 and BamH1 restriction endonucleases into 20 bp sequences. These sequences are then cloned into pUC19 plasmid, transfected into electro-competent cells and sequenced. My project has been to maximize a new procedure for purifying the pUC 19 after digestion with endonucleases. Purification is essential after digestion with Sac1 and BamH1, because a small piece of duplex DNA is left in solution which acts as a contaminant during ligation reactions. The gel purification of pUC19 has led to recoveries of between 5-50% with typical values around 30%. This project has been to test and maximize the technique of dephosphorylation as a means of purifying the vector. This cheaper and faster technique has led to yields of 27-73% with normal recoveries of over 50%.