Journal of Computational Chemistry

Cover image for Vol. 35 Issue 25

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: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

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

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  1. Full Papers

    1. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

      Wei Chen and Jana K. Shen

      Article first published online: 21 AUG 2014 | DOI: 10.1002/jcc.23713

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      Constant pH techniques are becoming an integral part of molecular dynamics. The effects of system net charge and electrostatic truncation on the explicit-solvent continuous constant pH molecular dynamics are reported. Enforcing charge neutrality via titratable co-ions significantly improves the accuracy of the calculated pKa values. Directions for future improvement of constant pH techniques are suggested.

    2. Kinetics of radical-molecule reactions in aqueous solution: A benchmark study of the performance of density functional methods

      Annia Galano and Juan Raúl Alvarez-Idaboy

      Article first published online: 21 AUG 2014 | DOI: 10.1002/jcc.23715

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      Six density functional approximations are recommended for kinetic calculations in aqueous solution: LC-ωPBE, M06-2X, BMK, B2PLYP, M05-2X, and MN12SX, in that order. This result was obtained using the SMD model, conventional transition state theory, zero-curvature tunneling correction, and experimental data as reference.

    3. Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes

      Alexander Hoffmann, Richard Grunzke and Sonja Herres-Pawlis

      Article first published online: 13 AUG 2014 | DOI: 10.1002/jcc.23706

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      Investigation of sterically encumbered guanidine-quinoline copper bis(chelate) complexes shows that the correct description requires modern dispersion correction using Becke–Johnson damping. The best structural description is obtained with the TPSSh functional but B3LYP is very suited as well in combination with the def2-TVP basis set. Optical and vibrational description is best with B3LYP/def2-TZVP and not much affected by dispersion.

    4. Plane-wave density functional theory investigation of adsorption of 2,4,6-trinitrotoluene on al-hydroxylated (0001) surface of (4 × 4) α-alumina

      Manoj K. Shukla and Frances Hill

      Article first published online: 13 AUG 2014 | DOI: 10.1002/jcc.23712

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      Alumina is one of the most important materials on the earth's surface, with wide applications in different areas of science and technology. The relative humidity in the environment controls the hydroxylation of the alumina surface. The results of adsorption of 2,4,6-trinitrotoluene, an energetic compound, are reported on the Al-hydroxylated (0001) surface of (4 × 4) α-alumina (α-Al2O3), obtained via the plane-wave level of density functional theory approach using PBE and a recently developed high accuracy vdW-DF2 van der Waals functional.

    5. Molecular sensing using armchair graphene nanoribbon

      Mohammad Reza Rezapour, Arunkumar Chitteth Rajan and Kwang S. Kim

      Article first published online: 13 AUG 2014 | DOI: 10.1002/jcc.23705

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      An electron transport system composed of an armchair graphene nanoribbon with a molecule or molecules attached onto its surface can be considered as a Fano–Anderson structure. Reductions appearing in the transmission profile of the system due to Fano resonance are unique for each molecule. These dips, representing molecular fingerprints, would be a promising tool to molecular recognition and configurational analysis.

    6. Illuminating the origins of spectral properties of green fluorescent proteins via proteochemometric and molecular modeling

      Chanin Nantasenamat, Saw Simeon, Wiwat Owasirikul, Napat Songtawee, Maris Lapins, Virapong Prachayasittikul and Jarl E. S. Wikberg

      Article first published online: 12 AUG 2014 | DOI: 10.1002/jcc.23708

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      Unified proteochemometric models for predicting spectral properties of green fluorescent protein variants are reported. Structural information from a chromophore-protein interaction network is introduced using proteochemometric cross-terms. The predictive models, for the first time, not only consider physicochemical properties of chromophores but also mutational information of GFP variants and their contributions on spectral properties. The strategy could be extended to other biological systems where the interplay of several biological entities is crucial for a protein's activity.

    7. SurfKin: An ab initio kinetic code for modeling surface reactions

      Thong Nguyen-Minh Le, Bin Liu and Lam K. Huynh

      Article first published online: 11 AUG 2014 | DOI: 10.1002/jcc.23704

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      A C/C++ based code, SurfKin, has been developed and shown promising capability to calculate rate constants of gas-surface elementary steps. SurfKin can be used to perform kinetic analysis on reaction networks that include adsorption, reaction, and desorption. Using density functional theory calculations as input, standard statistical mechanics and classic rate theories (i.e., transition state theory and collision theory) are incorporated and automated in the code for a wide range of heterogeneous catalysis systems.

    8. Adsorption of small molecules on helical gold nanorods: A relativistic density functional study

      Xiao-Jing Liu and Ian Hamilton

      Article first published online: 11 AUG 2014 | DOI: 10.1002/jcc.23711

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      The adsorption of a variety of small molecules on the helical gold nanorod Au40 is studied using relativistic density functional theory. All molecules preferentially adsorb at a single low-coordinated gold atom at an end of Au40. There is significant charge transfer between Au40 and the adsorbate and Au40-adsorbate can be described as a donor-accepter complex. The adsorption energy order is determined to be CO > NO2 > NH3 > NO> CH2[DOUBLE BOND]CH2 > CH2[DOUBLE BOND]CH[BOND]CHO > HC[TRIPLE BOND]CH > C5H5N > H2S > HCN > CH3OH > H2O > H2C[DOUBLE BOND]O > SO2 > CH4 >O2 > N2.

    9. Calculating core-level excitations and x-ray absorption spectra of medium-sized closed-shell molecules with the algebraic-diagrammatic construction scheme for the polarization propagator

      Jan Wenzel, Michael Wormit and Andreas Dreuw

      Article first published online: 7 AUG 2014 | DOI: 10.1002/jcc.23703

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      Core-excited states are generated by absorption of high-energy X-ray radiation. These states can be computed and X-ray absorption spectra can be simulated using the core-valence separated algebraic-diagrammatic construction scheme of second order CVS-ADC(2). A representative set of molecules from the field of organic electronics and biology has been chosen to demonstrate the wide range of applicability and the high accuracy of CVS-ADC(2).

  2. Software News and Updates

    1. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

      Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M. Venable, Jeffery B. Klauda and Wonpil Im

      Article first published online: 7 AUG 2014 | DOI: 10.1002/jcc.23702

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      CHARMM-GUI Membrane Builder is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulation through an automated optimized process.

  3. Letters to the Editor

    1. An updated version of the computational package SIMPRE that uses the standard conventions for Stevens crystal field parameters

      José J. Baldoví, Juan M. Clemente-Juan, Eugenio Coronado, Alejandro Gaita-Ariño and Andrew Palii

      Article first published online: 3 AUG 2014 | DOI: 10.1002/jcc.23699

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      The methodology used by SIMPRE is verified and found to be correct for all physical properties. Nevertheless, the presentation is now formally improved, adequately referencing, and defining the crystal field operators and parameters used by SIMPRE. New calculations are performed that confirm the small effect of including the excited spin-orbit states, that is, the effect of lifting a critical approximation of SIMPRE.

    2. Software package SIMPRE—Revisited

      Mirosław Karbowiak and Czesław Rudowicz

      Article first published online: 1 AUG 2014 | DOI: 10.1002/jcc.23700

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      Methodology used in the package SIMPRE for modeling the spectroscopic and magnetic properties of single ion and single-molecule magnets is analyzed. The nominally Stevens crystal-field parameters (CFPs) exhibit features characteristic for the Wybourne CFPs. To clarify this confusion, the properties of the Stevens CFPs inline image and the tesseral-tensor operators inline image are contrasted with those of the Wybourne CFPs Bkq and the spherical-tensor operators inline image. Effect of this confusion on reliability of SIMPRE is considered.

  4. 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

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      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.

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