Journal of Computational Chemistry

Cover image for Journal of Computational Chemistry

5 August 2012

Volume 33, Issue 21

Pages 1717–1780

  1. Full Papers

    1. Top of page
    2. Full Papers
    1. Spinor product computations for protein conformations (pages 1717–1729)

      Pieter Chys and Pablo Chacón

      Version of Record online: 8 MAY 2012 | DOI: 10.1002/jcc.23002

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      Spinor operators in geometric algebra can efficiently describe conformational changes of proteins by ordered products which act on individual bonds and represent their net rotations. This new mathematical framework enables to efficiently manipulate and generate protein conformations to any arbitrary degree. We show the intimate relationship between spinors and quaternions. Spinor calculations have a smaller computational cost and turn out to be slightly faster than current alternatives for both protein backbone construction and coordinate updating.

    2. Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory (pages 1730–1739)

      Jens Antony and Stefan Grimme

      Version of Record online: 9 MAY 2012 | DOI: 10.1002/jcc.23004

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      Dispersion corrected density functional theory (DFT-D3) is used for fully ab initio protein-ligand (PL) interaction energy calculation via molecular fractionation with conjugated caps (MFCC) and applied to PL complexes from the PDB comprising 3680, 1798, and 1060 atoms.

    3. Metabolic-intermediate complex formation with cytochrome P450: Theoretical studies in elucidating the reaction pathway for the generation of reactive nitroso intermediate (pages 1740–1747)

      Nikhil Taxak, Prashant V. Desai, Bhargav Patel, Michael Mohutsky, Valentine J. Klimkowski, Vijay Gombar and Prasad V. Bharatam

      Version of Record online: 21 MAY 2012 | DOI: 10.1002/jcc.23008

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      Aliphatic and aromatic amines can undergo biotransformation reactions to form reactive metabolites such as nitrosoalkanes, leading to mechanism-based inhibition of cytochromes. The mechanistic details for the formation of reactive nitroso intermediate and its coordination with heme-iron, forming metabolic-intermediate complex (MIC), were explored in detail using quantum chemical analysis. This study revealed that the MIC formation from a primary amine favors a proton shuttle pathway, and is a highly exothermic process, involving eight different steps and preferably takes place on the doublet spin surface of Cpd I.

    4. Rationalization of the behavior of M2(CH3CS2)4I (M = Ni, Pt) chains at room temperature from periodic density functional theory and ab initio cluster calculations (pages 1748–1761)

      Zahra Tabookht, Xavier López, Coen de Graaf, Nathalie Guihéry, Nicolas Suaud and Nadia Benamor

      Version of Record online: 21 MAY 2012 | DOI: 10.1002/jcc.23009

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      The MMX-like [Ni2(dta)4I] and [Pt2(dta)4I] chains have been theoretically studied by extraction of the electronic structure parameters by means of periodic density functional theory calculations and multiconfigurational ab initio methods with the effective Hamiltonian theory. Present results show that the nature of the charge ordering in either chain (alternate charge-polarization for Ni, averaged valence for Pt) explains the observed difference of 3 orders of magnitude in their electrical conductivities at room temperature.

    5. Computational investigations on covalent dimerization/oligomerization of polyacenes: Is it relevant to soot formation? (pages 1762–1772)

      D. Koley, E. Arunan and S. Ramakrishnan

      Version of Record online: 21 MAY 2012 | DOI: 10.1002/jcc.23014

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      Probable pathways for soot particle nucleation through covalent dimerization and oligomerizations of a variety of PAHs.

    6. Multi-zinc-expanded graphene patches: Tetraradical versus diradical character (pages 1773–1780)

      Hongfang Yang, Qisheng Song, Xinyu Song and Yuxiang Bu

      Version of Record online: 21 MAY 2012 | DOI: 10.1002/jcc.23018

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      Introduction of short zinc chains into the small graphene patches leads to different multi-Zn-expanded graphene patch derivatives which could have an open-shell broken-symmetry singlet diradical ground state or a quintet tetraradical ground state with high energy open-shell broken-symmetry singlet tetraradical character. This work provides an executable strategy to yield molecules which have stable polyradicaloid character and enhanced electronic properties of multi-Zn-expanded graphene patches.