Journal of Computational Chemistry

Cover image for Vol. 36 Issue 23

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

Impact Factor: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

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

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Recently Published Articles

  1. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)

    Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener and Michael E. Johnson

    Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24011

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    Computation prediction on ligand-protein binding activities (Molecular Mechanics Poisson-Boltzmann surface area (MM-PBSA), (Quantum Mechanics/) MM-Generalized Born surface area ((QM/)MM-GBSA), has gained attention in the pharmaceutical community due to its efficiency and accuracy. However, the effect of radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length on the MM-PBSA and (QM/)MM-GBSA performance has not been extensively studied. The article highlights the importance of these factors in the MM-PBSA and (QM/)MM-GBSA performance using the bacterial enoyl-ACP reductase and benzimidazole inhibitors as a test case.

  2. Bis(azulene) “submarine” metal dimer sandwich compounds (C10H8)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations

    Hongyan Wang, Hui Wang, R. Bruce King and Henry F. Schaefer III

    Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24013

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    The lowest energy (C10H8)2M2 submarine sandwich structures of the early transition metals Ti, V, Cr, and Mn have the azulene units functioning as bis(pentahapto) ligands to each metal atom. For the later transition metals Fe, Co, and Ni the lowest energy (C10H8)2M2 structures contain pentahapto-trihapto azulene ligands with an uncomplexed C[DOUBLE BOND]C double bond

  3. A new QM/MM method oriented to the study of ionic liquids

    M. Luz Sánchez, José C. Corchado, M. Elena Martín, Ignacio Fdez. Galván, Rute Barata-Morgado and Manuel A. Aguilar

    Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24023

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    A new quantum mechanic/molecular mechanic method, related to the average solvent electrostatic potential/molecular dynamics methodology, is presented to the study of pure ionic liquids. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate.

  4. A deeper insight into strain for the sila-bi[6]prismane ( Si18H12) cluster with its endohedrally trapped silicon atom, Si19H12

    Holger Vach, Lena V. Ivanova, Qadir K. Timerghazin, Fatme Jardali and Ha-Linh Thi Le

    Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24009

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    Formation of overcoordinated silicon hydride nanoclusters with nontetrahedral atomic configurations is the result of a self-assembly process in a silane/hydrogen plasma reactor operated close to dusty plasma conditions as shown in our ab initio molecular dynamics simulations. Both symmetric and asymmetric Si19H12 isomers are ultrastable and exhibit aromatic-like behavior. Ultrastability results from extensive electron delocalization that is induced by electron-deficient bonds.

  5. Strain in nonclassical silicon hydrides: An insight into the “ultrastability” of sila-bi[6]prismane (Si18H12) cluster with the endohedrally trapped silicon atom, Si19H12

    Grygoriy A. Dolgonos and Koshka Mekalka

    Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24014

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    Formation of a tubular silicon hydride nanocluster bearing nontetrahedral atomic configurations requires significant amount of energy. As in the case of recently proposed tubular “ultrastable” sila-bi[6]prismane with one encaged silicon atom, Si19H12, the energy difference with respect to the tetrahedral reference molecules (called “strain energy”) is high enough to cause isomerization or fragmentation reactions. Consequently, this isomer cannot be considered as “ultrastable” nor as aromatic. Two new low-lying Si19H12 isomers have been proposed.