Physical Chemistry

1. Physical Chemistry Faculty Research Interests

2. Prof. Judith A. Harrison Overview: We examine the atomic-scale origins of friction and wear of hydrocarbon-based materials using computer simulations (i.e., molecular dynamics) which utilize a potential energy function developed at USNA. Also used computer models to examine properties of alternative fuels. Projects: 1) Simulating chemical reactions:Students learn how to write molecular dynamics computer codes for simulating the movement of atoms on computers. Skills needed: Willingness to learn basic FORTRAN and some UNIX. 2) Computing the properties of Alternative Fuels (Hydrotreated Renewable Diesel) This project will develop a computer model that is capable of predicting the properties of alternative fuels of any composition. Compare results to experiments carried out in Chemistry Department. Collaborators: Profs. Trulove, LuningPrak, Cowart, Caton, O’Sullivan. Skills needed: Willingness to learn basic FORTRAN and some UNIX. 3) Using molecular dynamics simulationsto examine adhesion, friction, and wear in diamond and diamondlike carbon (DLC) and self-assembled monolayers). The effects of tip shape, chemical composition, roughness, temperature, and environment must all be considered. Experimental Collaborators: Univ. of Pennsylvannia Skills needed: Willingness to learn FORTRAN and UNIX. Past students:  L. Herman, J. Williams, P. Lombard, R. Willingham, B. Lassen 1993 1998 Fuel tank seawater 2008 HRD Biodiesel 60 sec

3. Prof. Mark Elert My research efforts involve molecular dynamics simulations of shock waves and detonation. Computer simulation of molecular motion in solid model systems is used to investigate the onset of detonation. The goal is to incorporate realistic bond-breaking and bond-forming processes so that the simulation can successfully model chemical effects in detonation, such as the role of impurities, voids, molecular orientation, and exothermicity, on the speed and stability of detonation wave propagation. A simulation of the detonation of solid acetylene is shown below. Recently I have been focusing on the role of strain energy in shock waves. A strained hydrocarbon system such as cubane (above) can release large amounts of energy on impact, comparable to the energy release in a conventional explosive. Conversely, an endothermic isomerization reaction could be used to absorb energy during shock impact of armor material.

4. Prof. Robert F. Ferrante- Spectroscopy - Overview: We utilize spectroscopy (chiefly FT-IR) of samples at very low temperatures (10K – 140K) to examine: - Small stable molecules that form ices on the surfaces of comets, outer solar system bodies, or interstellar dust particles to help identify them and their irradiation products in astronomical spectra. - Very unstable molecules, like reaction intermediates, to determine their structure, bonding and reactions. Current Projects: 1) Optical Properties of Hydrocarbon Ices: (NASA/GSFC) - developing a spectroscopic database of the “optical constants” of simple ices (e.g. C2H6, C2H4, etc) and ice mixtures (CH4/N2, etc.) which exist in comets and outer solar system objects. May also involve ice density measurements by quartz crystal microbalance (at USNA). This data is used by astronomers in modeling the composition of these objects. 2) Raman Spectroscopy of Ices: (USNA) testing the ability ofa simple Raman spectrometer to distinguish and identify thin ice coatings on mineral samples. This will help probe the feasibility of proposed application of Raman on a Mars lander. 3) Spectroscopy of Nitrenes and Nitrides: (USNA) working on a unique way to make these extremely unstable intermediates, and to study them spectroscopically. See me for more information!

5. Assoc Prof Roy McClean • Overview • Prof McClean’s research centers round two areas: • gas phase reaction kinetics using laser photolysis/laser-induced fluorescence methods • computational chemistry using density functional theory (DFT) • Possible Projects • Potential energy surface studies on • TM + CO2→ Products • TM + CS2→ Products • Prior Knowledge • SC345 - Thermodynamics & Kinetics • SC346 - Quantum Chemistry & Spectroscopy • Some UNIX - easy to learn

6. Assistant Professor Elizabeth Yates Biophysical Chemistry OVERVIEW:My research focus is aimed at studying amyloidogenic proteins associated with neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, etc.). These diseases are related to the rearrangement of specific proteins to non-native conformations. Such rearrangements promote aggregation and deposition within tissues and/or cellular compartments. Understanding the role of amyloidogenic protein interaction at solid/liquid interfaces and lipid membranes may provide valuable insight into the toxic mechanism between cellular surfaces and amyloids. PROJECTS: 1. Measuring amyloidogenic protein interaction with lipid membranes via colorimetric assay A biomimetic, vesicle-binding assay to investigate the interactions of protein aggregates with lipid membranes. Vesicles have varied colorimetric responses when exposed to proteins depending on the extent of the protein-lipid interaction. 2. Atomic force microscopy: modeling and experimentation of amyloid proteins on surfaces Atomic force microscope (AFM) virtual training and MATLAB programming. The aggregation of each protein will be studied and evaluated using an AFM. Future directions: Lipid-protein interactions affect surface chemistry of lipid monolayers If you are interested in biochemistry, nanoscience, medical applications of chemistry, or biophysics, please see me for more information! eyates@usna.edu Generic aggregation scheme for amyloid-forming proteins. The aggregation pathway for any given amyloid-forming protein can vary depending on the protein and its folding environment. No interaction Protein interaction Protein insertion AFM image of b-amyloid