Journal of Computational Chemistry

Cover image for Vol. 36 Issue 2

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 - 29
  1. Full Papers

    1. Persistent homology for the quantitative prediction of fullerene stability

      Kelin Xia, Xin Feng, Yiying Tong and Guo Wei Wei

      Article first published online: 19 DEC 2014 | DOI: 10.1002/jcc.23816

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      Geometric models often involve too much structural detail to be computationally efficient while topological models typically bear too little structural information to be quantitatively accurate. Persistent homology, a new branch of topology, bridges the gap between geometry and topology and offers a new strategy for handling big data. This work introduces persistent homology for qualitative analysis of fullerene topological fingerprints and quantitative prediction of fullerene stability.

    2. An incremental isoconversional method for kinetic analysis based on the orthogonal distance regression

      Tibor Dubaj, Zuzana Cibulková and Peter Šimon

      Article first published online: 18 DEC 2014 | DOI: 10.1002/jcc.23813

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      The parameters obtained from a kinetic analysis of thermoanalytical data often exhibit a conversion-dependent behavior. Modern isoconversional methods designed to deal with this problem are increasingly precise when applied to simulated data. Conversely, they do not take the errors of the measured data into account. The proposed incremental isoconversional method follows the error structure of the thermoanalytical measurements and the data are processed using the orthogonal distance regression without transformations.

    3. Search for the global minimum structures of AlB3H2n (n = 0 − 6) clusters

      İskender Muz, Osman Canko, Murat Atiş and Erdem Kamil Yıldırım

      Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23812

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      The global minimum structures of AlB3H2n (n = 0–6) clusters are investigated and the chemical bonding patterns of the most stable isomers are analyzed by the adaptive natural density partitioning method.

    4. New insights into the meaning and usefulness of principal component analysis of concatenated trajectories

      Gustavo Pierdominici-Sottile and Juliana Palma

      Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23811

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      Combined principal component analysis (combined-PCA) is a technique usually employed to analyze structural and dynamical differences between alternative conformations of a given protein. However, analytical formulas showing what is to be expected and what is not to be expected from a combined-PCA have never been provided. Here, we present and discuss such formulas. We believe that they will be useful to enlighten the discussions of the results of combined-PCA.

  2. Software News and Updates

    1. STOCK: Structure mapper and online coarse-graining kit for molecular simulations

      Staš Bevc, Christoph Junghans and Matej Praprotnik

      Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23806

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      STOCK is a web-based toolkit for setting up coarse-grained molecular simulations. One can define a molecular mapping from high to low resolution with the aid of a molecular visualizer. Additionally, one may generate effective potentials for coarse-grained simulations preserving structural properties of the underlying higher resolution model. The tool is available at http://stock.cmm.ki.si

  3. Full Papers

    1. k-Nearest neighbors optimization-based outlier removal

      Abraham Yosipof and Hanoch Senderowitz

      Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23803

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      A new iterative method for the identification and removal of outliers from quantitative structure activity relationship (QSAR) datasets is described. This method is based on a kNN optimization algorithm, and named kNN optimization-based outlier removal. The method is able to maintain the internal diversity of the parent dataset and at the same time produce QSAR models with better prediction statistics than other outlier removal methods.

  4. Software News and Updates

    1. BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials

      Pablo M. De Biase, Suren Markosyan and Sergei Noskov

      Article first published online: 15 DEC 2014 | DOI: 10.1002/jcc.23799

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      The transport of DNA and ions by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. BROMOC Suite is a software package designed to perform Brownian dynamics simulations up to several milliseconds long of large biological systems (BROMOC), to develop effective potentials for solute-ion interactions based on RDF from all-atom Molecular Dynamics (IMC-MACRO), and to do a wide variety of pre-processing and post-simulation analysis (BROMOC Tools).

  5. Erratum

    1. You have free access to this content
      Corrigendum: Geometrical and optical benchmarking of copper(II) guanidine–quinoline complexes: Insights from TD-DFT and many-body perturbation theory (Part II)

      Alexander Hoffmann, Martin Rohrmüller, Anton Jesser, Ines dos Santos Vieira, Wolf Gero Schmidt and Sonja Herres-Pawlis

      Article first published online: 12 DEC 2014 | DOI: 10.1002/jcc.23793

  6. Full Papers

    1. Local response dispersion method in periodic systems: Implementation and assessment

      Yasuhiro Ikabata, Yusuke Tsukamoto, Yutaka Imamura and Hiromi Nakai

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23807

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      The local response dispersion (LRD) method, which has been developed as a dispersion correction method for isolated molecules, is implemented in the package based on periodic boundary condition and plane-wave basis set. After atomic polarizabilities are calculated using the real-space grid, the dispersion energy is obtained as the sum of atomic pair contributions. The availability of LRD with PBE and revPBE functionals is assessed for simple substances, molecular crystals, and physical adsorption.

  7. Software News and Updates

    1. Automatic algorithms for completeness-optimization of Gaussian basis sets

      Susi Lehtola

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23802

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      The completeness-optimization procedure is based on a sequence of consecutive additions of functions into the basis set, illustrated here for augmentation with tight and diffuse functions, until the studied property attains convergence to the complete basis set limit. Once the limit has been achieved, the procedure is run in reverse to form computationally efficient basis sets for production-level calculations.

    2. pmx: Automated protein structure and topology generation for alchemical perturbations

      Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23804

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      Molecular dynamics-based alchemical free energy calculations present a powerful method to evaluate protein thermostability and changes in the interaction affinities upon an amino acid mutation. The approach requires a description of the mutatable amino acids as a two state system connected via an alchemical pathway. In the current work, we present a framework and its implementation to generate hybrid amino acid structures and topologies for a number of commonly used biomolecular force fields.

  8. Full Papers

    1. Force field development for organic molecules: Modifying dihedral and 1–n pair interaction parameters

      Siyan Chen, Shasha Yi, Wenmei Gao, Chuncheng Zuo and Zhonghan Hu

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23808

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      The energy correlation map between calculations from molecular mechanics force fields and quantum mechanical calculations illustrating the quality of the developed force field to describe the transition energies for condensed matter systems of ethane (right) and 3-hydroxypropionic acid (left). Especially for the 3-hydroxypropionic acid molecule, the parameters for the dihedral angle and 1−n interaction potentials in the new force field (MM) significantly help to improve the results in comparison to QM studies.

    2. Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer

      Víctor Duarte Alaniz, Tomás Rocha-Rinza and Gabriel Cuevas

      Article first published online: 2 DEC 2014 | DOI: 10.1002/jcc.23798

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      Eleven relative orientations of (CH4)2 were investigated through the topology of inline image and Symmetry Adapted Perturbation Theory (SAPT). The relations found between the components of SAPT and the properties of inline image are exploited to construct Mollier-like diagrams to evaluate the importance of hydrophobic interactions (HIs) in representative examples. These diagrams might prove useful in analyzing HIs, especially when ab-initio or SAPT calculations are unfeasible or prohibitively expensive.

    3. New algorithms for iterative matrix-free eigensolvers in quantum chemistry

      Dmitry Zuev, Eugene Vecharynski, Chao Yang, Natalie Orms and Anna I. Krylov

      Article first published online: 2 DEC 2014 | DOI: 10.1002/jcc.23800

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      Finding a few eigenpairs of large matrices is a common task in science and engineering. In the present work, new algorithms are introduced for iterative diagonalization that solve for a small set of eigenstates of a large matrix. A modified version of Davidson's algorithm enabling a user to solve for interior eigenpairs at low computational cost is presented. A new solver is also introduced, and its performance is compared against the canonical Davidson procedure.

  9. Software News and Updates

    1. The Iterative Protein Redesign and Optimization (IPRO) suite of programs

      Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford and Costas D. Maranas

      Article first published online: 2 DEC 2014 | DOI: 10.1002/jcc.23796

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      The Iterative Protein Redesign and Optimization suite of programs integrates various methods for protein engineering. All of these methods incorporate the same fundamental idea that improving the affinity for a small molecule can be achieved by repeatedly perturbing the protein's backbone, finding the optimal set of amino acids based on this new backbone conformation, making minor adjustments to the protein's structure and small molecule's orientation, and deciding to keep the results or not.

  10. Full Papers

    1. Features of CPB: A Poisson–Boltzmann solver that uses an adaptive cartesian grid

      Marcia O. Fenley, Robert C. Harris, Travis Mackoy and Alexander H. Boschitsch

      Article first published online: 27 NOV 2014 | DOI: 10.1002/jcc.23791

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      Electrostatic potential maps and polar solvation (ΔGel) and binding (ΔΔGel) energies computed with the Poisson–Boltzmann equation (PBE) are widely used in biophysical applications. By using an adaptive Cartesian grid and least-squares reconstruction schemes, the PBE solver CPB can produce high resolution surface electrostatic potential maps and predict ΔGel and ΔΔGel for large biomolecular assemblies, such as ribosomes and viruses, with lower computational demands than other PBE solvers.

    2. Pentaatomic planar tetracoordinate silicon with 14 valence electrons: A large-scale global search of SiXnYmq (n + m = 4; q = 0, ±1, −2; X, Y = main group elements from H to Br)

      Jing Xu and Yi-hong Ding

      Article first published online: 27 NOV 2014 | DOI: 10.1002/jcc.23792

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      The 14 electrons of planar tetracoordinate silicon were systematically searched for the first time, finding nine global minimum ptSi, that is, Li3SiAs2−, HSiY3 (Y = Al/Ga), Ca3SiAl, Mg4Si2−, C2LiSi, Si3Y2 (Y = Li/Na/K). The former six systems represent the first prediction. In light of the very limited global ptSi examples, the presently designed six systems with 14e are expected to enrich the exotic ptSi chemistry and welcome future laboratory confirmation.

    3. Improving the Q2MM method for transition state force field modeling

      Elaine Limé and Per-Ola Norrby

      Article first published online: 27 NOV 2014 | DOI: 10.1002/jcc.23797

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      The Quantum-to-molecular mechanics method for parameterization of force fields has been augmented by a projection along normal modes, allowing a close fit to natural force constants while retaining a positive curvature at the TS.

    4. Symmetry calculation for molecules and transition states

      Nick M. Vandewiele, Ruben Van de Vijver, Kevin M. Van Geem, Marie-Françoise Reyniers and Guy B. Marin

      Article first published online: 24 NOV 2014 | DOI: 10.1002/jcc.23788

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      The fast and accurate automated calculation of the rotational symmetry number of molecule opens up an array of applications in computational chemistry. This work discusses a novel algorithm for the determination of symmetry numbers based on an augmented graph representation of the chemical structure. The general applicability for a diverse range of molecules and transition states is illustrated. The application of the algorithm on a database of 50,000 molecules is presented as a test case.

    5. Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers

      Jing Huang, Likai Du, Deping Hu and Zhenggang Lan

      Article first published online: 21 NOV 2014 | DOI: 10.1002/jcc.23778

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      The systematical calculations with different levels of electronic-structure methods are conducted to understand the optoelectronic properties of conjugated dendrimers. The electronic characters of excited states, namely the contributions of intraunit local excitations and interunit charge-transfer excitations within all interacting conjugated branches, are analyzed by the one-electron transition density matrix. This work provides theoretical insights of photoinduced energy transfer in solar energy conversions for novel tree-like photovoltaic materials.

    6. An automated method to find transition states using chemical dynamics simulations

      Emilio Martínez-Núñez

      Article first published online: 21 NOV 2014 | DOI: 10.1002/jcc.23790

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      An automated method to optimize the transition states of a molecular system is proposed. Based on running high-energy chemical dynamics simulations, it sampled different areas of the potential energy surface. Then, an algorithm was used to select suitable candidate structures to be optimized as transition states. As dynamics simulations were involved in the procedure, additional information about the system was obtained, as the possibility of deviations from statistical behavior.

  11. Software News And Updates

    1. Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool

      Daniele Licari, Alberto Baiardi, Malgorzata Biczysko, Franco Egidi, Camille Latouche and Vincenzo Barone

      Article first published online: 18 NOV 2014 | DOI: 10.1002/jcc.23785

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      This article presents the setup and implementation of a new graphical user interface (VMS-Draw) for a multifrequency spectrometer. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line-shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools.

  12. Full Papers

    1. Semiempirical and DFT computations of the influence of Tb(III) dopant on unit cell dimensions of cerium(III) fluoride

      Andrii Shyichuk, Marcin Runowski, Stefan Lis, Jakub Kaczkowski and Andrzej Jezierski

      Article first published online: 18 NOV 2014 | DOI: 10.1002/jcc.23789

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      The AM1, RM1, PM3, PM6, and PM7 semiempirical computational methods with Sparkle model for Ln(III) and GGA/PBE ab initio DFT method were used to model the influence of the amount of dopant on crystal cell dimensions of CeF3 doped with Tb3+ ions, a known luminescent material. The cell dimensions of the material calculated using Sparkle/PM3 and the DFT methods were in the best agreement (about 1% error) with our experimental data on CeF3:Tb3+ obtained via co-precipitation or hydrothermal methods.

    2. Could the “Janus-like” properties of the halobenzene CX bond (X[DOUBLE BOND]Cl, Br) be leveraged to enhance molecular recognition?

      Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard G. Maroun and Nohad Gresh

      Article first published online: 18 NOV 2014 | DOI: 10.1002/jcc.23786

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      The CX bond in halobenzenes (X[DOUBLE BOND]Cl, Br) exhibits a dual character, electron-deficient along the CX direction, and electron-rich on its flanks. Both features were amplified upon resorting to electron-withdrawing and -donating substituents respectively. This was done by quantum chemistry computations in the recognition sites of three protein targets. A simple yet rigorous computational strategy is suggested to prescreen novel substituted halobenzenes in the context of drug design.

    3. Nature of the water/aromatic parallel alignment interactions

      Mariusz P. Mitoraj, Goran V. Janjić, Vesna B. Medaković, Dušan Ž. Veljković, Artur Michalak, Snežana D. Zarić and Miloš K. Milčić

      Article first published online: 13 NOV 2014 | DOI: 10.1002/jcc.23783

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      The nature of interactions in parallel water/benzene complexes is investigated using ab initio calculations and energy decomposition methods. The calculated energies of the interactions are significant at large horizontal displacement. These interactions are stronger than CH…O water/benzene interactions, but weaker than OH…π interactions. Both energy decomposition methods, SAPT and ETS-NOCV, agree that electrostatic is the most important force, responsible for bonding in water/benzene parallel complexes at large horizontal displacement.

    4. Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units

      Takeshi Yoshikawa and Hiromi Nakai

      Article first published online: 13 NOV 2014 | DOI: 10.1002/jcc.23782

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      The graphical processing units (GPU) implementations were performed for accelerating the Hartree–Fock (HF) calculations by combining the linear-scaling divide-and-conquer (DC) method with the effective resolution-of-the-identity (RI) technique. The speedups of DC-RI-HF on GPU compared with standard HF increased with increasing molecular size because of the sparse density matrix and local diagonalization by the DC method.

    5. Communication through molecular bridges: Different bridge orbital trends result in common property trends

      Jonny Proppe and Carmen Herrmann

      Article first published online: 7 NOV 2014 | DOI: 10.1002/jcc.23781

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      Communication through molecular bridges plays a crucial role in electron transfer, charge or spin delocalization in mixed-valence compounds, electron transport, and electron spin coupling through superexchange. For the latter two, common property trends are found to not result from common bridge molecular orbital energy trends, so transferring knowledge from electron transport to spin coupling based on bridge orbitals is not straightforward.

    6. Isolated pentagon rule violating endohedral metallofullerenes explained using the Hückel rule: A statistical mechanical study of the C84 Isomeric Set

      Timothy J. Fuhrer and Angel M. Lambert

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23774

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      A systematic, temperature dependent, statistical thermodynamic study is presented of the 24 possible isolated pentagon rule fullerene isomers of C84 as well as two of the experimentally known non-IPR isomers (51365 and 51383), at several different charges (0, −2, −4, and −6). Based on the results, the Hückel rule is a valid explanation for the stability of fused pentagons in endohedral metallofullerenes.

    7. Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory

      Yanliang Ren, Osama Melhem, Yongjian Li, Bo Chi, Xinya Han, Hao Zhu, Lingling Feng, Jian Wan and Xin Xu

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23770

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      The electronic energy transfer is a fundamental key in the development of synthetic light-harvesting devices. Insight into the EET pathways in APC trimer and hexamer was gained by the first principle calculations within the framework of Förster theory.

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