Journal of Computational Chemistry

Cover image for Vol. 34 Issue 29

5 November 2013

Volume 34, Issue 29

Pages i–iv, 2493–2575

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Rapid Communications
    4. Full Papers
    1. You have free access to this content
      Cover Image, Volume 34, Issue 29 (pages i–ii)

      Version of Record online: 24 SEP 2013 | DOI: 10.1002/jcc.23451

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      Amyloid peptides associated with Alzheimer's disease are intrinsically disordered proteins. The Cu(II)-bound Aβ(1–16) that hops on the rugged landscape sampled by molecular dynamics simulations reveals the polymorphic ensemble of the metal-bound amyloid. Based on newly developed AMBER force field parameters, the effects of different Cu(II) binding modes on both structural and thermodynamic properties of Aβ(1–16) are characterized from the perspective of computational simulations by Liang Xu, Xiaojuan Wang, Shengsheng Shan, and Xicheng Wang on page 2524. The relative Cu(II) binding affinity is compared in terms of the binding free energy calculations.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 29 (pages iii–iv)

      Version of Record online: 24 SEP 2013 | DOI: 10.1002/jcc.23452

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      Auxiliary basis functions for second-order Møller–Plesset perturbation theory with resolution-of-identity approximation (RI-MP2) suitable for 6-31G** and 6-311G** basis sets are developed for first-, second-, and third-row elements. On page 2568, Masato Tanaka, Michio Katouda, and Shigeru Nagase assess the performance of auxiliary basis functions for 114 small and 23 large molecules (shown on the cover). The largest RI errors (|ΔERI| = |E(2)RI−MP2E(2)MP2|) for 6-31G** and 6-311G** basis sets are only 0.809 and 1.895 mHartree, respectively. The developed auxiliary basis functions are applicable to the RI-MP2 calculations of very large molecules with high accuracy and low computational cost.

  2. Rapid Communications

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    2. Cover Image
    3. Rapid Communications
    4. Full Papers
    1. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29–42) peptides (pages 2493–2497)

      Satoru G. Itoh and Hisashi Okumura

      Version of Record online: 7 AUG 2013 | DOI: 10.1002/jcc.23402

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      The Hamiltonian replica-permutation method (or multidimensional replica-permutation method) for molecular dynamics and Monte Carlo simulations is proposed. Parameters in the Hamiltonian are permuted among more than two replicas with the Suwa–Todo algorithm and this method is applied to an alanine dipeptide and to two amyloid-β(29–42) molecules. The Hamiltonian replica-permutation method realizes more efficient sampling than the Hamiltonian replica-exchange method. The protein misfolding funnel of amyloid-β(29–42) is illustrated and its dimerization pathways revealed.

    2. Chemically intuitive indices for charge-transfer excitation based on SAC-CI and TD-DFT calculations (pages 2498–2501)

      Masahiro Ehara, Ryoichi Fukuda, Carlo Adamo and Ilaria Ciofini

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23423

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      A recently proposed charge-transfer (CT) index and some related quantities for the description of CT excitations in push–pull model systems are examined in a vacuum and in ethanol by the direct symmetry-adapted cluster configuration interaction method in the polarizable continuum model and compared with results obtained at the time-dependent density functional theory level. Both the effect of solvation and electron correlations on these quantities are significant.

  3. Full Papers

    1. Top of page
    2. Cover Image
    3. Rapid Communications
    4. Full Papers
    1. Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm (pages 2502–2513)

      Carlos Campañá and Ronald E. Miller

      Version of Record online: 5 SEP 2013 | DOI: 10.1002/jcc.23408

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      The transition rapidly exploring random eigenvector assisted tree algorithm was developed to perform energy landscape exploration along low-energy pathways connecting local minima in the molecular shape space. The algorithm uses robot path planning techniques to look for feasible low-curvature trajectories, which could be used to locate transition states mediating conformational changes and chemical reactions in molecular systems.

    2. On the centrality of vertices of molecular graphs (pages 2514–2523)

      Milan Randić, Marjana Novič, Marjan Vračko and Dejan Plavšić

      Version of Record online: 19 AUG 2013 | DOI: 10.1002/jcc.23413

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      The common vertex matrix of graphs, which was recently introduced, is further explored. Analysis offers novel characterization of the central vertex or vertices in acyclic and cyclic graphs. The centricity values are constructed for all vertices in acyclic and cyclic graphs. A selection of graphs is examined, and nonisomorphic graphs are found with vertices that have a 1:1 correspondence between their centricities.

    3. Characterization of the polymorphic states of copper(II)-bound Aβ(1–16) peptides by computational simulations (pages 2524–2536)

      Liang Xu, Xiaojuan Wang, Shengsheng Shan and Xicheng Wang

      Version of Record online: 27 AUG 2013 | DOI: 10.1002/jcc.23416

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      The overlap of the pre-organization free energies of different Cu2+-Aβ(1–16) systems shows the polymorphic property of Aβ(1–16) conformations that are ready for the binding of Cu2+.

    4. Dramatic substituent effects on the mechanisms of nucleophilic attack on Se—S bridges (pages 2537–2547)

      Otilia Mó, Al Mokhtar Lamsabhi, Manuel Yáñez, Gavin S. Heverly-Coulson and Russell J. Boyd

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23417

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      In contrast with the generally accepted view, the nucleophilic attack on Se—S bridges does not always lead to the S—Se bond cleavage, but to the fission of the Se—X bonds when the substituent X is very electronegative.

    5. A strategy to find minimal energy nanocluster structures (pages 2548–2556)

      José Rogan, Alejandro Varas, Juan Alejandro Valdivia and Miguel Kiwi

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23419

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      An unbiased search procedure to find global and local nanocluster minimal energies is developed. For the Lennard–Jones potential, this yields new local minima, an estimation of their number as the cluster size grows, and the scaling of the number of seeds that need to be explored to obtain the global minimum. The efficiency of the method is evaluated on the basis of the number of force evaluations required and the diversity generated.

    6. Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids (pages 2557–2567)

      Stefan Maintz, Volker L. Deringer, Andrei L. Tchougréeff and Richard Dronskowski

      Version of Record online: 10 SEP 2013 | DOI: 10.1002/jcc.23424

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      An analytical framework is derived to transfer chemical information from periodic plane-wave basis sets to local, Slater-type orbitals. This way, projected densities of states and projected crystal orbital Hamilton population analyses are readily available for a range of state-of-the-art materials simulations.

    7. Optimization of RI-MP2 Auxiliary Basis Functions for 6-31G** and 6-311G** Basis Sets for First-, Second-, and Third-Row Elements (pages 2568–2575)

      Masato Tanaka, Michio Katouda and Shigeru Nagase

      Version of Record online: 24 SEP 2013 | DOI: 10.1002/jcc.23430

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      The RI-MP2 auxiliary basis functions suitable for 6-31G** and 6-311G** basis sets are developed. Performance of the auxiliary basis functions is assessed for 114 small and 23 large molecules such as valinomycin (168 atoms). The largest resolution-of-identity (RI) errors (E(2)RI-MP2E(2)MP2) for 6-31G** and 6-311G** basis sets are only 0.809 and 1.895 mHartree, respectively. The developed auxiliary basis functions are applicable to the second-order Møller–Plesset perturbation theory with RI (RI-MP2) calculations of very large molecules with high accuracy.

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