Journal of Computational Chemistry

Cover image for Vol. 37 Issue 31

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

Impact Factor: 3.648

ISI Journal Citation Reports © Ranking: 2015: 40/163 (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. Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pKa shifts of protein residues

    Ity Sharma and George A. Kaminski

    Version of Record online: 27 OCT 2016 | DOI: 10.1002/jcc.24519

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    Our Fuzzy-Border continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second-order Interaction Model (POSSIM) framework. It was then used to compute pKa shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. In addition, we have studied aspartic acid residues of Rnase Sa. We conclude that the POSSIM force field and the Fuzzy-Border model are sufficiently robust and transferable.

  2. d-electron count, ion-pairing and diagonal twist angles in metallo-bis(dithiolene) complexes

    Charles C. Kirkpatrick, John N. Truong and Bruce A. Kowert

    Version of Record online: 27 OCT 2016 | DOI: 10.1002/jcc.24524

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    The shape of the d9 nickel-bis(dithiolene) compound, [Ni(mnt)2]3−, has not been determined but was assumed to be planar in electrochemical and spectroscopic studies. DFT calculations show it is nonplanar and predict a diagonal twist angle of 42° in the absence of ion pairing. Alkali metal and tetra alkylammonium cations interact with the trianion's regions of highest negative charge, the NS2 planes of the ligands, and influence the diagonal twist angle; the ion-pairing energy is cation-dependent.

  3. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches

    E. Prabhu Raman, Sirish Kaushik Lakkaraju, Rajiah Aldrin Denny and Alexander D. MacKerell Jr

    Version of Record online: 26 OCT 2016 | DOI: 10.1002/jcc.24522

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    Accurate and rapid prediction of ligand potencies by the pre-computed ensembles based methods, Single Step Free Energy Perturbation (SSFEP) and Site Identification by Ligand Competitive Saturation (SILCS), is evaluated for Ack1 and p38 Map Kinase targets. Both SILCS and SSFEP are competitive with or better than the FEP results for the studied systems while being 1000+ fold times faster. Potential application of these methods in the context of screening large numbers of transformations is also illustrated.

  4. Optimal allosteric stabilization sites using contact stabilization analysis

    Alex Dickson, Christopher T. Bailey and John Karanicolas

    Version of Record online: 24 OCT 2016 | DOI: 10.1002/jcc.24517

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    Proteins are prone to unfold and aggregate, especially when mutated or under stress. Stabilizing a proteins' functional state, either using engineered disulfide bonds or designed small-molecule stabilizers, is an important goal, but first we must determine an optimal stabilization site to impact activity. We use simulation to measure the stabilization capacity of every contact in the β-glucuronidase enzyme, and show that the stabilization capacity of a contact is only loosely related to its proximity from the active site.

  5. Evaluation of bonding, electron affinity, and optical properties of M@C28 (M = Zr, Hf, Th, and U): Role of d- and f-orbitals in endohedral fullerenes from relativistic DFT calculations

    Alvaro Muñoz-Castro and R. Bruce King

    Version of Record online: 24 OCT 2016 | DOI: 10.1002/jcc.24518

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    Borderline elements between d- and f-blocks retain particular characteristics from both groups.