Physics Commons^™

Fragmentation Properties Of Three-Membered Ring Heterocyclic Molecules By Partial Ion Yield Spectroscopy: C2h4o And C2h4s, Wayne C. Stolte, I. Dumitriu, S-W Yu, Gunnar Ohrwall, Maria Novella Piancastelli, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We investigated the photofragmentation properties of two three-membered ring heterocyclic molecules, C₂H₄O and C₂H₄S, by total and partial ion yield spectroscopy. Positive and negative ions have been collected as a function of photon energy around the C 1s and O 1s ionization thresholds in C₂H₄O, and around the S 2p and C 1s thresholds in C₂H₄S. We underline similarities and differences between these two analogous systems. We present a new assignment of the spectral features around the C K-edge and the sulfur L_{2 …}

Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

We present a combined theoretical and experimental study of molecular field effects on molecular core levels. Polarization-dependent resonant inelastic x-ray scattering is observed experimentally after resonant K-shell excitation of CF₃Cl and HCl. We explain the linear dichroism observed in spin-orbit level intensities as due to molecular field effects, including singlet-triplet exchange, and interpret this behavior in terms of population differences in the 2p_x,y,z inner-shell orbitals. We investigate theoretically the different factors that can affect the electronic populations and the dynamical R dependence of the spin-orbit ratio. Finally, the results obtained are used to interpret the L-shell …

Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie

Chemistry & Physics Faculty Publications

Here we summarize recent work on the continued development of our fast and simple empirical equation for predicting and structurally rationalizing protein–protein and protein–peptide binding affinities. Our empirical expression consists of six regression-weighted physical descriptors and derives from two key simplifying assumptions: (1) the assumption of rigid-body association and (2) the assumption that all contributions not explicitly considered in the equation make a net contribution to binding of ≈0 kcal. Within the strict framework of rigid-body association, we tested relative binding affinity predictions using our empirical equation against the corresponding experimental binding free energy data for 197 interface alanine mutants. …

The Initial And Final States Of Electron And Energy Transfer Processes: Diabatization As Motivated By System-Solvent Interactions, Joseph E. Subotnik, Robert J. Cave, Ryan P. Steele, Neil Shenvi

All HMC Faculty Publications and Research

For a system which undergoes electron or energy transfer in a polar solvent, we define the diabatic states to be the initial and final states of the system, before and after the nonequilibrium transfer process. We consider two models for the system-solvent interactions: A solvent which is linearly polarized in space and a solvent which responds linearly to the system. From these models, we derive two new schemes for obtaining diabatic states from ab initio calculations of the isolated system in the absence of solvent. These algorithms resemble standard approaches for orbital localization, namely, the Boys and Edmiston–Ruedenberg (ER) formalisms. …

The Rotational Spectrum Of The Fed Radical In Its X4Δ State, Measured By Far-Infrared Laser Magnetic Resonance, Michael Jackson, Lyndon R. Zink, Jonathan P. Towle, Neil Riley, John M. Brown

All Faculty Scholarship for the College of the Sciences

Transitions between the spin-rotational levels of the FeD radical in the v = 0level of the X ⁴Δ ground state have been detected by the technique of laser magnetic resonance at far-infrared wavelengths. Pure-rotational transitions have been observed for the three lowest spin components. Lambda-type doubling is resolved on all the observed transitions; nuclear hyperfine structure is not observed. The energy levels of FeD are strongly affected by the breakdown of the Born–Oppenheimer approximation and cannot be modeled accurately by an effective Hamiltonian. The data are therefore fitted to an empirical formula to yield term values and g-factors for …

Visualizing Atomic Orbitals Using Second Life, Andrew Lang, David C. Kobilnyk

College of Science and Engineering Faculty Research and Scholarship

We demonstrate the usefulness of Second Life as a platform for enlivening major concepts in chemistry education. These concepts include absorption spectra, selection rules, quantum numbers, and atomic orbital shapes. We have built several exhibits in Second Life which provide 3-dimensional interactivity for each of those areas: an interactive experiment showing the absorption spectrum of hydrogen, an interactive model of selection rules showing allowed and forbidden transitions for each state, a 3-dimensional grid of orbitals showing the constraints on the values of quantum numbers, and a large-scale interactive orbital display allowing the user to choose and rotate to-scale atomic orbitals …

Volume 02, Joseph A. Mann, Kathryn J. Greenly, Scott E. Jenkins, Andrew E. Puckette, Daniel M. Honey, Jeffery P. Ravenhorst, Jamie Elizabeth Mesrobian, Thomas Scott, Jay Crowell, Sarah Spangenberg, Amy S. Eason, Kenny Wolfe, Liz Hale, Rachel Bouchard, Will Semonco, Carley York, Ryan Higgenbothom, Adrienne Heinbaugh, Melissa Dorton, Madeline Hunter, June Ashmore, Clark Barkley, Jay Haley

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Mike's Nite: New Jazz for an Old Instrument by Joseph A. Mann

Investigation of the use of Cucumis Sativus for Remediation Of Chromium from Contaminated Environmental Matrices: An Interdisciplinary Instrumental Analysis Project by Kathryn J. Greenly, Scott E. Jenkins, and Andrew E. Puckette

Development of GC-MS and Chemometric Methods for the Analysis of Accelerants in Arson Cases by Scott Jenkins

Building and Measuring Scalable Computing Systems by Daniel M. Honey and Jeffery P. Ravenhorst

Nomini Hall: A Case Study in the Use of Archival Resources as Guides for Excavation at An Archaeological Site by …

Development And Validation Of An Empirical Free Energy Function For Calculating Protein–Protein Binding Free Energy Surfaces, Joseph Audie

Chemistry & Physics Faculty Publications

In a previous paper, we described a novel empirical free energy function that was used to accurately predict experimental binding free energies for a diverse test set of 31 protein–protein complexes to within ≈1.0 kcal. Here, we extend that work and show that an updated version of the function can be used to (1) accurately predict native binding free energies and (2) rank crystallographic, native-like and non-native binding modes in a physically realistic manner. The modified function includes terms designed to capture some of the unfavorable interactions that characterize non-native interfaces. The function was used to calculate one-dimensional binding free …

Abc's Of Dew (Adi) Software, John Pickle

STEM Digital

Introduction to three color light, pixels, DEW (ADI) tools

A Review Of Helium Hamiltonians, Carl W. David

Chemistry Education Materials

Helium Hamiltonian transformations are discussed in extreme detail.

Partial Ion Yield Sspectroscopy Around The Cl 2p And C 1s Ionization Thresholds In Cf3cl, D. Ceolin, Maria Novella Piancastelli, Wayne C. Stolte, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We present a partial ion yield experiment on freon 13, CF₃Cl, excited in the vicinity of the C 1s and Cl 2p ionization thresholds. We have collected a large amount of cationic fragments and a few anionic fragments at both edges. We have observed a strong intensity dependence of Rydberg transitions with ion fragment size for the CF_nCl⁺ and CF_n⁺/F⁺ (n=0–3) series at both the Cl 2p and C 1s ionization edges. Selectivity in the fragmentation processes involving the C–Cl and C–F bonds are highlighted by the intensities of the C …

Yttrium And Hydrogen Superstructure And Correlation Of Lattice Expansion And Proton Conductivity In The Bazr0.9y0.1o2.95 Proton Conductor, A. Braun, A. Ovalle, V. Pomjakushin, A. Cervellino, S. Erat, Wayne C. Stolte, T. Graule

Chemistry and Biochemistry Faculty Research

Bragg reflections in Y-resonant x-ray diffractograms of BaZr_0.9Y_0.1O_2.95 (BZY10) reveal that Y is organized in a superstructure. Comparison with neutron diffraction superstructure reflections in protonated/deuterated BZY10 suggests that both superstructures are linked, and that protons move in the landscape imposed by the Y. The thermal lattice expansion decreases abruptly for protonated BZY10 at T≥648±20 K, coinciding with the onset of lateral proton diffusion and suggesting a correlation of structural changes and proton conductivity. The chemical shift in the Y L₁-shell x-ray absorption spectra reveals a reduction from Y³⁺ toward Y²⁺ upon …