International Journal of Quantum Chemistry

Cover image for Vol. 112 Issue 24

Special Issue: Proceedings of the 2012 Sanibel Symposium

15 December 2012

Volume 112, Issue 24

Pages i–iv, 3721–3903

Issue edited by: N. Yngve Öhrn, John R. Sabin

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Preface
    4. Full Papers
    1. You have free access to this content
      Cover Image, Volume 112, Issue 24 (pages i–ii)

      Article first published online: 9 NOV 2012 | DOI: 10.1002/qua.24349

      Thumbnail image of graphical abstract

      This snapshot structure of the 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC) lipid bilayer containing gramicidin A (GA), a peptide that forms ion channels for monovalent cations, is presented by Hiroaki Saito and colleagues on page 3834. The water molecules and hydrogen atoms are hidden, and GA is drawn as a ribbon structure in the figure. The arrows indicate the lateral pressures in the polar and hydrophobic regions of the membrane. This molecular dynamics study reveals that the lateral pressure in the hydrophobic region compresses the GA in the membrane and changes the pore size of the channel, which influences the ion permeation through the GA channel.

    2. You have free access to this content
      Inside Cover, Volume 112, Issue 24 (pages iii–iv)

      Article first published online: 9 NOV 2012 | DOI: 10.1002/qua.24359

      Thumbnail image of graphical abstract

      Cytochrome c oxidase (CcO) catalyzes the four-electron reduction of molecular oxygen to water and couples it to the transmembrane proton transfer in the respiratory chain of mitochondria and bacteria. The CuA site functions as the proximate electron-transfer intermediate from an electron source in CcO. It has characteristic structural features, providing an electronic structure suitable for rapid electron transfer. X-ray crystallographic structures show the structural variety of the Cu2S2 core of the CuA site. On page 3756, Yu Takano and colleagues address the origin of the structural variety of the Cu2S2 core of the CuA site, using the density functional theory.

  2. Preface

    1. Top of page
    2. Cover Image
    3. Preface
    4. Full Papers
    1. You have free access to this content
      Special Issue: 2012 Sanibel Symposium (page 3721)

      N. Y. Öhrn and J. R. Sabin

      Article first published online: 9 NOV 2012 | DOI: 10.1002/qua.24346

  3. Full Papers

    1. Top of page
    2. Cover Image
    3. Preface
    4. Full Papers
    1. Algebra of physical space and the geometric spacetime solution of Dirac's equation (pages 3722–3728)

      Burke Ritchie and Charles A. Weatherford

      Article first published online: 22 MAY 2012 | DOI: 10.1002/qua.24156

      Thumbnail image of graphical abstract

      The Dirac Equation and Zitterbewegung—what is Dirac trying to tell us? Does a continuum and a bound electron move with a quivering motion? A high fidelity simulation of the Dirac hydrogen atom says it does.

    2. Density functional theory and ab initio study on the reaction mechanisms of the homogeneous, unimolecular elimination kinetics of selected 1-chloroalkenes in the gas phase (pages 3729–3738)

      Jose R. Mora, Jesus Lezama, Neydher Berroteran, Tania Cordova and Gabriel Chuchani

      Article first published online: 24 MAY 2012 | DOI: 10.1002/qua.24175

      Thumbnail image of graphical abstract

      Density functional theory study on the HCl unimolecular elimination mechanism of selected alkenyl chlorides in the gas phase was performed. The transition state involves stabilization due to electron delocalization from the neighboring π-electrons. Calculated parameters were in good agreement with experimental values.

    3. Realization of population inversion under nonadiabatic conditions induced by the coupling between vibrational modes via Raman fields (pages 3739–3743)

      Vishesha Patel and Svetlana A. Malinovskaya

      Article first published online: 15 JUN 2012 | DOI: 10.1002/qua.24198

      Thumbnail image of graphical abstract

      In a simplistic picture, the laser process can be approximated by a two-level system. Here, the effects of the coupling between Raman-active vibrational modes on the population transfer are investigated using two coupled two-level systems with non-degenerate ground states. The population inversion is induced by two ultrafast laser pulses having chirps equal in magnitude and opposite in sign, and thus demonstrated in a more generic case of the averaged initial relative phase.

    4. Geometric single-qubit gates for an electron spin in a quantum dot (pages 3744–3749)

      Vladimir S. Malinovsky and Sergey Rudin

      Article first published online: 15 JUN 2012 | DOI: 10.1002/qua.24202

      Thumbnail image of graphical abstract

      Using the analytic expression of the evolution operator for the electron spin in a quantum dot, a new scheme is proposed to design a universal set of single-qubit gates based solely on the geometric phase that the qubit state acquires after a cyclic evolution in the parameter space. The scheme is using ultrafast linearly chirped pulses providing adiabatic excitation of the qubit states and the geometric phase is fully controlled by the relative phase between pulses.

    5. Constructing protein nano-fiber and estimation of the electronic state around metal ions (pages 3750–3755)

      Yu Komatsu, Masaki Fukuda, Hironao Yamada, Shuhei Kawamoto, Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Satoshi Yokojima, Satoshi Akanuma and Akihiko Yamagishi

      Article first published online: 5 JUN 2012 | DOI: 10.1002/qua.24206

      Thumbnail image of graphical abstract

      Nano-fiber can be self-assembled by mixing two kinds of proteins. Binding between the two α-helices of one protein and two α-helices of second protein yields a four-helix bundle, which is thermally stable. Coarse grained molecular dynamics simulations and electronic structure calculations are used to provide insight on this system, in particular, around their metal ions.

    6. Density functional studies of the structural variety of the Cu2S2 core of the CuA site (pages 3756–3762)

      Yu Takano, Orio Okuyama, Yasuteru Shigeta and Haruki Nakamura

      Article first published online: 8 JUN 2012 | DOI: 10.1002/qua.24214

      Thumbnail image of graphical abstract

      The effects of structural variations on the electronic structure of the Cu2S2 core of biological CuA site are analyzed using DFT calculations. The σu* oxidized state is find to be more robust to the structural change than the πu oxidized state. This result suggests that the reorganization energy between the oxidized and reduced states of the CuA site is very small, and that the structural variety of the core comes from the surrounding protein.

    7. Computing redox potentials for dyes used in p-type dye-sensitized solar cells (pages 3763–3768)

      Frédéric B. Anne, Nicolas Galland and Denis Jacquemin

      Article first published online: 15 JUN 2012 | DOI: 10.1002/qua.24215

      Thumbnail image of graphical abstract

      The redox potentials of ruthenium dyes used in p-type dye-sensitized solar cells are investigated with a variety of density functional theory approaches. An efficient computational protocol has been designed, and it is shown that the selected functional's impact on the predicted localization of the oxidation and/or reduction.

    8. Theoretical estimation of the acidities of alcohols and azoles in gas phase, DMSO, and water (pages 3769–3776)

      Paul G. Seybold and W. C. Kreye

      Article first published online: 9 JUN 2012 | DOI: 10.1002/qua.24216

      Thumbnail image of graphical abstract

      The acid-base behaviors of compounds are of central importance for their performances as drugs, biochemicals, and environmental species, so ways to estimate acid-base behavior theoretically are important aids in approaching this performance. In this report, the acidities of alcohols and azoles in gas phase, water, and DMSO are examined using molecular descriptors and quantitative structure-property relationships.

    9. A material design on new sodium ion conductor for sodium–sulfur battery. I. NaAlO(CN)2 and NaxAl1-x/3(CN)3 perovskite (pages 3777–3781)

      Taku Onishi

      Article first published online: 8 JUN 2012 | DOI: 10.1002/qua.24217

      Thumbnail image of graphical abstract

      The design of a solid electrolyte with stable structure and high sodium ion-conductivity is a fundamental step in the development of future sodium–sulfur batteries. A new sodium ion-conductive NaAlO(CN)2 perovskite is introduced in this work.

    10. Beyond the thermal set point: Significance of the compensatory temperatures of water vapor condensation in biological interactions (pages 3782–3790)

      Paul W. Chun

      Article first published online: 14 JUN 2012 | DOI: 10.1002/qua.24218

      Thumbnail image of graphical abstract

      This communication reports for the first time a link that has gone unrecognized between the compensatory temperatures of water vapor condensation and the thermal set point in interacting biological systems. In addition to determining the unique thermal set point for water vapor, which falls at 260 K, results indicate that in any biological interaction, the thermal set point must fall between the limits defined by the compensatory temperatures of water vapor, that is between 30 K and 380 K. Only between these limits is the net chemical driving force favorable for biological interaction to occur.

    11. Molecular dynamics analyses of the dissociation process of ADP from Hsp90 (pages 3791–3795)

      Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Megumi Nishimura, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu and Hidemi Nagao

      Article first published online: 19 JUN 2012 | DOI: 10.1002/qua.24229

      Thumbnail image of graphical abstract

      Hsp90 is a molecular chaperon and an attractive target for the therapeutics against cancer and virus infectious diseases. The functional cycle of Hsp90 is driven by binding of ATP and hydrolysis to ADP. Molecular dynamics simulations of Hsp90 with ADP are performed. Results of calculations reveal the dissociation process of ADP from Hsp90 at atomic resolution. ADP has two possible conformation and pathways during the dissociation process.

    12. Laplacian-based models for the exchange energy (pages 3796–3806)

      A. C. Cancio, Chris E. Wagner and Shaun A. Wood

      Article first published online: 26 JUN 2012 | DOI: 10.1002/qua.24230

      Thumbnail image of graphical abstract

      Development of simple, accurate density functional theories for molecules and solids is of highest interest in quantum chemistry. A standard approach—building models from the local density and its gradient—is updated to use a hybrid of the density gradient and Laplacian. This better represents the underlying physics of the exchange-correlation hole and obtains a more robust parameter with which to work, shown here by exchange potential calculations for small atoms.

    13. Molecular determinants for ligand binding at serotonin 5-HT2A and 5-HT2C GPCRs: Experimental affinity results analyzed by molecular modeling and ligand docking studies (pages 3807–3814)

      Tania Córdova-Sintjago, Rajeev Sakhuja, Krishnakanth Kondabolu, Clinton E. Canal and Raymond G. Booth

      Article first published online: 19 JUN 2012 | DOI: 10.1002/qua.24237

      Thumbnail image of graphical abstract

      The neurotransmitter serotonin mediates some of its psychological effects by activation of the 5-HT2 family of G protein coupled receptors (GPCRs). In this work, the overall receptor structures and ligand binding sites of several 5-HT2 GPCRs for drug are compared via homology modeling, molecular dynamics, and docking studies. This approach produces reliably predictable homology models, useful for the study of drug–receptor interaction for drug design purposes.

    14. Unified treatment of exactly solvable quantum potentials with confluent hypergeometric eigenfunctions: Generalized potentials (pages 3815–3821)

      J. J. Peña, J. Morales, J. García-Martínez and J. García-Ravelo

      Article first published online: 22 JUN 2012 | DOI: 10.1002/qua.24238

      Thumbnail image of graphical abstract

      A canonical transform to convert a general differential equation into Schrödinger-like equation is applied in the unified treatment of potentials having confluent hypergeometric wavefunctions. The results are generalized potentials of Harmonic, Morse, and Coulomb-type that reduce to well-known potentials, as particular cases. The approach is general and can be extended to other kind of differential equations with the aim to obtain generalized potentials accepting different special functions solutions.

    15. Theoretical calculation of the zero-temperature isotherm and phase stability of silver up to 2 Gbar using the linear combinations of gaussian type orbitals method (pages 3822–3828)

      Jonathan C. Boettger

      Article first published online: 19 JUN 2012 | DOI: 10.1002/qua.24239

      Thumbnail image of graphical abstract

      A systematic procedure is developed for calculating the zero temperature isotherm of a crystalline solid to arbitrarily high compressions using a linear combinations of Gaussian type orbitals electronic structure method. This procedure is used to determine the sequence of structural phase transitions exhibited by silver up to a pressure of 2 Gbar. The predicted sequence of structures is fcc to hcp to fcc to hcp to bcc.

    16. Molecular dynamics approach to sodium–water reaction compensating macroscopic heat and mass flow dynamics for LMFBR safety (pages 3829–3833)

      Kimichika Fukushima, Yukio Ugawa, Hiroshi Endo, Yoshihisa Shindo, Isao Tatewaki, Kazuo Haga and Masaaki Inoue

      Article first published online: 19 JUN 2012 | DOI: 10.1002/qua.24240

      Thumbnail image of graphical abstract

      In a liquid metal cooled fast breeder nuclear reactor pressurized water vapor can accidentally leak into the sodium in the secondary system, generating heat. Thus, understanding the sodium–water reaction in a heat exchanging steam generator is of paramount importance to ensure the safety of the facility. The potential energy and reaction rate of the reaction are calculated in this work using a combination of DFT, classical molecular dynamics, and macroscopic flow dynamics.

    17. Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile (pages 3834–3839)

      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Megumi Nishimura, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, Taku Mizukami and Hidemi Nagao

      Article first published online: 22 JUN 2012 | DOI: 10.1002/qua.24248

      Thumbnail image of graphical abstract

      Gramicidin is a peptide that forms ion channels specific for monovalent cations in biological membranes. The effect of gramicidin on the structure and lateral pressure profile of lipid bilayers is studied by molecular dynamics simulations. Due to the hydrophobic mismatch between gramicidin and the lipid bilayer, the membrane surface is largely distorted. The lateral pressure in the hydrophobic region of the membrane is found to decrease the pore size around the ion channel entrance.

    18. Electron detachment energies of aqueous and cluster halide anions from electron propagator calculations with the polarizable continuum model (pages 3840–3848)

      Olga Dolgounitcheva, Viatcheslav G. Zakrzewski and Joseph Vincent Ortiz

      Article first published online: 26 JUN 2012 | DOI: 10.1002/qua.24254

      Thumbnail image of graphical abstract

      The reactivity and spectra of gas-phase molecules and ions differ markedly from their counterparts in solution. The vertical electron detachment energies (VEDEs), and thus the computed photoelectron spectra, of fluoride and chloride anions in isolation, and coordinated by water molecules are calculated with and without the polarizable continuum model of solvation in water. The use of the dielectric cavity accounts for large shifts in VEDEs as well as important changes in the coordination geometries of the chloride ion.

    19. Spin hamiltonian models for artificial and native water splitting systems revealed by hybrid DFT calculations. Oxygen activation by high-valent Mn and Ru ions (pages 3849–3866)

      K. Yamaguchi, S. Yamanaka, H. Isobe, K. Tanaka and N. Ueyama

      Article first published online: 17 JUL 2012 | DOI: 10.1002/qua.24270

      Thumbnail image of graphical abstract

      Broken-symmetry hybrid density functional calculations are used to analyze proposed reaction mechanisms of water splitting reaction in artificial photosynthesis systems, involving putative ruthenium complexes, and discuss the similarities between artificial and native water splitting systems.

    20. Computational modeling of wet TiO2 (001) anatase surfaces functionalized by transition metal doping (pages 3867–3873)

      Yuchi Zhang and Dmitri S. Kilin

      Article first published online: 24 JUL 2012 | DOI: 10.1002/qua.24289

      Thumbnail image of graphical abstract

      Titanium dioxide anatase nanostructure is a photocatalyst under UV light. Given the importance of cheaply producing hydrogen from nonpetrochemical sources, this fact can be exploited for water splitting on its crystals, subject to the choice of a proper surface and functionalization. This study considers the problem of doping the surface with transition metal species, tuning the bandgap/density of states, and optimizing the nanostructure to maximize splitting, which facilitate the efficiency of photocatalytic water splitting on TiO2 crystals.

    21. Anatase (100) thin film surface computational model for photoelectrochemical cell (pages 3874–3878)

      Stephanie Jensen and Dmitri Kilin

      Article first published online: 20 JUL 2012 | DOI: 10.1002/qua.24290

      Thumbnail image of graphical abstract

      The TiO2 anatase surfaces are a good candidate for use in a photoelectrochemical cell; however, it has a too large bandgap to efficiently split water. Doping can be used to reduce the material's bandgap and largely improve its photocatalytic activity. In this study, the effectiveness of doping by ruthenium and platinum is considered by analyzing the surface charge transfer states at the substitution sites.

    22. Computational simulation of the p-n doped silicon quantum dot (pages 3879–3888)

      Jiangchao Chen, Andrew Schmitz and Dmitri S. Kilin

      Article first published online: 3 AUG 2012 | DOI: 10.1002/qua.24291

      Thumbnail image of graphical abstract

      This article describes a novel theoretical treatment of charge transfer at the center of quantum dots. The presented approach combines density matrix formalism and ab initio electronic structure calculations, in a procedure that uses the time average of reduced density matrix elements and incorporation of relaxation phenomena. This allows for the calculation of important experimental observables such as the electronic charge redistribution in two models of codoped and undoped silicon crystalline quantum dots.

    23. Optical properties of host material for phosphor computational modeling (pages 3889–3895)

      Ge Yao, Mary T. Berry, P. Stanley May and Dmitri S. Kilin

      Article first published online: 20 JUL 2012 | DOI: 10.1002/qua.24292

      Thumbnail image of graphical abstract

      β-NaYF4 is well known as the descent host material for fluorescent phosphors. In this work, the model of the periodical disorder structure of this material is reported, based on density functional theory calculations. The analysis of the partial charge densities suggests that charge transfer occurs from ligand to metal during the HOMO to LUMO excitation over the p–d channel. Calculations also show that NaYF4 is transparent in a wide spectral range, making it an appropriate host material for phosphors.

    24. Sequential hydrogen dissociation from a charged Pt13H24 cluster modeled by ab initio molecular dynamics (pages 3896–3903)

      Qingguo Meng, P. Stanley May, Mary T. Berry and Dmitri Kilin

      Article first published online: 13 AUG 2012 | DOI: 10.1002/qua.24301

      Thumbnail image of graphical abstract

      Platinum is one of the most valuable catalysts in use in industry for the reaction of hydrogenation and photo-catalytical water splitting. The electronic properties of selected Pt clusters, and their reactivity in the desorption and dissociation (A,B) of molecular hydrogen (C,D) are studied in this work using ab initio molecular dynamics (MD). The desorption rate of H2 is found to be related to the temperature and total charge of the model.

SEARCH

SEARCH BY CITATION