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Biological and Chemical Physics

2008

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Articles 1 - 23 of 23

Full-Text Articles in Physics

Constructing Diabatic States From Adiabatic States: Extending Generalized Mulliken–Hush To Multiple Charge Centers With Boys Localization, Joseph E. Subotnik, Robert J. Cave, Sina Yeganeh, Mark A. Ratner Dec 2008

Constructing Diabatic States From Adiabatic States: Extending Generalized Mulliken–Hush To Multiple Charge Centers With Boys Localization, Joseph E. Subotnik, Robert J. Cave, Sina Yeganeh, Mark A. Ratner

All HMC Faculty Publications and Research

This article shows that, although Boys localization is usually applied to single-electron orbitals, the Boys method itself can be applied to many electron molecular states. For the two-state charge-transfer problem, we show analytically that Boys localization yields the same charge-localized diabatic states as those found by generalized Mulliken–Hush theory. We suggest that for future work in electron transfer, where systems have more than two charge centers, one may benefit by using a variant of Boys localization to construct diabatic potential energy surfaces and extract electronic coupling matrix elements. We discuss two chemical examples of Boys localization and propose a ...


Reconstructing Three-Dimensional Shape Envelopes From Time-Resolved Small-Angle X-Ray Scattering Data, Jessica Lamb, Lisa W. Kwok, Xiangyun Qiu, Kurt Andresen, Hye Yoon Park, Lois Pollack Dec 2008

Reconstructing Three-Dimensional Shape Envelopes From Time-Resolved Small-Angle X-Ray Scattering Data, Jessica Lamb, Lisa W. Kwok, Xiangyun Qiu, Kurt Andresen, Hye Yoon Park, Lois Pollack

Physics and Astronomy Faculty Publications

Modern computing power has made it possible to reconstruct low-resolution, three-dimensional shapes from solution small-angle X-ray scattering (SAXS) data on biomolecules without a priori knowledge of the structure. In conjunction with rapid mixing techniques, SAXS has been applied to time resolve conformational changes accompanying important biological processes, such as biomolecular folding. In response to the widespread interest in SAXS reconstructions, their value in conjunction with such time-resolved data has been examined. The group I intron from Tetrahymena thermophila and its P4–P6 subdomain are ideal model systems for investigation owing to extensive previous studies, including crystal structures. The goal of ...


Abrupt Transition From A Free, Repulsive To A Condensed, Attractive Dna Phase, Induced By Multivalent Polyamine Cations, Xiangyun Qiu, Kurt Andresen, Jessica S. Lamb, Lisa W. Kwok, Lois Pollack Nov 2008

Abrupt Transition From A Free, Repulsive To A Condensed, Attractive Dna Phase, Induced By Multivalent Polyamine Cations, Xiangyun Qiu, Kurt Andresen, Jessica S. Lamb, Lisa W. Kwok, Lois Pollack

Physics and Astronomy Faculty Publications

We have investigated the energetics of DNA condensation by multivalent polyamine cations. Solution small angle x-ray scattering was used to monitor interactions between short 25 base pair dsDNA strands in the free supernatant DNA phase that coexists with the condensed DNA phase. Interestingly, when tetravalent spermine is used, significant inter-DNA repulsion is observed in the free phase, in contrast with the presumed inter-DNA attraction in the coexisting condensed phase. DNA condensation thus appears to be a discrete, first-order-like, transition from a repulsive gaseous to an attractive condensed solid phase, in accord with the reported all-or-none condensation of giant DNA. We ...


Direct Observation Of H2 Binding To A Metal Oxide Surface, J. Z. Larese, T. Arnold, L. Frazier, R. J. Hinde, A. J. Ramirez-Cuesta Oct 2008

Direct Observation Of H2 Binding To A Metal Oxide Surface, J. Z. Larese, T. Arnold, L. Frazier, R. J. Hinde, A. J. Ramirez-Cuesta

Chemistry Publications and Other Works

Inelastic neutron scattering is used to probe the dynamical response of H2 films adsorbed on MgO(100) as a function of film thickness. Concomitant diffraction measurements and a reduced-dimensionality quantum dynamical model provide insight into the molecule-surface interaction potential. At monolayer thickness, the rotational motion is strongly influenced by the surface, so that the molecules behave like quasiplanar rotors. These findings have a direct impact on understanding how molecular hydrogen binds to the surface of materials used in catalytic and storage applications.


Dynamics Of Apomyoglobin In The Α-To-Β Transition And Of Partially Unfolded Aggregated Protein, E. Fabiani, A. M. Stadler, D. Madern, M. M. Koza, M. Tehei, M. Hirai, G. Zaccai Oct 2008

Dynamics Of Apomyoglobin In The Α-To-Β Transition And Of Partially Unfolded Aggregated Protein, E. Fabiani, A. M. Stadler, D. Madern, M. M. Koza, M. Tehei, M. Hirai, G. Zaccai

Faculty of Science - Papers (Archive)

Changes of molecular dynamics in the α-to-β transition associated with amyloid fibril formation were explored on apo-myoglobin (ApoMb) as a model system. Circular dichroism, neutron and X-ray scattering experiments were performed as a function of temperature on the protein, at different solvent conditions. A significant change in molecular dynamics was observed at the α-to-β transition at about 55 ˚C, indicating a more resilient high temperature β structure phase. A similar effect at approximately the same temperature was observed in holo-myoglobin, associated with partial unfolding and protein aggregation. A study in a wide temperature range between 20 K and 360 K ...


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 Sep 2008

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 Publications

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.


Inverse Velocity Dependence Of Vibrationally Promoted Electron Emission From A Metal Surface, N. H. Nahler, J. D. White, Jerry L. Larue, Daniel J. Auerbach, Alec M. Wodtke Aug 2008

Inverse Velocity Dependence Of Vibrationally Promoted Electron Emission From A Metal Surface, N. H. Nahler, J. D. White, Jerry L. Larue, Daniel J. Auerbach, Alec M. Wodtke

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

All previous experimental and theoretical studies of molecular interactions at metal surfaces show that electronically nonadiabatic influences increase with molecular velocity. We report the observation of a nonadiabatic electronic effect that follows the opposite trend: The probability of electron emission from a low–work function surface—Au(111) capped by half a monolayer of Cs—increases as the velocity of the incident NO molecule decreases during collisions with highly vibrationally excited NO(X2π½, V = 18; V is the vibrational quantum number of NO), reaching 0.1 at the lowest velocity studied. We show that these results are ...


An Extended Multireference Study Of The Electronic States Of Para-Benzyne, Carol A. Parish, Evan B. Wang, Hans Lischka Jul 2008

An Extended Multireference Study Of The Electronic States Of Para-Benzyne, Carol A. Parish, Evan B. Wang, Hans Lischka

Chemistry Faculty Publications

A state-averaged, multireference complete active space (CAS) approach was used for the determination of the vertical excitation energies of valence and Rydberg states of para-benzyne. Orbitals were generated with a 10- and 32-state averaged multiconfigurational self-consistent field approach. Electron correlation was included using multireference configuration interaction with singles and doubles, including the Pople correction for size extensivity, multireference averaged quadratic coupled cluster (MR-AQCC) and MR-AQCC based on linear response theory. There is a very high density of electronic states in this diradical system—there are more than 17 states within 7 eV of the ground state including two 3 ...


Mono- And Trivalent Ions Around Dna: A Small-Angle Scattering Study Of Competition And Interactions, Kurt Andresen, Xiangyun Qiu, Suzette A. Pabit, Jessica S. Lamb, Hye Yoon Park, Lisa W. Kwok, Lois Pollack Jul 2008

Mono- And Trivalent Ions Around Dna: A Small-Angle Scattering Study Of Competition And Interactions, Kurt Andresen, Xiangyun Qiu, Suzette A. Pabit, Jessica S. Lamb, Hye Yoon Park, Lisa W. Kwok, Lois Pollack

Physics and Astronomy Faculty Publications

The presence of small numbers of multivalent ions in DNA-containing solutions results in strong attractive forces between DNA strands. Despite the biological importance of this interaction, e.g., DNA condensation, its physical origin remains elusive.Wecarried out a series of experiments to probe interactions between short DNA strands as small numbers of trivalent ions are included in a solution containing DNA and monovalent ions. Using resonant (anomalous) and nonresonant small angle x-ray scattering, we coordinated measurements of the number and distribution of each ion species around the DNA with the onset of attractive forces between DNA strands. DNA-DNA interactions occur ...


Temperature Response Of 129 Xe Depolarization Transfer And Its Application For Ultrasensitive Nmr Detection, Leif Schröder, Tyler Meldrum, Monica Smith, Thomas J. Lowery, David E. Wemmer, Alexander Pines Jun 2008

Temperature Response Of 129 Xe Depolarization Transfer And Its Application For Ultrasensitive Nmr Detection, Leif Schröder, Tyler Meldrum, Monica Smith, Thomas J. Lowery, David E. Wemmer, Alexander Pines

Arts & Sciences Articles

Trapping xenon in functionalized cryptophane cages makes the sensitivity of hyperpolarized (HP) 129Xe available for specific NMR detection of biomolecules. Here, we study the signal transfer onto a reservoir of unbound HP xenon by gating the residence time of the nuclei in the cage through the temperature-dependant exchange rate. Temperature changes larger than ∼0.6  K are detectable as an altered reservoir signal. The temperature response is adjustable with lower concentrations of caged xenon providing more sensitivity at higher temperatures. Ultrasensitive detection of functionalized cryptophane at 310 K is demonstrated with a concentration of 10 nM, corresponding to a ∼4000 ...


Stability And Equation Of State Of A Nanocrystalline Ga-Ge Mullite In A Vitroceramic Composite: A Synchrotron X-Ray Diffraction Study, Kristina E. Lipinska-Kalita, Patricia Kalita, Cedric Gobin, Oliver Hemmers, Thomas Hartmann, Gino Mariotto Apr 2008

Stability And Equation Of State Of A Nanocrystalline Ga-Ge Mullite In A Vitroceramic Composite: A Synchrotron X-Ray Diffraction Study, Kristina E. Lipinska-Kalita, Patricia Kalita, Cedric Gobin, Oliver Hemmers, Thomas Hartmann, Gino Mariotto

Environmental Studies Faculty Publications

Synchrotron x-ray diffraction and diamond anvil cell techniques were used to characterize the phase transformations and to evaluate the structural stability at elevated pressures of a developed nanocrystalline composite. The optically transparent material was built of a germanium oxide-based amorphous host matrix with homogeneously dispersed 13±3 nm Ga-Ge mullite-type nanocrystals, which had a structure similar to the conventional Al2O3-SiO2 mullite. The equation of state of the nanocrystals and the overall structural integrity of the nanocomposite were investigated in quasihydrostatic conditions on compression to 36 GPa and on the following decompression to ambient conditions. The ...


Interactions Of Β-Helical Antifreeze Protein Mutants With Ice, Maya Bar, Yeliz Celik, Deborah Fass, Ido Braslavsky Apr 2008

Interactions Of Β-Helical Antifreeze Protein Mutants With Ice, Maya Bar, Yeliz Celik, Deborah Fass, Ido Braslavsky

Physics Faculty Research

The fold of the β-helical antifreeze protein from Tenebrio molitor (TmAFP) proved to be surprisingly tolerant of multiple amino acid substitutions, enabling the construction of a panel of mutants displaying grids of single amino acid types in place of the threonines on the ice-binding face. These mutants, maintaining the regularity of amino acid spacing found in the wild-type protein but with different functional groups on the surface, were tested for antifreeze activity by measuring thermal hysteresis and observing ice grown in their presence. We found that no mutant exhibited the dramatic activity of the wild-type version of this hyperactive antifreeze ...


Equation Of State Of Gallium Oxide To 70 Gpa: Comparison Of Quasihydrostatic And Nonhydrostatic Compression, Kristina E. Lipinska-Kalita, Patricia Kalita, Oliver Hemmers, Thomas Hartmann Mar 2008

Equation Of State Of Gallium Oxide To 70 Gpa: Comparison Of Quasihydrostatic And Nonhydrostatic Compression, Kristina E. Lipinska-Kalita, Patricia Kalita, Oliver Hemmers, Thomas Hartmann

Environmental Studies Faculty Publications

Synchrotron x-ray diffraction and diamond-anvil cell techniques were used to characterize pressure induced structural modifications in gallium oxide. Gallium oxide was studied on compression up to 70 GPa and on the following decompression. The effect of the pressure-transmitting medium on the structural transformations was investigated in two sets of compression and decompression runs, one with nitrogen as a quasihydrostatic pressure-transmitting medium and the other in nonhydrostatic pressure conditions. The x-ray diffraction data showed gradual phase transition from a low-density, monoclinic β-Ga2O3 to a high-density, rhombohedral α-Ga2O3. With the use of nitrogen as a pressure ...


Functional Cloning And Characterization Of The Multidrug Efflux Pumps Norm From Neisseria Gonorrhoeae And Ydhe From Escherichia Coli, Feng Long, Corrinne Rouquette-Loughlin, William M. Shafer, Edward Yu Jan 2008

Functional Cloning And Characterization Of The Multidrug Efflux Pumps Norm From Neisseria Gonorrhoeae And Ydhe From Escherichia Coli, Feng Long, Corrinne Rouquette-Loughlin, William M. Shafer, Edward Yu

Physics and Astronomy Publications

Active efflux of antimicrobial agents is one of the most important adapted strategies that bacteria use to defend against antimicrobial factors that are present in their environment. The NorM protein of Neisseria gonorrhoeae and the YdhE protein of Escherichia coli have been proposed to be multidrug efflux pumps that belong to the multidrug and toxic compound extrusion (MATE) family. In order to determine their antimicrobial export capabilities, we cloned, expressed, and purified these two efflux proteins and characterized their functions both in vivo and in vitro. E. coli strains expressing norM or ydhE showed elevated (twofold or greater) resistance to ...


Conformational Change Of The Acrr Regulator Reveals A Possible Mechanism Of Induction, Ruoyu Gu, Ming Li, Chih-Chia Su, Feng Long, Matthew D. Routh, Feng Yang, Gerry Mcdermott, Edward Yu Jan 2008

Conformational Change Of The Acrr Regulator Reveals A Possible Mechanism Of Induction, Ruoyu Gu, Ming Li, Chih-Chia Su, Feng Long, Matthew D. Routh, Feng Yang, Gerry Mcdermott, Edward Yu

Physics and Astronomy Publications

The Escherichia coli AcrR multidrug-binding protein represses transcription of acrAB and is induced by many structurally unrelated cytotoxic compounds. The crystal structure of AcrR in space group P2221 has been reported previously. This P2221 structure has provided direct information about the multidrug-binding site and important residues for drug recognition. Here, a crystal structure of this regulator in space group P31 is presented. Comparison of the two AcrR structures reveals possible mechanisms of ligand binding and AcrR regulation.


Crystallization And Preliminary X-Ray Diffraction Analysis Of The Multidrug Efflux Transporter Norm From Neisseria Gonorrhoeae, Chih-Chia Su, Feng Long, Gerry Mcdermott, William M. Shafer, Edward Yu Jan 2008

Crystallization And Preliminary X-Ray Diffraction Analysis Of The Multidrug Efflux Transporter Norm From Neisseria Gonorrhoeae, Chih-Chia Su, Feng Long, Gerry Mcdermott, William M. Shafer, Edward Yu

Physics and Astronomy Publications

The crystallization and preliminary X-ray data analysis of the NorM multidrug efflux pump produced by Neisseria gonorrhoeae are reported. NorM is a cytoplasmic membrane protein that consists of 459 amino-acid residues. It is a member of the recently classified multidrug and toxic compound extrusion (MATE) family of transporters and recognizes a number of cationic toxic compounds such as ethidium bromide, acriflavin, 2-N-methylellipticinium and ciprofloxacin. Recombinant NorM protein was expressed in Escherichia coli and purified by metal-affinity and gel-filtration chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron ...


A Six-Dimensional H2–H2 Potential Energy Surface For Bound State Spectroscopy, Robert Hinde Jan 2008

A Six-Dimensional H2–H2 Potential Energy Surface For Bound State Spectroscopy, Robert Hinde

Chemistry Publications and Other Works

We present a six-dimensional potential energy surface for the (H2)2 dimer based on coupled-cluster electronic structure calculations employing large atom-centered Gaussian basis sets and a small set of midbond functions at the dimer’s center of mass. The surface is intended to describe accurately the bound and quasibound states of the dimers (H2)2, (D2)2, and H2–D2 that correlate with H2 or D2 monomers in the rovibrational levels (v, j) =(0,0), (0,2), (1,0), and (1,2). We employ a close-coupled approach to compute the energies of these ...


Stable Long-Time Semiclassical Description Of Zero-Point Energy In High-Dimensional Molecular Systems, Sophya V. Garashchuk, V. A. Rassolov Jan 2008

Stable Long-Time Semiclassical Description Of Zero-Point Energy In High-Dimensional Molecular Systems, Sophya V. Garashchuk, V. A. Rassolov

Faculty Publications

Semiclassical implementation of the quantum trajectory formalism [J. Chem. Phys.120, 1181 (2004)] is further developed to give a stable long-time description of zero-point energy in anharmonic systems of high dimensionality. The method is based on a numerically cheap linearized quantum force approach; stabilizing terms compensating for the linearization errors are added into the time-evolution equations for the classical and nonclassical components of the momentum operator. The wave function normalization and energy are rigorously conserved. Numerical tests are performed for model systems of up to 40 degrees of freedom.


Variation Of The Magnetic Ordering In Gdt2zn20 (T=Fe, Ru, Os, Co, Rh And Ir) And Its Correlation With The Electronic Structure Of Isostructural Yt2zn20, Shuang Jia, Ni Ni, G. D. Samolyuk, A. Safa-Sefat, K. Dennis, Hyunjin Ko, Gordon J. Miller, Sergey L. Bud'ko, Paul C. Canfield Jan 2008

Variation Of The Magnetic Ordering In Gdt2zn20 (T=Fe, Ru, Os, Co, Rh And Ir) And Its Correlation With The Electronic Structure Of Isostructural Yt2zn20, Shuang Jia, Ni Ni, G. D. Samolyuk, A. Safa-Sefat, K. Dennis, Hyunjin Ko, Gordon J. Miller, Sergey L. Bud'ko, Paul C. Canfield

Chemistry Publications

Magnetization, resistivity, and specific heat measurements were performed on solution-grown single crystals of six GdT2Zn20 (T=Fe, Ru, Os, Co, Rh, and Ir) compounds, as well as on their Y analogs. For the Gd compounds, the Fe column members manifest a ferromagnetic (FM) ground state (with an enhanced Curie temperature TC for T=Fe and Ru), whereas the Co column members manifest an antiferromagnetic (AFM) ground state. Thermodynamic measurements on YT2Zn20 revealed that the enhanced TC for GdFe2Zn20 and GdRu2Zn20 can be understood within the framework of Heisenberg moments embedded in a nearly ferromagnetic Fermi liquid. Furthermore, electronic structure calculations ...


Single-Molecule Dendrimer-Hydrocarbon Interaction, Karthikeyan Pasupathy, Nicholas W. Suek, John L. Lyons, Justin Ching, Aaron Jones, Qi Lu, Monica H. Lamm, Pu Chun Ke Jan 2008

Single-Molecule Dendrimer-Hydrocarbon Interaction, Karthikeyan Pasupathy, Nicholas W. Suek, John L. Lyons, Justin Ching, Aaron Jones, Qi Lu, Monica H. Lamm, Pu Chun Ke

Chemical and Biological Engineering Publications

We report our single-molecule fluorescence microscopy and molecular dynamics simulation studies on the interaction of poly(amidoamine) dendrimer and squalane hydrocarbon in aqueous solution. Our spectrophotometry measurements indicate that this interaction increases with the pH of the solvent. Our simulations show that squalane resides primarily on the perimeter of the dendrimer at low to neutral pH, but becomes encapsulated by the dendrimer at high pH. Using single-molecule fluorescence microscopy, we have identified that the binding between PAMAM and squalane is reversible. At a pH value of 8, the approaching, binding, and characteristic times of a single fluorescently-labeled dendrimer to squalane ...


Nanoparticle Ordering Via Functionalized Block Copolymers In Solution, Rastko Sknepnek, Joshua A. Anderson, Monica H. Lamm, Jorg Schmalian, Alex Travesset Jan 2008

Nanoparticle Ordering Via Functionalized Block Copolymers In Solution, Rastko Sknepnek, Joshua A. Anderson, Monica H. Lamm, Jorg Schmalian, Alex Travesset

Chemical and Biological Engineering Publications

We consider nanoparticles and functionalized copolymers, block copolymers with attached end groups possessing a specific affinity for nanoparticles, in solution. Using molecular dynamics, we show that nanoparticles are able to direct the self-assembly of the polymer/ nanoparticle composite. We perform a detailed study for a wide range of nanoparticle sizes and concentrations. We show that the nanoparticles order in a number of distinct phases: simple cubic, layered hexagonal, hexagonal columnar, gyroid, and a novel square columnar. Our results show that nanoparticles ordered with functionalized block copolymers can provide a simple and efficient tool for assembling novel materials with nanometer scale ...


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 Jan 2008

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 Publications

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 L2,3-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 ...


Crystal Structure Of The Catalytic Trimer Of Methanococcus Jannaschii Aspartate Transcarbamoylase, Jacqueline Vitali, Michael Colaneri Colaneri, Evan Kantrowitz Jan 2008

Crystal Structure Of The Catalytic Trimer Of Methanococcus Jannaschii Aspartate Transcarbamoylase, Jacqueline Vitali, Michael Colaneri Colaneri, Evan Kantrowitz

Physics Faculty Publications

The catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase is extremely heat stable, maintaining 75% of its activity after heat treatment for 60 min at 75 degrees C. We undertook its structural analysis in order to understand the molecular basis of its thermostability and gain insight on how its catalytic function adapts to high temperature. Several structural elements potentially contributing to thermostability were identified. These include: (i) changes in the amino acid composition such as a decrease in the thermolabile residues Gln and Asn, an increase in the charged residues Lys and Glu, an increase in Tyr and a decrease in ...