Journal of Computational Chemistry

Cover image for Vol. 35 Issue 27

October 15, 2014

Volume 35, Issue 27

Pages i–iv, 1943–2017

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 35, Issue 27 (pages i–ii)

      Article first published online: 13 SEP 2014 | DOI: 10.1002/jcc.23746

      Thumbnail image of graphical abstract

      On page 1997 (DOI: 10.1002/jcc.23712), 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 report on the CHARMM-GUI Membrane Builder, 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. The cover image illustrates the building process of a protein/membrane system by reading the protein structure, generating pore water/bilayer/bulk water/ions, and combining all the components.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 27 (pages iii–iv)

      Article first published online: 13 SEP 2014 | DOI: 10.1002/jcc.23747

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      A theoretical study of sterically encumbered guanidine-quinoline copper bis(chelate) complexes is reported on page 1943 (DOI: 10.1002/jcc.23706) by Alexander Hoffmann, Richard Grunzke, and Sonja Herres-Pawlis. This investigation shows that the correct description requires modern dispersion correction using Becke-Johnson damping in order to describe the rather “soft” interaction of ligand moieties. 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 is barely affected by dispersion.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes (pages 1943–1950)

      Alexander Hoffmann, Richard Grunzke and Sonja Herres-Pawlis

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

      Thumbnail image of graphical abstract

      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.

    2. Illuminating the origins of spectral properties of green fluorescent proteins via proteochemometric and molecular modeling (pages 1951–1966)

      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.

    3. Adsorption of small molecules on helical gold nanorods: A relativistic density functional study (pages 1967–1976)

      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; 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. Plane-wave density functional theory investigation of adsorption of 2,4,6-trinitrotoluene on al-hydroxylated (0001) surface of (4 × 4) α-alumina (pages 1977–1985)

      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. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics (pages 1986–1996)

      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.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations (pages 1997–2004)

      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

      Thumbnail image of graphical abstract

      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.

    2. SPILLO-PBSS: Detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach (pages 2005–2017)

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

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

      Thumbnail image of graphical abstract

      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.

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