Atomic, Molecular and Optical Physics Commons^™

Water Diffusion In And Out Of The Β-Barrel Of Gfp And The Fast Maturing Fluorescent Protein, Turbogfp, Marc Zimmer, Binsen Li, Ramza Shahid, Paola Peshkepija

Chemistry Faculty Publications

The chromophore of fluorescent proteins is formed by an internal cyclization of the tripeptide 65SYG67 fragment and a subsequent oxidation. The oxidation is slow – the kinetics of this step is presumably improved in fast maturing GFPs. Water molecules can aid in the chromophore formation. We have used 50ns molecular dynamics simulations of the mature and immature forms of avGFP and TurboGFP to examine the diffusion of water molecules in-and-out of the protein β-barrel. Most crystal structures of GFPs have well-structured waters within hydrogen-bonding distance of Glu222 and Arg96. It has been proposed that they have an important role in …

Computational Study Of The Hydration Of Sulfuric Acid Dimers: Implications For Acid Dissociation And Aerosol Formation, Berhane Temelso, Thuong Ngoc Phan, George C. Shields

Faculty Journal Articles

We have investigated the thermodynamics of sulfuric acid dimer hydration using ab initio quantum mechanical methods. For (H₂SO₄)₂(H₂O)_n where n = 0−6, we employed high-level ab initio calculations to locate the most stable minima for each cluster size. The results presented herein yield a detailed understanding of the first deprotonation of sulfuric acid as a function of temperature for a system consisting of two sulfuric acid molecules and up to six waters. At 0 K, a cluster of two sulfuric acid molecules and one water remains undissociated. Addition of a second …

Symmetry-Based Techniques For Qualitative Understanding Of Rovibrational Effects In Spherical-Top Molecular Spectra And Dynamics, Justin Chadwick Mitchell

Graduate Theses and Dissertations

Using light to probe the structure of matter is as natural as opening our eyes. Modern physics and chemistry have turned this art into a rich science, measuring the delicate interactions possible at the molecular level.

Perhaps the most commonly used tool in computational spectroscopy is that of matrix diagonalization. While this is invaluable for calculating everything from molecular structure and energy levels to dipole moments and dynamics, the process of numerical diagonalization is an opaque one. This work applies symmetry and semi-classical techniques to elucidate numerical spectral analysis for high-symmetry molecules.

Semi-classical techniques, such as the Potential Energy Surfaces, …

Ultrafast Rempi In Benzene And The Monohalobenzenes Without The Focal Volume Effect, Timothy D. Scarborough, James Strohaber, David B. Foote, Collin J. Mcacy, Cornelis J. Uiterwaal

C.J.G.J. Uiterwaal Publications

We report on the photoionization and photofragmentation of benzene (C₆H₆) and of the monohalobenzenes C₆H₅–X (X = F, Cl, Br, I) under intense-field, single-molecule conditions. We focus 50-fs, 804-nm pulses from a Ti:sapphire laser source, and record ion mass spectra as a function of intensity in the range ~10¹³ W/cm² to ~10¹⁵ W/cm². We count ions that were created in the central, most intense part of the focal area; ions from other regions are rejected. For all targets, stable parent ions (C₆H₅X+) are …

Site-Specific Photocatalytic Splitting Of Methanol On Tio2(110), Chuanyao Zhou, Zefeng Ren, Shijing Tan, Zhibo Ma, Xinchun Mao, Dongxu Dai, Hongjun Fan, Xueming Yang, Jerry L. Larue, Russell Cooper, Alec M. Wodtke, Zhou Wang, Zhenyu Li, Bing Wang, Jinlong Yang, Jianguo Hou

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Clean hydrogen production is highly desirable for future energy needs, making the understanding of molecular-level phenomena underlying photocatalytic hydrogen production both fundamentally and practically important. Water splitting on pure TiO₂ is inefficient, however, adding sacrificial methanol could significantly enhance the photocatalyzed H₂ production. Therefore, understanding the photochemistry of methanol on TiO₂ at the molecular level could provide important insights to its photocatalytic activity. Here, we report the first clear evidence of photocatalyzed splitting of methanol on TiO₂ derived from time-dependent two-photon photoemission (TD-2PPE) results in combination with scanning tunneling microscopy (STM). STM tip induced molecular manipulation …

Full Multiple Scattering Analysis Of Xanes At The Cd L 3- And O K- Edges In Cdo Films Combined With A Soft-X-Ray Emission Investigation, I. N. Demchenko, J. D. Denlinger, M. Chernyshova, K. M. Yu, D. T. Speaks, P. Olalde-Velasco, Oliver Hemmers, W. Walukiewicz, A. Derkachova, K. Lawniczak-Jablonska

Environmental Studies Faculty Publications

X-ray absorption near edge structure (XANES) at the cadmium L3 and oxygen K edges for CdO thin films grown by pulsed laser deposition method, is interpreted within the real-space multiple scattering formalism, FEFF code. The features in the experimental spectra are well reproduced by calculations for a cluster of about six and ten coordination shells around the absorber for L3 edge of Cd and K edge of O, respectively. The calculated projected electronic density of states is found to be in good agreement with unoccupied electronic states in experimental data and allows to conclude that the orbital character of the …

Sulfur K-Edge Photo-Fragmentation Of Ethylene Sulfide, Wayne C. Stolte, Gunnar Ohrwall

Chemistry and Biochemistry Faculty Research

We have investigated the photofragmentation properties of the three-membered ring heterocyclic molecule ethylene sulfide or thiirane, C₂H₄S, by time-of-flight mass spectroscopy. Positive ions have been collected as a function of photon energy around the S K ionization threshold. Branching ratios were derived for all detected ions, which are informative of the decay dynamics and photofragmentation patterns of the core-excited species. We present a new assignment of the spectral features around the S K-edge.

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 …

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 …

Linear Dichroism In Resonant Inelastic X-Ray Scattering To Molecular Spin-Orbit States, Renaud Guillemin, Stephane Carniato, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

Polarization-dependent resonant inelastic x-ray scattering (RIXS) is shown to be a new probe of molecular-field effects on the electronic structure of isolated molecules. A combined experimental and theoretical analysis explains the linear dichroism observed in Cl 2p RIXS following Cl 1s excitation in HCl and CF₃Cl as due to molecular-field effects, including singlet-triplet exchange, indicating polarized-RIXS provides a direct probe of spin-orbit-state populations applicable to any molecule.

Real-Time Plasma Controlled Chemistry In A Two-Frequency, Confined Plasma Etcher, Vladimir Milosavljevic, Albert R. Ellingboe, Cezar Gaman, John V. Ringwood

Articles

The physics issues of developing model-based control of plasma etching are presented. A novel methodology for incorporating real-time model-based control of plasma processing systems is developed. The methodology is developed for control of two dependent variables (ion flux and chemical densities) by two independent controls (27 MHz power and O2flow). A phenomenological physics model of the nonlinear coupling between the independent controls and the dependent variables of the plasma is presented. By using a design of experiment, the functional dependencies of the response surface are determined. In conjunction with the physical model, the dependencies are used to deconvolve the sensor …

Activation Energy Of Surface Diffusion And Terrace Width Dynamics During The Growth Of In (4×3) On Si (100) - (2×1) By Femtosecond Pulsed Laser Deposition, M. A. Hafez, H. E. Elsayed-Ali

Electrical & Computer Engineering Faculty Publications

The nucleation and growth of indium on a vicinal Si (100) - (2×1) surface at high temperature by femtosecond pulsed laser deposition was investigated by in situ reflection high energy electron diffraction (RHEED). RHEED intensity relaxation was observed for the first ∼2 ML during the growth of In (4×3) by step flow. From the temperature dependence of the rate of relaxation, an activation energy of 1.4±0.2 eV of surface diffusion was determined. The results indicate that indium small clusters diffused to terrace step edges with a diffusion frequency constant of (1.0±0.1) × 10¹¹ s^-1. The RHEED specular …

Photofragmentation Of Sif4 Upon Si 2p And F 1s Core Excitation: Cation And Anion Yield Spectroscopy, Maria Novella Piancastelli, Wayne C. Stolte, Renaud Guillemin, A. Wolska, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We have studied the fragmentation dynamics of core-excited SiF₄ by means of soft-x-ray photoexcitation and partial positive and negative ion yield measurements around the Si L_2,3-shell and F K-shell ionization thresholds. All detectable ionic fragments are reported and we observe significant differences between the various partial ion yields near the Si 2p threshold. The differences are similar to our previous results from CH₃Cl showing more extended fragmentation in correspondence to transitions to Rydberg states. At variance with smaller systems, we observe negative ion production in the shape resonance region. This can be related …

Design And Performance Of A Curved-Crystal X-Ray Emission Spectrometer, A. C. Hudson, Wayne C. Stolte, Dennis W. Lindle, Renaud Guillemin

Chemistry and Biochemistry Faculty Research

A curved-crystal x-ray emission spectrometer has been designed and built to measure 2–5 keV x-ray fluorescence resulting from a core-level excitation of gas phase species. The spectrometer can rotate 180°, allowing detection of emitted x rays with variable polarization angles, and is capable of collecting spectra over a wide energy range (20 eV wide with 0.5 eV resolution at the Cl K edge) simultaneously. In addition, the entire experimental chamber can be rotated about the incident-radiation axis by nearly 360° while maintaining vacuum, permitting measurements of angular distributions of emitted x rays.

Formation Of In- (2×1) And In Islands On Si (100) - (2×1) By Femtosecond Pulsed Laser Deposition, M. A. Hafez, H. E. Elsayed-Ali

Electrical & Computer Engineering Faculty Publications

The growth of indium on a vicinal Si (100) - (2×1) surface at room temperature by femtosecond pulsed laser deposition (fsPLD) was investigated by in situ reflection high-energy electron diffraction (RHEED). Recovery of the RHEED intensity was observed between laser pulses and when the growth was terminated. The surface diffusion coefficient of deposited In on initial two-dimensional (2D) In- (2×1) layer was determined. As growth proceeds, three-dimensional In islands grew on the 2D In- (2×1) layer. The RHEED specular profile was analyzed during film growth, while the grown In islands were examined by ex situ atomic force microscopy. The full …

Low-Energy Nondipole Effects In Molecular Nitrogen Valence-Shell Photoionization, Oliver Hemmers, Renaud Guillemin, D. Rolles, A. Wolska, Dennis W. Lindle, E. P. Kanter, B. Krassig, S. H. Southworth, R. Wehlitz, B. Zimmermann, V. Mckoy, P. W. Langhoff

Environmental Studies Faculty Publications

Observations are reported for the first time of significant nondipole effects in the photoionization of the outer-valence orbitals of diatomic molecules. Measured nondipole angular-distribution parameters for the 3σ_g, 1π_u, and 2σ_u shells of N₂ exhibit spectral variations with incident photon energies from thresholds to ∼200  eV which are attributed via concomitant calculations to particular final-state symmetry waves arising from (E1)⊗(M1,E2) radiation-matter interactions first-order in photon momentum. Comparisons with previously reported K-edge studies in N₂ verify linear scaling with photon momentum, accounting in part for the significantly enhanced nondipole behavior observed in inner-shell ionization …

Femtosecond Nuclear Motion Of Hcl Probed By Resonant X-Ray Raman Scattering In The Cl 1s Region, Marc Simon, Loic Journel, Stephane Carniato, Richard Taieb, I. Minkov, Faris Gel'mukhanov, P. Salek, H. Agren, Renaud Guillemin, Wayne C. Stolte, A. C. Hudson, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

Femtosecond dynamics are observed by resonant x-ray Raman scattering (RXS) after excitation along the dissociative Cl 1s→6ơ* resonance of gas-phase HCl. The short core-hole lifetime results in a complete breakdown of the common nondispersive behavior of soft-x-ray transitions between parallel potentials. We evidence a general phenomenon of RXS in the hard-x-ray region: a complete quenching of vibrational broadening. This opens up a unique opportunity for superhigh resolution x-ray spectroscopy beyond vibrational and lifetime limitations.

Growth Of Ge Quantum Dots On Si(100)-(2×1) By Pulsed Laser Deposition, M. S. Hegazy, H. E. Elsayed-Ali

Electrical & Computer Engineering Faculty Publications

Self-assembled germanium quantum dots (QDs) were grown on Si(100)-(2×1) by pulsed laser deposition. In situ reflection-high energy electron diffraction (RHEED) and postdeposition atomic force microscopy are used to study the growth of the QDs. Several films of different thicknesses were grown at a substrate temperature of 400 °C using a Q-switched Nd:yttrium aluminum garnet laser (λ= 1064 nm, 40 ns pulse width, 23 J/cm ² fluence, and 10 Hz repetition rate). At low film thicknesses, hut clusters that are faceted by different planes, depending on their height, are observed after the completion of the wetting layer. With increasing film thickness, …

Multivalued Logic, Neutrosophy And Schrodinger Equation, Florentin Smarandache, Victor Christianto

Branch Mathematics and Statistics Faculty and Staff Publications

This book was intended to discuss some paradoxes in Quantum Mechanics from the viewpoint of Multi-Valued-logic pioneered by Lukasiewicz, and a recent concept Neutrosophic Logic. Essentially, this new concept offers new insights on the idea of ‘identity’, which too often it has been accepted as given. Neutrosophy itself was developed in attempt to generalize Fuzzy-Logic introduced by L. Zadeh. While some aspects of theoretical foundations of logic are discussed, this book is not intended solely for pure mathematicians, but instead for physicists in the hope that some of ideas presented herein will be found useful. The book is motivated by …

Anion And Cation-Yield Spectroscopy Of Core-Excited Sf6, Maria Novella Piancastelli, Wayne C. Stolte, Renaud Guillemin, A. Wolska, M. M. Sant'anna, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

We report an extensive study on total and partial-ion-yield spectroscopy around both the S 2p and F 1s thresholds in SF₆. All positive and negative single-ion channels have been measured. Below the F 1s threshold we detect a large variation in relative intensity of the resonant structures according to the specific channel monitored, indicating selective fragmentation. Above threshold, at variance with previous cases described by us, we detect high-intensity structures related to shape resonances not only in the cation channels but also for the anions. We discuss the applicability and limits of a model we …

Fragmentation Dynamics Of H2s Following S 2p Photoexcitation, Renaud Guillemin, S-W Yu, Wayne C. Stolte, Dennis W. Lindle

Chemistry and Biochemistry Faculty Research

The fragmentation dynamics of core-excited H₂S has been studied by means of partial anion and cation yield measurements around the S L_2,3-subshell ionization thresholds. All detectable ionic fragments are reported, and significant differences between partial ion yields are observed. Possible dissociation pathways are discussed by comparison to previous studies of electron spectra.

Near-Edge X-Ray Absorption Fine Structure Study Of Ion-Beam-Induced Phase Transformation In Gd2(Ti1-Yzry)2o7, Ponnusamy Nachimuthu, S. Thevuthasan, V. Shutthanandan, E. M. Adams, W. J. Weber, B. D. Begg, D. K. Shuh, Dennis W. Lindle, Eric M. Gullikson, Rupert C. Perera

Chemistry and Biochemistry Faculty Research

The structural and electronic properties of Gd₂(Ti_1−yZr_y)₂O₇ (y=0–1) pyrochlores following a 2.0-MeV Au²⁺ ion-beam irradiation (~5.0 X 10¹⁴ Au²⁺/cm²) have been investigated by Ti 2p and O 1s near-edge x-ray absorption fine structure (NEXAFS). The irradiation of Gd₂(Ti_1−yZr_y)₂O₇ leads to the phase transformation from the ordered pyrochlore structure (Fd3m) to the defect fluorite structure (Fm3m) regardless of Zr concentration. Irradiated Gd₂(Ti_{1−y …}

Nondipole Effects In The Photoionization Of Xe 4d5/2 And 4d3/2: Evidence For Quadrupole Satellites, Oliver Hemmers, Renaud Guillemin, D. Rolles, A. Wolska, Dennis W. Lindle, K. T. Cheng, W. R. Johnson, H. L. Zhou, S. T. Manson

Environmental Studies Faculty Publications

Measurements of nondipole parameters in spin-orbit-resolved Xe 4d photoionization demonstrate dynamical differences arising from relativistic effects. The experimental data do not agree with relativistic random-phase approximation calculations of single ionization dipole and quadrupole channels. It is suggested that the discrepancy is due to the omission of multiple-excitation quadrupole channels, i.e., quadrupole satellite transitions.

Probing Cation Antisite Disorder In Gd2ti2o7 Pyrochlore By Site-Specific Nexafs And Xps, Ponnusamy Nachimuthu, S. Thevuthasan, Mark H. Engelhard, W. J. Weber, D. K. Shuh, N. M. Hamdan, B. S. Mun, E. M. Adams, D. E. Mccready, V. Shutthanandan, Dennis W. Lindle, G. Balakrishnan, R. C. Ewing

Chemistry and Biochemistry Faculty Research

Disorder in Gd₂Ti₂O₇ is investigated by near-edge x-ray-absorption fine structure (NEXAFS) and x-ray photoelectron spectroscopy (XPS). NEXAFS shows Ti⁴⁺ ions occupy octahedral sites with a tetragonal distortion induced by vacant oxygen sites. O 1s XPS spectra obtained with a charge neutralization system from Gd₂Ti₂O₇(100) and the Gd₂Ti₂O₇ pyrochlore used by Chen et al. [Phys. Rev. Lett. 88, 105901 (2002)], both yielded a single peak, unlike the previous result on the latter that found two peaks. The current results give no evidence for …

Nearest-Neighbor-Atom Core-Hole Transfer In Isolated Molecules, Renaud Guillemin, Oliver Hemmers, D. Rolles, S. W. Yu, A. Wolska, I. Tran, A. C. Hudson, J. Baker, Dennis W. Lindle

Environmental Studies Faculty Publications

A new phenomenon sensitive only to next-door-neighbor atoms in isolated molecules is demonstrated using angle-resolved photoemission of site-selective core electrons. Evidence for this interatomic core-to-core electron interaction is observable only by measuring nondipolar angular distributions of photoelectrons. In essence, the phenomenon acts as a very fine atomic-scale sensor of nearest-neighbor elemental identity.

Performance Characteristics Of Beamline 6.3.1 From 200 Ev To 2000 Ev At The Advanced Light Source, Ponnusamy Nachimuthu, J. H. Underwood, C. D. Kemp, Eric M. Gullikson, Dennis W. Lindle, David K. Shuh, Rupert C. Perera

Chemistry and Biochemistry Faculty Research

Bend magnet beamline 6.3.1 at the Advanced Light Source operates from 200 eV to 2000 eV, primarily used for x-ray absorption fine structure investigations. The beamline optics consist of a compact, entrance-slitless, Hettrick-Underwood type variable-line-spacing plane-grating monochromator and refocusing mirrors to provide a 25 μm × 500 μm spot at the focal point in the reflectometer end station. Wavelength is scanned by the simple rotation of the grating and illuminates a fixed exit slit. The LabView based beamline control and data acquisition computer code has been implemented to provide a convenient interface to the user. The dedicated end station is …

Dramatic Nondipole Effects In Low-Energy Photoionization: Experimental And Theoretical Study Of Xe 5s, Oliver Hemmers, Renaud Guillemin, E. P. Kanter, B. Krassig, Dennis W. Lindle, S. H. Southworth, R. Wehlitz, J. Baker, A. C. Hudson, M. Lotrakul, D. Rolles, Wayne C. Stolte, I. Tran, A. Wolska, S. Yu, M. Ya Amusia, K. T. Cheng, L. V. Chernysheva, W. R. Johnson, S. T. Manson

Environmental Studies Faculty Publications

The Xe 5s nondipole photoelectron parameter γ is obtained experimentally and theoretically from threshold to ∼200  eV photon energy. Significant nondipole effects are seen even in the threshold region of this valence shell photoionization. In addition, contrary to previous understanding, clear evidence of interchannel coupling among quadrupole photoionization channels is found.