Journal of Computational Chemistry

Cover image for Vol. 36 Issue 1

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 - 18
  1. Full Papers

    1. 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.

    2. 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.

    3. 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.

    4. Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

      Robin M. Betz and Ross C. Walker

      Article first published online: 21 NOV 2014 | DOI: 10.1002/jcc.23775

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      Classical molecular dynamics parameters are obtained by fitting so that the energy of a set of structures calculated with the parameters matches a set of input energies calculated at a quantum level of theory. Our program, Paramfit, automates this fitting process using a novel hybrid of genetic and simplex algorithms to fit multiple parameters simultaneously to any set of input molecule conformations that can include different molecules, enabling rapid, accurate force field development.

  2. 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.

  3. 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.

  4. Erratum

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  5. Software News and Updates

    1. Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library

      Ilya A. Kaliman and Lyudmila V. Slipchenko

      Article first published online: 13 NOV 2014 | DOI: 10.1002/jcc.23772

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      A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing that uses a master/slave model. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time- and length-scales.

  6. Full Papers

    1. 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.

    2. 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.

    3. How does hybrid bridging core modification robust the nonlinear optical properties in donor-π-acceptor configuration? A case study of dinitrophenol derivatives

      Shabbir Muhammad, Ahmad Irfan, Mohd Shkir, Aijaz R. Chaudhry, Abul Kalam, Salem AlFaify, Abdullah G. Al-Sehemi, A. E. Al-Salami, I. S. Yahia, Hong-Liang Xu and Zhong-Min Su

      Article first published online: 10 NOV 2014 | DOI: 10.1002/jcc.23777

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      A fundamental quantum chemical structure–property relationship spotlights the surprising effect of bridging core modification to robust nonlinear optical properties of dinitrophenol derivatives.

    4. 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.

    5. Expected degree for RNA secondary structure networks

      Peter Clote

      Article first published online: 7 NOV 2014 | DOI: 10.1002/jcc.23776

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      The first efficient dynamic programming algorithm is presented to compute the expected network degree, for the exponentially large network of all secondary structures of a given RNA sequence. The program RNAexpNumNbors is written in C, runs in cubic time and quadratic space, can compute the expected number of neighbors, or expected network degree, of an input sequence, and is publicly available.

    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. Protein folding pathways extracted by OFLOOD: Outlier FLOODing method

      Ryuhei Harada, Tomotake Nakamura, Yu Takano and Yasuteru Shigeta

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23773

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      The Outlier FLOODing method (OFLOOD) is proposed as an efficient conformational sampling method to extract biologically rare events such as protein folding. OFLOOD consists of (i) detections of outliers from conformational distributions and (ii) conformational resampling from the outliers by MD simulations. As demonstrations, OFLOOD was applied to folding of Chignolin and HP35. In both cases, OFLOOD automatically extracted folding pathways from unfolded structures with ns-order computational costs, although µs-order canonical MD failed to extract them.

    8. 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.

    9. Computing pKA values of hexa-aqua transition metal complexes

      Gegham Galstyan and Ernst-Walter Knapp

      Article first published online: 19 OCT 2014 | DOI: 10.1002/jcc.23764

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      Aqueous pKA values for hexa-aqua complexes of first and second row transition metals were computed using a combination of quantum chemical and electrostatic methods. Computed pKA values show very good agreement with measured pKA values with a root mean square deviation of 1 pH unit. Compared to previous approaches from the same lab, the precision of the method was systematically improved.

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