Journal of Computational Chemistry
Copyright © 2014 Wiley Periodicals, Inc., A Wiley Company
Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner
Impact Factor: 3.835
ISI Journal Citation Reports © Ranking: 2012: 34/152 (Chemistry Multidisciplinary)
Online ISSN: 1096-987X
Recently Published Articles
- Toward the understanding of the environmental effects on core ionizations
Adèle D. Laurent, Vitaly N. Glushkov, Thibaut Very and Xavier Assfeld
Article first published online: 18 APR 2014 | DOI: 10.1002/jcc.23604
A systematic methodology is used to evaluate core ionization energies of amino acids in the gas phase or in part of the human serum albumin protein. This is performed with the help of QM/MM tools and, more precisely, with the asymptotic projection formalism, accounting for orthogonality constraints between states. This work shows that environment effects are not trifling when computing core ionization energies, as they might be as large as 10 eV.
- All-atom polarizable force field for DNA based on the classical drude oscillator model
Alexey Savelyev and Alexander D. MacKerell Jr.
Article first published online: 18 APR 2014 | DOI: 10.1002/jcc.23611
The classical Drude oscillator model is used to incorporate electronic polarizability in a force field for DNA. Each polarizable (non-hydrogen) atom is supplemented with a Drude particle, which moves self consistently in the electric field, and, for hydrogen bond acceptors, lone-pair particles. Atomic polarizability is equivalent to the Drude charge, qD, divided by the force constant on the harmonic spring, kD, connecting the Drude particle and parent atom. Because of polarization effects the dipole moment of water is perturbed in the vicinity of DNA.
- Reactivity index based on orbital energies (pages 1093–1100)
Takao Tsuneda and Raman K. Singh
Article first published online: 17 APR 2014 | DOI: 10.1002/jcc.23599
Chemical reactivity depends on the orbital energy gap contributing to the reaction in the initial reaction process. This is because the small orbital energy gap gradient indicates the precursory charge transfer process, while the large gradient implies the initial structural transformation. Analyses using a normalized reaction diagram show that large orbital energy gap gradients are given for specific reactions, including several SN2 reactions, which are experimentally established to get around the optimum reaction pathways.
- Using operators to expand the block matrices forming the Hessian of a molecular potential
Article first published online: 16 APR 2014 | DOI: 10.1002/jcc.23609
Compact expressions for the derivatives of a molecular potential are important for use in theoretical and practical applications. In this work, the second-order derivatives are expanded in terms of operators. This leads to a new set of formulas that can be implemented efficiently in high-level programming languages.
- SN1-SN2 and SN2-SN3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides
Shinichi Yamabe, Guixiang Zeng, Wei Guan and Shigeyoshi Sakaki
Article first published online: 14 APR 2014 | DOI: 10.1002/jcc.23607
Transition states of hydrolysis reactions ZC6H4XCl are investigated with specific water molecules (n = 6, 9, 11, 17, 23, and 29), where X = CH2, and SO2 and Z = O2N, Cl, H, H3C, and H3CO. In the case of a large n value and an electron-donating Z group, the hydrolysis reaction occurs through a SN2 mechanism. However, the combination of a small n value and an electron-withdrawing Z group converts the reaction mechanism to SN3.