Journal of Computational Chemistry

Cover image for Vol. 36 Issue 11

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. Full Papers

    1. Toward assessment of density functionals for vibronic coupling in two-photon absorption: A case study of 4-nitroaniline

      Robert Zaleśny, Guangjun Tian, Christof Hättig, Wojciech Bartkowiak and Hans Ågren

      Article first published online: 31 MAR 2015 | DOI: 10.1002/jcc.23903

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      CC2 method and several exchange-correlation functionals are used to predict vibronic two-photon absorption spectra of 4-nitroaniline.

    2. Robustness in the fitting of molecular mechanics parameters

      Kenno Vanommeslaeghe, Mingjun Yang and Alexander D. MacKerell Jr.

      Article first published online: 31 MAR 2015 | DOI: 10.1002/jcc.23897

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      Automated methods for the parametrization of empirical force fields have attracted renewed interest of the community. However, the robustness issues associated with the often ill-conditioned nature of parameter optimization have been vastly underappreciated. This article discusses these issues and proposes a novel restraining scheme that mitigates ill-conditioned behavior in concerted Linear Least Squares fitting of bonded parameters in a continuous fashion and without affecting the quality of the results.

    3. You have full text access to this OnlineOpen article
      New ways to boost molecular dynamics simulations

      Elmar Krieger and Gert Vriend

      Article first published online: 30 MAR 2015 | DOI: 10.1002/jcc.23899

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      Molecular simulations with empirical force fields were originally a task for experts with huge computer clusters, but have nowadays become easily accessible for all interested scientists on their personal computers. The long simulation time scales needed to draw useful conclusions can be reached with faster hardware or faster software. This article concentrates on the latter and describes algorithms to speed up simulations, implemented in the molecular modeling program YASARA.

    4. From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg–Coxeter fullerenes up to C980

      Lukas N. Wirz, Ralf Tonner, Andreas Hermann, Rebecca Sure and Peter Schwerdtfeger

      Article first published online: 26 MAR 2015 | DOI: 10.1002/jcc.23894

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      A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C20.

    5. Theoretical comparative studies on transport properties of pentacene, pentathienoacene, and 6,13-dichloropentacene

      Xu Zhang, Xiaodi Yang, Hua Geng, Guangjun Nan, Xingwen Sun, Jinyang Xi and Xin Xu

      Article first published online: 24 MAR 2015 | DOI: 10.1002/jcc.23870

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      The hole and electron transport properties are theoretically studied for pentacene, pentathienoacene and 6,13-dichloropentacene. A detailed comparative calculation is carried out to gain insights in the theoretical design of organic transport materials.

    6. Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study

      Claudia Loerbroks, Andreas Heimermann and Walter Thiel

      Article first published online: 21 MAR 2015 | DOI: 10.1002/jcc.23898

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      Acid hydrolysis of cellulose yields glucose. This process is investigated computationally in water using two cellulose models (cellobiose and a 40-unit glucose chain) and explicit solvation. Hydrogen bonding is found to have a large impact on the reaction mechanism and on the barriers to hydrolysis. The results are compared to those from to a previous study with implicit solvation.

    7. Protein alignment: Exact versus approximate. An illustration

      Milan Randić and Tomaž Pisanski

      Article first published online: 19 MAR 2015 | DOI: 10.1002/jcc.23892

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      From the list of sequential labels for each adjacent pair of amino acid of two proteins one finds for all pairs of amino acids locations at which they have the same difference in labels. By ordering pairs having the same difference one finds segments at which two proteins have the same amino acids fragments. This information allows construction of the exact alignment of two proteins.

    8. An anisotropic coarse-grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

      Hujun Shen, Yan Li, Peijun Xu, Xiaofang Li, Huiying Chu, Dinglin Zhang and Guohui Li

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23895

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      The promising performance of an anisotropic coarse-grained model (so-called GBEMP) has been demonstrated in modeling a DMPC lipid bilayer. A 72-DMPC bilayer system was used for testing the performance of the GBEMP model, and it has shown a few important structural properties. In addition, the atomistic and experimental results for electron density profiles and order parameters can be reproduced reasonably well by this GBEMP model.

    9. Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material

      Jose L. Mendoza-Cortes, Qi An, William A. Goddard III, Caichao Ye and Sergey Zybin

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23893

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      The two most stable isomers of Di-tetrazine-tetroxide (DTTO), c1 and c2, were used to predict the most stable polymorphs of DTTO. For the c1 isomer, the most stable polymorph has P212121 space group with a density of 1.96 g/cm3. Conversely, for the c2 isomer, the most stable polymorph has Pbca space group with a density of 1.98 g/cm3. These predicted densities are among the highest of current energetic materials.

    10. Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation

      Antonio Cardone, Aaron Bornstein, Harish C. Pant, Mary Brady, Ram Sriram and Sergio A. Hassan

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23883

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      A method is developed to study protein complexation in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific sparsely populated binding modes. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks in concentrated multispecies, multiprotein systems.

    11. Gradient gravitational search: An efficient metaheuristic algorithm for global optimization

      Tirtharaj Dash and Prabhat K. Sahu

      Article first published online: 17 MAR 2015 | DOI: 10.1002/jcc.23891

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      The adaptation of novel techniques developed in the field of computational chemistry to solve the concerned problems for large and flexible molecules is taking center stage with regard to efficient algorithms, computational cost, and accuracy. The gradient-based gravitational search (GGS) algorithm, using analytical gradients for a fast minimization to the next local minimum, has been reported. The GGS approach has been applied to computational chemistry problems for finding the minimal value potential energy of two-dimensional and three-dimensional off-lattice protein models.

    12. Bonding charge density from atomic perturbations

      Yi Wang, William Yi Wang, Long-Qing Chen and Zi-Kui Liu

      Article first published online: 16 MAR 2015 | DOI: 10.1002/jcc.23880

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      Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. A first-principles approach to calculating the charge transfer is presented. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, the amount of electron charge associated with a particular atom or a group of atoms is determined. The topological electron loss versus gain is demonstrated using ethylene, graphene, MgO, and SrTiO3 as examples.

    13. A cascaded QSAR model for efficient prediction of overall power conversion efficiency of all-organic dye-sensitized solar cells

      Hongzhi Li, Ziyan Zhong, Lin Li, Rui Gao, Jingxia Cui, Ting Gao, Li Hong Hu, Yinghua Lu, Zhong-Min Su and Hui Li

      Article first published online: 14 MAR 2015 | DOI: 10.1002/jcc.23886

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      A cascaded support vector machine CasSVM model is built to establish the relationship between structures of all-organic dye molecules and the overall power conversion efficiency (PCE) of dye sensitized solar cells (DSSCs). The prediction mean absolute error (MAE) is about 10% of the mean value of experimental PCE. The validation parameters show the unique model could efficiently predict the PCE values of DSSCs with little cost, which may be practically useful for developing novel organic dyes.

    14. LS-VISM: A software package for analysis of biomolecular solvation

      Shenggao Zhou, Li-Tien Cheng, Hui Sun, Jianwei Che, Joachim Dzubiella, Bo Li and J. Andrew McCammon

      Article first published online: 12 MAR 2015 | DOI: 10.1002/jcc.23890

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      Recent development of a dielectric boundary-based, variational implicit-solvent approach and its robust level-set method implementation have enabled efficient and accurate predictions of the solvation free energies and stable conformations of biomolecules in aqueous solution. This article reviews the new implicit solvation theory and numerical methods, and introduces and details the resulting level-set variational implicit-solvent model, a software package for analysis of biomolecular interactions.

    15. Why many semiempirical molecular orbital theories fail for liquid water and how to fix them

      Matthew Welborn, Jiahao Chen, L.-P. Wang and Troy Van Voorhis

      Article first published online: 12 MAR 2015 | DOI: 10.1002/jcc.23887

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      Semiempirical methods offer a cheap, yet physically accurate description of electronic effects in liquid water. However, the popular neglect of diatomic differential overlap (NDDO) method PM6 incorrectly describes water's basic structure. This work examines why PM6 fails for water, and uses force matching to create an improved NDDO model of water.

    16. The topology of the Ehrenfest force density revisited. A different perspective based on Slater-type orbitals

      Jan Dillen

      Article first published online: 9 MAR 2015 | DOI: 10.1002/jcc.23869

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      The topology of the Ehrenfest force density is studied with Slater-type orbitals and is found to be mainly homeomorphic with the topology of the electron density. Atomic interaction lines are observed to exist in support of the hydrogen–hydrogen bond and are also found in some inclusion complexes of alkanes with helium. However, interaction lines are lacking in several other controversial cases.

    17. The performance of low-cost commercial cloud computing as an alternative in computational chemistry

      Russell Thackston and Ryan C. Fortenberry

      Article first published online: 9 MAR 2015 | DOI: 10.1002/jcc.23882

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      Cloud computing is currently a viable alternative to the purchase of in-house hardware for quantum chemistry. As cloud technology improves and the costs of such stabilize or decrease, it is expected that its usage in this field will continue to climb while traditional means may decrease relative to current levels of cloud usage.

  2. Software News and Updates

    1. Introduction of periodic boundary conditions into UNRES force field

      Adam K. Sieradzan

      Article first published online: 8 MAR 2015 | DOI: 10.1002/jcc.23864

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      The implementation of translational periodic conditions allowed for the simulation of multichain system in a UNRES force field with greater reality in association pattern and a removal of the colliding course trajectories.

  3. Full Papers

    1. The behavior of benzene confined in single wall carbon nanotube

      Yury D. Fomin, Elena N. Tsiok and Valentin N. Ryzhov

      Article first published online: 5 MAR 2015 | DOI: 10.1002/jcc.23872

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      The behavior of benzene confined in single wall carbon nanotube is studied by means of molecular dynamics simulation. Structural and dynamical properties are considered. The density and the temperature effects on the structure and diffusion of benzene are considered.

  4. 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.

  5. 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. 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.

    6. 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.

    7. 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.

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