Journal of Computational Chemistry

Cover image for Vol. 35 Issue 26

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. Electronic spectra and intersystem spin-orbit coupling in 1,2- and 1,3-squaraines

      Marta E. Alberto, Gloria Mazzone, Angelo D. Quartarolo, Flavio Fortes Ramos Sousa, Emilia Sicilia and Nino Russo

      Article first published online: 1 SEP 2014 | DOI: 10.1002/jcc.23725

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      The main photophysical properties of a series of recently synthetized 1,2- and 1,3-squaraines have been investigated by means of density functional theory (DFT) and time-dependent DFT approaches. Two singlet-triplet intersystem crossings have been found, which could contribute to the excited singlet oxygen production.

  2. Software News and Updates

    1. The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

      Saleh Riahi and Christopher N. Rowley

      Article first published online: 1 SEP 2014 | DOI: 10.1002/jcc.23716

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      The interface between CHARMM and TURBOMOLE allows researchers to perform extensive QM/MM molecular dynamics simulations using accurate quantum mechanical methods. This code also makes it possible to use a molecular mechanical model that is capable of describing induced electronic polarization within a simulation. Time-averaged electronic absorption, circular dichroism, and emission spectra can also be calculated.

    2. SPILLO-PBSS: Detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach

      Alessandro Di Domizio, Alessandro Vitriolo, Giulio Vistoli and Alessandro Pedretti

      Article first published online: 1 SEP 2014 | DOI: 10.1002/jcc.23714

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      The search for drug-binding proteins attracts great interest for its manifold applications including polypharmacology analysis, side-effects prediction/clarification, and drug repositioning. Starting from a defined reference binding site, the method presented involves a fully flexible structural search for potential binding sites on target proteins. This method surpassed the performance of available approaches, the rigidity of which prevents them from suitably recognizing distorted binding sites. The reported tests also suggest the possibility of fruitful applications on proteome-wide scale.

  3. 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. 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.

    6. 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.

  4. 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.

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