Journal of Computational Chemistry

Cover image for Vol. 35 Issue 23

Early View (Online Version of Record published before inclusion in an issue)

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

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


  1. 1 - 14
  1. Full Papers

    1. Hydrogen–hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods

      Kiamars Eskandari and Christian Van Alsenoy

      Article first published online: 29 JUL 2014 | DOI: 10.1002/jcc.23698

      Thumbnail image of graphical abstract

      In contrast to the classical view, both interacting quantum atoms and Hirshfeld atomic energy partitioning confirms Bader's hypothesis of H[[BOND]]H bonding in the planar biphenyl; there is a net attractive interaction between the ortho-hydrogens. In other words, the H[[BOND]]H bond paths (indicated by dashed lines) in the planar biphenyl are indicative of H[[BOND]]H bonding.

    2. Factors affecting the computation of the 13C shielding in disaccharides

      Pablo G. Garay, Osvaldo A. Martin, Harold A. Scheraga and Jorge A. Vila

      Article first published online: 28 JUL 2014 | DOI: 10.1002/jcc.23697

      Thumbnail image of graphical abstract

      Knowledge of the three-dimensional structures of carbohydrate molecules, as for maltose shown in the figure, is indispensable for a full understanding, at the molecular level, of the biological processes in which carbohydrates are involved. For this purpose, it is important to determine, first, which carbons can be used as probes to sense conformational changes and, second, all factors that affect the computation of the shielding, at the density functional theory (DFT) level of theory, of those carbons.

    3. Basis set error estimation for DFT calculations of electronic g-tensors for transition metal complexes

      Morten N. Pedersen, Erik D. Hedegård and Jacob Kongsted

      Article first published online: 25 JUL 2014 | DOI: 10.1002/jcc.23688

      Thumbnail image of graphical abstract

      The calculation of the electronic g-tensor for electron paramagnetic resonance (EPR) is a promising route to aid experimental investigations, especially within bio-inorganic chemistry. However, as the number of basis functions greatly increase for compounds containing d-block elements, it would be desirable if smaller basis set could be used for the ligands in a so-called locally dense basis set approach. This article reports the accuracy of several locally dense basis set schemes and compare these to an extrapolated complete basis set value.

    4. Benchmarking dispersion and geometrical counterpoise corrections for cost-effective large-scale DFT calculations of water adsorption on graphene

      Marco Lorenz, Bartolomeo Civalleri, Lorenzo Maschio, Mauro Sgroi and Daniele Pullini

      Article first published online: 23 JUL 2014 | DOI: 10.1002/jcc.23686

      Thumbnail image of graphical abstract

      The adsorption of water on graphene is computationally investigated via density functional theory combined with empirical corrections. This allows for going beyond the quality of classical or semiclassical simulations, while still keeping the computational costs under control. To model the water adsorption, we used 1 and 10 water molecules per cell, as well as a full coverage of the graphene surface. Additionally, we apply the same setup to hexagonal boron nitride supported graphene.

    5. Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems

      Soroosh Pezeshki and Hai Lin

      Article first published online: 23 JUL 2014 | DOI: 10.1002/jcc.23685

      Thumbnail image of graphical abstract

      Flexible-boundary QM/MM allows on-the-fly exchange of partial charges between the QM and MM subsystems in molecular dynamics. An average total charge of −0.9 e is observed for a chloride ion and its first solvation shell treated by QM, while on average the bulk water modeled by MM carries a total charge of −0.1 e.

  2. Software News and Updates

    1. CAST: A new program package for the accurate characterization of large and flexible molecular systems

      Christoph Grebner, Johannes Becker, Daniel Weber, Daniel Bellinger, Maxim Tafipolski, Charlotte Brückner and Bernd Engels

      Article first published online: 23 JUL 2014 | DOI: 10.1002/jcc.23687

      Thumbnail image of graphical abstract

      The program package Conformational Analysis and Search Tool (CAST) provides many approaches for the description of large and flexible (macro) molecules. For the determination of thermally accessible minima, it contains the standard approaches molecular dynamics or Monte Carlo and the new TabuSearch-based global optimization routine. Reaction paths can be determined via nudged elastic band or PathOpt. Beside many standard force fields, CAST includes the SAPT-FF force field. Interfaces to MOPAC and TeraChem are also available.

  3. Full Papers

    1. To be or not to be butterfly: New mechanistical insights in the Aza-Michael asymmetric addition of lithium (R)-N-benzyl-N-(α-methylbenzyl)amide

      Carlos T. Nieto, David Díez and Narciso M. Garrido

      Article first published online: 22 JUL 2014 | DOI: 10.1002/jcc.23694

      Thumbnail image of graphical abstract

      The asymmetric Aza-Michael addition of homochiral lithium benzylamides to α,β-unsaturated esters represents an extended protocol to obtain enantioenriched β-amino esters. A QM/MM transition state protocol is presented, revising the original proposed mechanism. Theoretical results a Si/Re 99:1 diastereoselective ratio, in good agreement with experimental results, is reported. Two TS conformers in a “V-stacked” orientation of the amide's phenyl rings, differing in the THF molecule arrangement coordinated to lithium, are the most suitable TS geometries.

    2. Shape-based virtual screening with volumetric aligned molecular shapes

      David Ryan Koes and Carlos J. Camacho

      Article first published online: 22 JUL 2014 | DOI: 10.1002/jcc.23690

      Thumbnail image of graphical abstract

      Volumetric aligned molecular shapes provide a way to screen libraries of molecular shapes that approaches the speed of the fastest shape-based methods and the accuracy of the most successful shape-based methods which are orders of magnitude slower. Volumetric aligned molecular shapes also offer a novel minimum/maximum shape constraint search that allows the user to precisely specify the desired shape and search millions of shapes in a fraction of a second.

    3. CCSD-CTOCD static dipole shielding polarizability for quantification of the chiral NMR effects in oxaziridine derivatives

      Stefano Pelloni and Inmaculada García Cuesta

      Article first published online: 22 JUL 2014 | DOI: 10.1002/jcc.23689

      Thumbnail image of graphical abstract

      Chiral discrimination by NMR spectroscopy might be achieved through the pseudo-scalar derived from the dipole shielding polarizability tensor, which has opposite sign in each enantiomer and is zero for achiral molecules. An accurate theoretical description of the magnitude is of fundamental importance to be susceptible of being unequivocally confirmed by experiment. CCSD calculations of the pseudo-scalar in oxaziridine derivatives show important effects caused by the chiral nuclei 19F and 31P.

    4. Coarse-grained molecular dynamics simulations of protein–ligand binding

      Tatsuki Negami, Kentaro Shimizu and Tohru Terada

      Article first published online: 20 JUL 2014 | DOI: 10.1002/jcc.23693

      Thumbnail image of graphical abstract

      Coarse-grained molecular dynamics simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. Spatial distributions of the CG ligand molecules revealed potential ligand-binding sites on the protein surfaces other than the real ligand-binding sites. The ligands bound most strongly to the real ligand-binding sites. Analysis of the ligand fluxes demonstrated that the CG ligand molecules tended to enter the ligand-binding pockets through grooves on the protein surfaces.

    5. DFT assessment of the spectroscopic constants and absorption spectra of neutral and charged diatomic species of group 11 and 14 elements

      Athanassios C. Tsipis

      Article first published online: 10 JUL 2014 | DOI: 10.1002/jcc.23684

      Thumbnail image of graphical abstract

      The spectroscopic constants and absorption spectra of neutral and charged diatomic molecules of group 11 and 14 elements formulated as [M2]+/0/− (M = Cu, Ag, Au), and [E2]+/0/− (E = C, Si, Ge, Sn, Pb) have been thoroughly investigated by means of electronic structure calculation methods at the DFT and TDDFT levels.

    6. Red and blue shifted hydridic bonds

      Mirosław Jabłoński

      Article first published online: 10 JUL 2014 | DOI: 10.1002/jcc.23678

      Thumbnail image of graphical abstract

      The elongation of a hydride bond on its interaction seems to be much more typical effect than its shortening. Contrary to what might have been expected on the basis of studies in uniform electric field, this elongation is accompanied by a blue instead of red shift of the R[BOND]H stretching vibration frequency. The “additional” elongation of the R[BOND]H hydridic bond results from the significant charge outflow from the sigma bonding orbital of R[BOND]H that weakens this bond.

    7. Including ligand-induced protein flexibility into protein tunnel prediction

      Laura J. Kingsley and Markus A. Lill

      Article first published online: 5 JUL 2014 | DOI: 10.1002/jcc.23680

      Thumbnail image of graphical abstract

      IterTunnel combines geometric tunnel prediction with steered MD to incorporate ligand migration and protein flexibility into tunnel prediction. We demonstrate that the ligand itself can reshape tunnels due to its interaction with the protein resulting in the exposure of new, energetically favorable tunnels.

    8. PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements

      Sean M. Law, Aaron T. Frank and Charles L. Brooks III

      Article first published online: 4 JUL 2014 | DOI: 10.1002/jcc.23683

      Thumbnail image of graphical abstract

      Protein secondary structure elements (SSEs) are typically assigned based on backbone hydrogen-bonding patterns. However, when it comes to assigning SSEs using only the Cα positions, the current state-of-the-art is lacking in both accuracy and speed. To this end, protein C-alpha secondary structure output (PCASSO) is presented—a fast and accurate Cα-based SSE assignment tool that can be used for universal SSE assignments, high-throughput SSE studies, analysis of coarse-grained simulations, and so forth.


  1. 1 - 14