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    132 results match your criteria Chemical physics letters[Journal]

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    Solvent Dependence of Cyanoindole Fluorescence Lifetime.
    Chem Phys Lett 2017 Oct 18;685:133-138. Epub 2017 Jul 18.
    Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.
    Several cyanotryptophans have been shown to be useful biological fluorophores. However, how their fluorescence lifetimes vary with solvent has not been examined. In this regard, herein we measure the fluorescence decay kinetics as well as the absorption and emission spectra of six cyanoindoles in different solvents. Read More

    Isotope-Labeled Aspartate Sidechain as a Non-Perturbing Infrared Probe: Application to Investigate the Dynamics of a Carboxylate Buried Inside a Protein.
    Chem Phys Lett 2017 Sep 23;683:193-198. Epub 2017 Mar 23.
    Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.
    Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultantC=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum. Read More

    Comparative Dynamics of Methionine Side-Chain in FMOC-Methionine and in Amyloid Fibrils.
    Chem Phys Lett 2017 Apr 14;673:108-112. Epub 2017 Feb 14.
    Department of Mathematics, 1201 Larimer Street, University of Colorado at Denver, Denver, CO 80204, USA.
    We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition. Read More

    Reactive molecular dynamics models frommolecular dynamics data using relative entropy minimization.
    Chem Phys Lett 2017 Sep 22;683:573-578. Epub 2017 Apr 22.
    Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, 60637 USA.
    We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly frommolecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields. Read More

    Formation of environmentally persistent free radicals (EPFRs) on ZnO at room temperature: Implications for the fundamental model of EPFR generation.
    Chem Phys Lett 2017 Feb 31;670:5-10. Epub 2016 Dec 31.
    Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA.
    Environmentally persistent free radicals (EPFRs) have significant environmental and public health impacts. In this study, we demonstrate that EPFRs formed on ZnO nanoparticles provide two significant surprises. First, EPR spectroscopy shows that phenoxy radicals form readily on ZnO nanoparticles at room temperature, yielding EPR signals similar to those previously measured after 250°C exposures. Read More

    Tautomeric stabilities of 4-fluorohistidine shed new light on mechanistic experiments with labeled ribonuclease A.
    Chem Phys Lett 2016 Dec 27;666:58-61. Epub 2016 Oct 27.
    Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States.
    Ribonuclease A is the oldest model for studying enzymatic mechanisms, yet questions remain about proton transfer within the active site. Seminal work by Jackson(Science, 1994) labeled Ribonuclease A with 4-fluorohistidine, concluding that active-site histidines act as general acids and bases. Calculations of 4-fluorohistidine indicate that the π-tautomer is predominant in all simulated environments (by ~17 kJ/mol), strongly suggesting that fluoro-labeled ribonuclease A functions with His119 in π-tautomer. Read More

    Lithium batteries: Improving solid-electrolyte interphases via underpotential solvent electropolymerization.
    Chem Phys Lett 2016 Sep;661:65-69
    Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA 91125, USA.
    Understanding the mechanism of formation of solid-electrolyte interphases (SEI) is key to the prospects of lithium metal batteries (LMB). Here, we investigate via cyclic voltammetry, impedance spectroscopy and chronoamperometry the role of kinetics in controlling the properties of the SEI generated from the reduction of propylene carbonate (PC, a typical solvent in LMB). Our observations are consistent with the operation of a radical chain PC electropolymerization into polymer units whose complexity increases at lower initiation rates. Read More

    A Computational Model for Predicting Experimental RNA Nearest-Neighbor Free Energy Rankings: Inosine•Uridine Pairs.
    Chem Phys Lett 2015 Oct;639:157-60
    Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri, 63103, United States.
    A computational model for predicting RNA nearest neighbor free energy rankings has been expanded to include the nonstandard nucleotide inosine. The model uses average fiber diffraction data and molecular dynamic simulations to generate input geometries for Quantum mechanic calculations. This resulted in calculated intrastrand stacking, interstrand stacking, and hydrogen bonding energies that were combined to give total binding energies. Read More

    Probing environmentally significant surface radicals: Crystallographic and temperature dependent adsorption of phenol on ZnO.
    Chem Phys Lett 2015 Oct;638:56-60
    Louisiana State University, Department of Physics and Astronomy, 202 Nicholson Hall, Tower Dr., Baton Rouge, LA 70803, United States.
    Environmentally persistent free radicals (EPFRs) are toxic organic/metal oxide composite particles that have been discovered to form from substituted benzenes chemisorbed to metal oxides. Here, we perform photoelectron spectroscopy, electron energy loss spectroscopy, and low energy electron diffraction of phenol chemisorbed to ZnO(1 0 1̱ 0) and (0 0 0 1̱)-Zn to observe electronic structure changes and charge transfer as a function adsorption temperature. We show direct evidence of charge transfer from the ZnO surfaces to the phenol. Read More

    Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine.
    Chem Phys Lett 2015 Apr;626:20-24
    Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US ; Department of Biomedical Informatics, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, US.
    Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable. Read More

    Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution.
    Chem Phys Lett 2015 Apr;625:143-146
    Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 ; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536.
    To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. Read More

    A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.
    Chem Phys Lett 2014 Nov;616-617:67-74
    Department of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 ; Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697.
    A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. Read More

    Ions increase strength of hydrogen bond in water.
    Chem Phys Lett 2014 Aug;610-611:159-162
    Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000, Slovenia.
    Knowledge of water-water potential is important for an accurate description of water. Potential between two molecules depends upon the distance, relative orientation of each molecule and local environment. In simulation, water-water hydrogen bonds are handled by point-charge water potentials and by polarizable models. Read More

    High electrical permittivity of ultrapure water at the water-platinum interface.
    Chem Phys Lett 2014 Oct;613:19-23
    Department of Bioengineering, University of Washington, Seattle WA 98195.
    The discharge of a platinum parallel-plate capacitor filled with ultrapure water has been measured. The observed discharge trend can be described by a Modified Poisson-Boltzmann Equation (MPB) only when the voltage is very low. Increasing the applied voltage creates an "exclusion zone," in which the MPB equation no longer fits, and the system capacitance shows a dependence on the spacing between the two platinum plates. Read More

    Nonlinear optical properties of multipyrrole dyes.
    Chem Phys Lett 2014 Jul;608:303-307
    Department of Physics, University of Massachusetts Boston, Boston, MA 02125.
    The nonlinear optical properties of a series of pyrrolic compounds consisting of BODIPY and aza-BODIPY systems are investigated using 532 nm nanosecond laser and the Z-scan technique. Results show that 3,5-distyryl extension of BODIPY to the red shifted MeOBODIPY dye has a dramatic impact on its nonlinear absorption properties changing it from a saturable absorber to an efficient reverse saturable absorbing material with a nonlinear absorption coefficient of 4.64 × 10m/W. Read More

    Excited state properties of a short π-electron conjugated peridinin analogue.
    Chem Phys Lett 2014 Feb;593:132-139
    Department of Chemistry, University of Connecticut, Storrs, CT, 06269-3060, USA.
    C-peridinin is a synthetic analogue of the important, naturally-occurring carotenoid, peridinin, found in several marine algal species. C-peridinin has five conjugated carbon-carbon double bonds compared to eight possessed by peridinin and also lacks the methyl group functionalities typically present along the polyene chain of carotenoids. These structural modifications lead to unique excited state properties and important insights regarding the factors controlling the photophysics of peridinin and other carbonyl-containing carotenoids, which are critical components of the light-harvesting systems of many photosynthetic organisms. Read More

    Sensitivity enhancement of a grating-based surface plasmon-coupled emission (SPCE) bionsor chip using gold thickness.
    Chem Phys Lett 2014 Jan;591:5-9
    Department of Molecular and Cell Biology University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125.
    We describe a novel approach to enhance the sensitivity of a grating-based surface plasmon-coupled emission (SPCE) sensor by increasing the thickness of the metal film used in this system. The calculated optical properties of grating-based SPR spectra were significantly affected by both grating depth and by gold thickness. Higher angular sensitivity could be achieved at short wavelengths and undermeasurement (analysis under aqueous condition). Read More

    Analyses of mineral specific surface area and hydroxyl substitution for intact bone.
    Chem Phys Lett 2013 Nov;588
    Department of Physics, Oklahoma State University, Stillwater, OK, USA 74078.
    Bone minerals possess two primary hydrogen sources: hydroxide ions in the nanocrystalline core and structural water in the amorphous surface layer. In order to accurately measure their concentrations using hydrogen to phosphorus cross polarization NMR spectroscopy, it is necessary to analyze the dependence of signal intensities on serial contact times, namely, cross polarization kinetics. A reliable protocol is developed to iteratively decompose the severely overlapped spectra and to analyze the cross-polarization kinetics, leading to measurement of hydroxyl and structural water concentrations. Read More

    Radical re-appraisal of water structure in hydrophilic confinement.
    Chem Phys Lett 2013 Dec;590:1-15
    ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK.
    The structure of water confined in MCM41 silica cylindrical pores is studied to determine whether confined water is simply a version of the bulk liquid which can be substantially supercooled without crystallisation. A combination of total neutron scattering from the porous silica, both wet and dry, and computer simulation using a realistic model of the scattering substrate is used. The water in the pore is divided into three regions: core, interfacial and overlap. Read More

    How do proteins locate specific targets in DNA?
    Chem Phys Lett 2013 May;570
    Department of Chemistry, Columbia University, New York, NY 10032, United States.
    Many aspects of biology depend on the ability of DNA-binding proteins to locate specific binding sites within the genome. Interest in this target search problem has been reinvigorated through the recent development of microscopy-based technologies capable of tracking individual proteins in real-time as they search for binding sites. In this review we discuss how two different proteins, lac repressor and RNA polymerase, have solved the target search problem through seemingly different mechanisms, with an emphasis on how recentsingle-molecule studies have influenced our understanding of these reactions. Read More

    Controlling the femtosecond laser-driven transformation of dicyclopentadiene into cyclopentadiene.
    Chem Phys Lett 2013 Feb;558:1-7
    Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India.
    Dynamics of the chemical transformation of dicyclopentadiene into cyclopentadiene in a supersonic molecular beam is elucidated using femtosecond time-resolved degenerate pump-probe mass spectrometry. Control of this ultrafast chemical reaction is achieved by using linearly chirped frequency modulated pulses. We show that negatively chirped femtosecond laser pulses enhance the cyclopentadiene photo-product yield by an order of magnitude as compared to that of the unmodulated or the positively chirped pulses. Read More

    Amide I Band and Photoinduced Disassembly of a Peptide Hydrogel.
    Chem Phys Lett 2013 Aug;580:135-140
    Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.
    Peptide hydrogels are promising candidates for a wide range of medical and biotechnological applications. To further expand the potential utility of peptide hydrogels, herein we demonstrate a simple yet effective strategy to render peptide hydrogels photodegradable, making controlled disassembly of the gel structure of interest feasible. In addition, we find that the high-frequency amide I' component (i. Read More

    Fluorescent Polyelectrolyte Capped Silver Nanoclusters: Optimization and Spectroscopic Evaluation.
    Chem Phys Lett 2012 Oct;549:72-76
    Center for Commercialization of Fluorescence Technologies, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, Texas, USA, 76107.
    In the present work, we have synthesized water soluble Ag nanoclusters using PMAA as a template with different Ag+: COO-ratios, to optimize it for highest brightness using less UV exposure time. Fluorescence polarization was 0.30 for and was found to vary with excitation and emission wavelength with few hundred picoseconds average fluorescence lifetime. Read More

    Optical switching of radical pair conformation enhances magnetic sensitivity.
    Chem Phys Lett 2013 May;572:106-110
    Institut für Quantenoptik und Quanteninformation der Österreichischen Akademie der Wissenschaften, Innsbruck, Austria ; Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria.
    The yield of radical pair reactions is influenced by magnetic fields well beyond the levels expected from energy considerations. This dependence can be traced back to the microscopic dynamics of electron spins and constitutes the basis of chemical compasses. Here we propose a new experimental approach based on molecular photoswitches to achieve additional control on the chemical reaction and allow short-time resolution of the spin dynamics. Read More

    Detection of some stable species during the oxidation of methane by coupling a jet-stirred reactor (JSR) to cw-CRDS.
    Chem Phys Lett 2012 May;534:1-7
    KINCOM 'Kinetics of Combustion', CNRS - LRGP ENSIC, 1, rue Grandville, BP 20451, 54001 Nancy, France.
    We present the coupling of a jet-stirred reactor to detection by cw-CRDS in the near infrared and first results obtained during the oxidation of methane. The mixture is rapidly expanded from the jet-stirred reactor into a 80 cm-long cw-CRDS cell maintained at a the pressure around 1.33 kPa, thus freezing the reaction and decreasing pressure broadening of the absorption lines. Read More

    Quenching of-Cyanophenylalanine Fluorescence by Various Anions.
    Chem Phys Lett 2013 Mar;563:93-96
    Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.
    To expand the spectroscopic utility of the non-natural amino acid-cyanophenylalanine (Phe), we examine the quenching efficiencies of a series of commonly encountered anions toward its fluorescence. We find that iodide exhibits an unusually large Stern-Volmer quenching constant, making it a convenient choice in Phefluorescence quenching studies. Indeed, using the villin headpiece subdomain as a testbed we demonstrate that iodide quenching of Phefluorescence offers a convenient means to reveal protein conformational heterogeneity. Read More

    Computational study of the cerium(III) ion in aqueous environment.
    Chem Phys Lett 2012 Jun;539-540(8):50-53
    Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
    This work comprises the first quantum chemical simulation study of the Ceion in aqueous environment. The structural and dynamical properties have been investigated by means of the quantum mechanical charge field (QMCF) molecular dynamics (MD) approach and the results, where applicable, have been compared to experimental data. Besides conventional analytical tools, angular radial distribution functions have been employed to gain deeper insight into the structure of the hydrate. Read More

    Hydration of trivalent lanthanum revisited - AnQMCF-MD approach.
    Chem Phys Lett 2012 May;536(4):50-54
    Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
    The previously investigated La-hydrate has been re-evaluated by means of the quantum mechanical charge field (QMCF) molecular dynamics (MD) approach. Improved description of the hydration characteristics has been realised by including the full second hydration shell into the quantum mechanically treated region and by introducing the influence of the surrounding bulk via an electrostatic embedding technique. Analytical tools such as the ligand angular radial distribution analysis have been employed to gain deeper insight into the structural features of the hydrate. Read More

    Ultrafast E to Z photoisomerization dynamics of the Cph1 phytochrome.
    Chem Phys Lett 2012 Oct 31;549:86-92. Epub 2012 Aug 31.
    Department of Chemistry, One Shields Ave, University of California, Davis, CA 95616, United States.
    Femtosecond photodynamics of the reverse (P→P) reaction of the red/far-red phytochrome Cph1 fromwere resolved with visible broadband transient absorption spectroscopy. Multi-phasic dynamics were resolved and separated via global target analysis into a fast-decaying (260 fs) excited-state population that bifurcates to generate the isomerized Lumi-F primary photoproduct and a non-isomerizing vibrationally excited ground state that relaxes back into thePground state on a 2.8-ps time scale. Read More

    Two Photon Induced Luminescence of BSA Protected Gold Clusters.
    Chem Phys Lett 2013 Mar;561-562:74-76
    Center for Commercialization of Fluorescence Technologies, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, Texas, USA, 76107 ; Department of Cell Biology and Anatomy, University of North Texas Health Science Center. 3500 Camp Bowie Blvd. Fort Worth, Texas, USA, 76107.
    In this short letter, we have synthesized the BSA protected Aunanoclusters and studied their two photon luminescence behavior. We demonstrate that BSA Aunanoclusters can be used as a probe with two photon excitation capability. Our results show a quadratic relation between excitation power and emission intensity whereas with one photon excitation shows a linear dependence. Read More

    Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.
    Chem Phys Lett 2013 Jan 7;555:274-281. Epub 2012 Nov 7.
    Chemical Physics and Mateiral Physics Graduate Program, University of California, Irvine, CA, 92697 ; Department of Chemistry, University of California, Irvine, CA, 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697.
    Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Read More

    On-the-fly free energy parameterization via temperature accelerated molecular dynamics.
    Chem Phys Lett 2012 Sep;547:114-119
    Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States.
    We discuss a method for parametric calculation of free energy functions in arbitrary collective variables using molecular simulations. The method uses a variant of temperature accelerated molecular dynamics to evolve on-the-fly the parameters of the free energy function to their optimum values by minimization of a cumulative gradient error. We illustrate how the method performs using simple examples and discuss its application in the derivation of effective pairwise potentials for multiscale molecular simulations. Read More

    Solvation Structure and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface.
    Chem Phys Lett 2012 Feb;527:22-26
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
    Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic decrease in coordination number and an increasingly anisotropic distribution of solvating water molecules is shown to accompany movement of the ions towards vapor conditions; these effects are most noticeable with increases in ion size/decreases in magnitude of hydration free energy. Read More

    MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.
    Chem Phys Lett 2012 Aug 19;545:118-124. Epub 2012 Jul 19.
    Department of Mathematics, University of Pittsburgh, Pittsburgh, PA 15260, USA ; National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
    Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Read More

    Metal-enhanced intrinsic fluorescence of nucleic acids using platinum nanostructured substrates.
    Chem Phys Lett 2012 Oct;548:45-50
    Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD, 21201, USA.
    We investigated the feasibility of using platinum nanostructures to accomplish the metal-enhanced fluorescence (MEF) in the UV spectral region. We examine the possibility for detection of the intrinsic fluorescence from nucleotides and G-quadruplex DNA on platinum nanoparticles. Guanosine monophosphate (GMP) showed significant increases (~20-fold) in fluorescence intensities in the presence of platinum nanostructures when compared to quartz controls. Read More

    Computational Study on the Conformations of Gambogic Acid.
    Chem Phys Lett 2011 Aug;511(4-6):405-412
    Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University MS 38677-1848 USA.
    The conformations of gambogic acid were studied using force fields, MM3*, AMBER*, MMFFs and OPLS2005, and B3LYP methods. In a model molecule, only the MM3* and AMBER* methods produced the same number of conformers as B3LYP, generating two conformations for rings 1 and 2, and a single conformation for rings 3 and 4. The preferred conformations of these rings are maintained in a conformer of the actual gambogic acid generated using the AMBER* and B3LYP methods. Read More

    A gold cyano complex in nitromethane: MD simulation and X-ray diffraction.
    Chem Phys Lett 2012 Jun;539-540:24-29
    Department of Chemistry, The Ångström Laboratory, Uppsala University, Box 531, S-75121 Uppsala, Sweden ; Department of Theoretical Chemistry, The Royal Institute of Technology (KTH), Roslagstullsbacken 15, S-106 91 Stockholm, Sweden.
    The solvation structure around the dicyanoaurate(I) anion (Au(CN)) in a dilute nitromethane (CHNO) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute-solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. Read More

    Modified Becke'05 method of nondynamic correlation in density functional theory with self-consistent implementation.
    Chem Phys Lett 2012 Feb 5;525-526:150-152. Epub 2012 Jan 5.
    Q-Chem Inc., 5001 Baum boulevard, Suite 690, Pittsburgh, PA 15213, USA.
    Becke's B05 method for nondynamic correlation is simplified for self-consistent implementation. An alternative form is proposed for the nondynamic correlation factors that do not require solving a complicated nonlinear algebraic equation. The four linear parameters of B05 are re-optimized together with one extra parameter entering a modified expression for the second-order same-spin energy contribution. Read More

    Influence of water on the work function of certain metals.
    Chem Phys Lett 2012 May 3;536:65-67. Epub 2012 Apr 3.
    Dipartimento di Fisica ed Astronomia -Università di Catania and Laboratori Nazionali del Sud - INFN. Via S. Sofia 64, 95123, Catania, Italy.
    Experiments were carried out to explore the effect of light on Au, Pt and Cu surfaces immersed in water, in order to study the changes of work function arising from the interaction between the metallic surfaces and water. The results show an action of liquid water about three times larger than that of low-temperature ice. Theoretical calculations, present in literature, have predicted values much lower than those we measured. Read More

    Modulations in restricted amide rotation by steric induced conformational trapping.
    Chem Phys Lett 2012 Jan;523(27):124-127
    Department of Chemistry, California State University, Fresno CA 93740.
    The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. Read More

    Hydration of highly charged ions.
    Chem Phys Lett 2011 Aug;512(4-6):139-145
    Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
    Based on a series of ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulations, the broad spectrum of structural and dynamical properties of hydrates of trivalent and tetravalent ions is presented, ranging from extreme inertness to immediate hydrolysis. Main group and transition metal ions representative for different parts of the periodic system are treated, as are 2 threefold negatively charged anions. The results show that simple predictions of the properties of the hydrates appear impossible and that an accurate quantum mechanical simulation in cooperation with sophisticated experimental investigations seems the only way to obtain conclusive results. Read More

    Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies.
    Chem Phys Lett 2011 Oct;514(4-6):368-373
    Department of Physics, Shanghai Normal University, Shanghai, 200234, China.
    Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first reviewed the theory for the computation of dielectric boundary forces based on the definition of the Maxwell stress tensor. Read More

    Carotenoid response to retinal excitation and photoisomerization dynamics in xanthorhodopsin.
    Chem Phys Lett 2011 Nov;516(1-3):96-101
    Institute of Physical Biology, University of South Bohemia, Zámek 136, 373 33 Nové Hrady, Czech Republic.
    We present a comparative study of xanthorhodopsin, a proton pump with the carotenoid salinixanthin serving as an antenna, and the closely related bacteriorhodopsin. Upon excitation of retinal, xanthorhodopsin exhibits a wavy transient absorption pattern in the region between 470 and 540 nm. We interpret this signal as due to electrochromic effect of the transient electric field of excited retinal on salinixanthin. Read More

    Thermal stability of functionalized carbon nanotubes studied by in-situ transmission electron microscopy.
    Chem Phys Lett 2011 Sep;513(1-3):88-93
    Microscopy and Imaging Center and Materials Science and Engineering Program, Texas A&M University, College Station, TX 77843-2257, USA.
    The thermal stability of funtionalized carbon nanotubes (CNTs) has been studied experimentally by direct in-situ observations using a heating stage in a transmission electron microscope, from room temperature (RT) to about 1000 °C. It was found that the thermal stability of the functionalized CNTs was significantly reduced during the in-situ heating process. Their average diameter dramatically expanded from RT to about 500 °C, and then tended to be stable until about 1000 °C. Read More

    The Effects of Regularly Spaced Glutamine Substitutions on Alpha-Helical Peptide Structures. A DFT/ONIOM Study.
    Chem Phys Lett 2011 Aug;512(4-6):255-257
    Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York NY 10065.
    The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. Read More

    Modulation of cross polarization in motionally averaged solids by Variable Angle Spinning NMR.
    Chem Phys Lett 2011 May;508(4-6):314-319
    Department of Chemistry, University of California, Irvine 92697-2025.
    In systems where the dipolar couplings are partially averaged by molecular motion, cross-polarization is modulated by sample spinning. The cross-polariation efficiency in Variable Angle Spinning (VAS) and Switched Angle Spinning (SAS) experiments on mobile samples is therefore strongly dependent on the spinning angle. We describe simulations and experimental measurements of these effects over a range of spinning angles from 0° to 90°. Read More

    Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity.
    Chem Phys Lett 2011 Apr;506(4-6):135-138
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599.
    Catechol O-methyltransferase (COMT) metabolizes catechol moieties by methylating a single hydroxyl group at the meta- or para- hydroxyl position. Hydrophobic amino acids near the active site of COMT influence the regioselectivity of this reaction. Our sequence analysis highlights their importance by showing that these residues are highly conserved throughout evolution. Read More

    Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields.
    Chem Phys Lett 2011 May;508(4-6):289-294
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
    We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5-5. Read More

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