Journal of Computational Chemistry

Cover image for Journal of Computational Chemistry

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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  1. 1 - 22
  1. Full Papers

    1. Electronic reorganization triggered by electron transfer: The intervalence charge transfer of a Fe3+/Fe2+ bimetallic complex

      Alex Domingo, Celestino Angeli, Coen de Graaf and Vincent Robert

      Article first published online: 5 MAR 2015 | DOI: 10.1002/jcc.23871

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      The electronic reorganization induced by the intervalence charge transfer of a synthetic nonheme binuclear mixed-valence Fe3+/Fe2+ complex determines the energy cost of the electron transfer. The largest electronic reorganization occurs in the pyrimidinic N atoms and the bridge O of the first coordination shell, being weaker in the metal centres. The adaptation of the molecular orbitals to the electron transfer is sufficient to inverse the spectroscopy and generate a metastable electron transfer state.

  2. Software News and Updates

    1. QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input

      Louis Vanduyfhuys, Steven Vandenbrande, Toon Verstraelen, Rochus Schmid, Michel Waroquier and Veronique Van Speybroeck

      Article first published online: 5 MAR 2015 | DOI: 10.1002/jcc.23877

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      QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent terms are derived from ab initio data. As a result, accurate force fields are generated with minimal effort.

  3. Full Papers

    1. State-specific multireference perturbation theory with improved virtual orbitals: Taming the ground state of F2, Be2, and N2

      Sudip Chattopadhyay, Rajat K Chaudhuri and Uttam Sinha Mahapatra

      Article first published online: 5 MAR 2015 | DOI: 10.1002/jcc.23873

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      Improved virtual orbital-complete active space configuration interaction-based state-specific multireference perturbation theory in the frame of Rayleigh–Schrödinger perturbative expansion has been used to investigate the spectroscopic constants and vibrational spectrum of F2, Be2, and N2 through the computation of dissociation energy surfaces.

    2. Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

      Maria T. Panteva, George M. Giambaşu and Darrin M. York

      Article first published online: 4 MAR 2015 | DOI: 10.1002/jcc.23881

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      Mg2+ ions are essential for nucleic acid structure and function and this has motivated the development of several Mg2+ models for use in molecular simulations. As a first step in developing improved Mg2+ models for biomolecular simulations, we focus on the ability to which 17 different pairwise potential Mg2+ models, which belong to the most mature force fields for modeling nucleic acid dynamics, can simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. These represent a balanced set of solution properties that serve as a useful departure point from which robust models for molecular dynamics simulations of biological processes can be developed by tuning pairwise interaction parameters.

    3. Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05-2X computational study

      Liudmyla K. Sviatenko, Olexandr Isayev, Leonid Gorb, Frances C. Hill, Danuta Leszczynska and Jerzy Leszczynski

      Article first published online: 3 MAR 2015 | DOI: 10.1002/jcc.23878

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      Reduction and oxidation properties of trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) were studied in gas phase, in water, and adsorbed on a silica surface state. It was found that adsorption and solvation promote redox transformation of nitrocompounds. Nitrocompounds dissolved in water are easier to transform than adsorbed ones. Reactivity in an electron attachment and electron detachment processes increases in the rows: DNT < DNAN ≈ NTO < TNT and TNT < DNT < DNAN < NTO, respectively.

    4. Symmetry classification of electron and phonon states in TiO2-based nanowires and nanotubes

      Robert A. Evarestov and Andrej I. Panin

      Article first published online: 3 MAR 2015 | DOI: 10.1002/jcc.23875

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      General approach to the phonon symmetry analysis for nanowires and nanotubes is outlined. It is illustrated on the example of TiO2 rutile-based nanorods and TiO2 anatase-based nanotubes with the hexagonal and rectangular morphology, respectively. The number and symmetry of Infrared active, Raman active, and silent modes is found, which is important for the vibrational spectra interpretations of the systems in consideration. There are four acoustic modes with zero frequencies for k = 0: three longitudinal acoustic and one twisting.

    5. Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine

      Wiktor Zierkiewicz, Dariusz C. Bieńko, Danuta Michalska and Thérèse Zeegers-Huyskens

      Article first published online: 27 FEB 2015 | DOI: 10.1002/jcc.23860

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      The halogen-bonded complexes between six carbonyl bases and molecular chlorine are investigated theoretically. The study includes the optimized geometries and the interaction energies along with an extended natural bond orbital analysis. The interaction energies calculated at the CCSD(T)/aug-cc-pVTZ level range between −1.61 and −3.50 kcal mol−1. These energies are related to the ionization potential and the proton affinity of the carbonyl bases.

    6. Fep1d: A script for the analysis of reaction coordinates

      Polina V. Banushkina and Sergei V. Krivov

      Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23868

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      Multidimensional dynamical processes can be analyzed by projecting them onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script which can be used to answer questions appearing during such an analysis. In particular, the determination of the associated free energy profile and the diffusion coefficient and establishing whether the used coordinate is optimal.

    7. Toward the complete range separation of non-hybrid exchange–correlation functional

      Bun Chan, Jong-Won Song, Yukio Kawashima and Kimihiko Hirao

      Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23867

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      Range separation for the exchanged functional has contributed significantly to the advancement of DFT. A simple “Range-separated eXchange–Correlation” (RXC) scheme is used to divide a total exchange–correlation functional. For properties that are short-range in nature, the performance of the RXC-DFT protocol resembles that of the short-range component, and vice versa. The general RXC scheme can be easily implemented in computational chemistry software packages.

    8. An ab initio study of nuclear volume effects for isotope fractionations using two-component relativistic methods

      Keisuke Nemoto, Minori Abe, Junji Seino and Masahiko Hada

      Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23858

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      Nuclear volume term is a main term in the chemical equilibrium constants of isotope fractionations with heavy-element isotopes. The nuclear volume term can be calculated by the four-component Dirac-Hartree-Fock method. In this work, various types of two-component quasi-relativistic methods are performed in an attempt to find alternatives to the time-consuming four-component method. One of the infinite-order Douglass-Kroll-Hess methods is found to be accurate, but 30 times faster than the four-component method.

    9. How does a hydrocarbon staple affect peptide hydrophobicity?

      Adelene Y. L. Sim and Chandra Verma

      Article first published online: 23 FEB 2015 | DOI: 10.1002/jcc.23859

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      Protein–peptide interfaces have nonuniform chemical properties and geometry, posing challenges to understanding the driving forces of hydrophobicity, particularly at atomic-level detail. The dynamics of water between an E3 ubiquitin ligase (MDM2) and peptides derived from the tumor suppressor protein p53 (including a hydrocarbon “stapled” one) are studied using molecular dynamics. The interdomain densities show two-state behavior, and the relative fraction of wet and dry states is used to compare the extent of hydrophobicity.

    10. Electronic structure and microscopic charge-transport properties of a new-type diketopyrrolopyrrole-based material

      Jin-Dou Huang, Wen-Liang Li, Shu-Hao Wen and Bin Dong

      Article first published online: 23 FEB 2015 | DOI: 10.1002/jcc.23825

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      The electronic structures and microscopic charge-transport properties of a diketopyrrolopyrrole-based material (compound 1) were investigated using density functional theory and charge-transport models. It is the first time that the transport parameters of compound 1 were calculated in the context of band model and hopping models. Our investigations here, provide guidance for the understanding of the structure–function relationship and intermolecular charge-transport behaviors, and are instructive to further explore the potential of other higher diketopyrrolopyrrole-containing molecules.

    11. A coarse-grained MARTINI-like force field for DNA unzipping in nanopores

      Anna Stachiewicz and Andrzej Molski

      Article first published online: 23 FEB 2015 | DOI: 10.1002/jcc.23874

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      In nanopore force spectroscopy (NFS), a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. A new model is presented that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all-atom simulations. The model was applied to simulations of DNA hairpin unzipping in nanopores.

    12. Bonding and singlet–triplet gap of silicon trimer: Effects of protonation and attachment of alkali metal cations

      Nguyen Minh Tam, Tran Dieu Hang, Hung Tan Pham, Huyen Thi Nguyen, My Phuong Pham-Ho, Pablo A. Denis and Minh Tho Nguyen

      Article first published online: 19 FEB 2015 | DOI: 10.1002/jcc.23856

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      Both 1A1 and 3 inline image states of Si3 are degenerate. The H+, Li+, and Na+ cations favor the singlet state, whereas K+ favors the triplet. Some thermochemical parameters are predicted: PA(Si3) = 830 ± 4, LiCA(Si3) = 108 ± 8, NaCA(Si3) = 79 ± 8, and KCA(Si3) = 44 ± 8 kJ/mol. The ring current shows that the singlet three-membered Si3 ring is, at most, nonaromatic. Attachment of H+ and Li+ renders it anti-aromatic.

    13. Stability of ion triplets in ionic liquid/lithium salt solutions: Insights from implicit and explicit solvent models and molecular dynamics simulations

      Andrzej Eilmes and Piotr Kubisiak

      Article first published online: 18 FEB 2015 | DOI: 10.1002/jcc.23853

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      Ion triplets [LiAn1An2] in five ionic liquids were investigated through Molecular Dynamics simulations and quantum-chemical calculations in continuous or explicit solvent. The relative binding energies of triplets obtained from the two solvent models were in general agreement.

    14. One-electron images in real space: Natural adaptive orbitals

      Marcos Menéndez, Roberto Álvarez Boto, Evelio Francisco and Ángel Martín Pendás

      Article first published online: 18 FEB 2015 | DOI: 10.1002/jcc.23861

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      A hierarchical set of one-electron functions called natural adaptive orbitals is introduced. n-center NAdOs decompose real space n-center bonding indices into one-electron contributions. NAdOs maintain their meaning both for correlated and noncorrelated descriptions.

    15. Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin

      Ryuhei Harada, Yu Takano and Yasuteru Shigeta

      Article first published online: 18 FEB 2015 | DOI: 10.1002/jcc.23854

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      An enhanced conformational search method referred as TaBoo SeArch (TBSA) algorithm is proposed. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited. As a demonstration, TBSA was applied to the folding of chignolin and automatically sampled the native structure with nanosecond order computational costs, although a long-time 1-µs normal MD simulation failed to sample the native structure.

    16. Solvatochromic shifts of Br2 and I2 in water cages of type 512, 51262, 51263, and 51264

      Nils Middendorf, Katharina Krause and Sebastian Höfener

      Article first published online: 18 FEB 2015 | DOI: 10.1002/jcc.23863

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      Solvatochromic shifts are estimated for molecular bromine and iodine trapped in selected clathrate hydrate cages using frozen-density embedding, allowing for the combination of scalar-relativistic and nonrelativistic methods for heavy halogens and light water molecules, respectively.

    17. The multieffects of DMF and DBU on the [5 + 1] benzannulation of nitroethane and α-alkenoyl ketene-(S,S)-acetals: Hydrogen bonding and electrostatic interactions

      Haiyan Yuan, Yiying Zheng, Bo Li, Wenliang Li and Jingping Zhang

      Article first published online: 16 FEB 2015 | DOI: 10.1002/jcc.23846

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      The multieffects of DMF and DBU on the [5 + 1] Benzannulation of Nitroethane and α-alkenoyl ketene-(S,S)-acetals are investigated by the DFT calculations under unassisted, DBU assisted, and DBU with DMF cocatalyzed conditions. The calculated results suggest that DMF and DBU act as not only solvent and non-nucleophilic base, respectively but also catalysts in the reaction by stabilizing the transition states and intermediates via intermolecular hydrogen bonds and electrostatic interactions.

    18. Deformation of single-walled carbon nanotubes by interaction with graphene: A first-principles study

      Xiao Wang, Juan Yang, Ruoming Li, Hong Jiang and Yan Li

      Article first published online: 16 FEB 2015 | DOI: 10.1002/jcc.23844

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      First-principles calculations were performed to investigate the interaction between single-walled carbon nanotubes (SWNTs) and graphene. Zigzag SWNTs show stronger interactions with SLG than armchair SWNTs of similar diameters, whereas armchair SWNTs display stronger interactions with DLG than zigzag SWNTs, which can be interpreted by the mechanical properties of SWNTs and graphene.

    19. Hydrogen–hydrogen bonding: The current density perspective

      Paolo Della Porta, Riccardo Zanasi and Guglielmo Monaco

      Article first published online: 16 FEB 2015 | DOI: 10.1002/jcc.23841

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      Hydrogen atoms involved in H[BOND]H bonding are embraced by a small delocalized diatropic current, which can be used to assess the stabilizing character of their interaction.

    20. Origin-independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method

      Petr Štěpánek and Petr Bouř

      Article first published online: 7 FEB 2015 | DOI: 10.1002/jcc.23845

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      The sum over state method using states from the time-dependent density functional theory is convenient for fast simulations of molecular magnetic circular dichroism spectra. In the original formulation, the molecule was kept at the coordinate origin to obtain reproducible results. In this work, an alternative way is explored, providing fully origin-independent natural electronic and magnetic circular dichroic intensities.

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