Journal of Computational Chemistry

Cover image for Vol. 37 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: 3.648

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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  1. 1 - 15
  1. Full Papers

    1. Informatics-Based Energy Fitting Scheme for Correlation Energy at Complete Basis Set Limit

      Junji Seino and Hiromi Nakai

      Version of Record online: 25 JUL 2016 | DOI: 10.1002/jcc.24455

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      The n-scheme fitting models were developed based on informatics techniques using hierarchical basis sets with small cardinal numbers to reproduce correlation energies at the complete basis set limits. Systematic assessments on the Gaussian-3X and Gaussian-2 sets revealed that the fitting models drastically reduced errors with equal or smaller computational effort.

    2. Geometrical control of the interatomic coulombic decay process in quantum dots for infrared photodetectors

      Praphasiri Dolbundalchok, Daniel Peláez, Emad F. Aziz and Annika Bande

      Version of Record online: 25 JUL 2016 | DOI: 10.1002/jcc.24410

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      A next-generation quantum dot (QD) infrared photodedector is proposed in which radiation absorption and electron emission are localized on either of two vertically-aligned singly-charged GaAs QDs among which an efficient energy transfer process, the interatomic Coulombic decay, is operative. Speed-optimized highly-accurate electron dynamics calculations on numerous architectures reveal how the performance may be custom-made through tuning the QDs’ geometries.

    3. The nature of structure and bonding between transition metal and mixed Si-Ge tetramers: A 20-electron superatom system

      Xiaojun Li, Zhijun Yan and Shuna Li

      Version of Record online: 25 JUL 2016 | DOI: 10.1002/jcc.24456

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      A novel superatom species with 20-electron system, SixGeyM+ (x + y = 4; M = Nb, Ta), is proposed and possesses spherically double (π and σ) aromaticity with high stability.

    4. A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules

      Jorge I. Martínez-Araya

      Version of Record online: 22 JUL 2016 | DOI: 10.1002/jcc.24453

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      The so-called dual descriptor reveals the most susceptible regions to undergo nucleophilic (dark-colored lobes) and electrophilic attacks (white-colored lobes), but its original operational formula based on electronic densities does not take into account degeneracies in frontier molecular orbitals, thus providing an incorrect description of the local reactivity as depicted by the middle image for C60. This article proposes an operational formula that takes into account those degeneracies as indicated by the right-most image.

    5. Design of [2]rotaxane through image threshold segmentation of electrostatic potential image

      Pingying Liu, Qiufeng Chen and Jing Ma

      Version of Record online: 21 JUL 2016 | DOI: 10.1002/jcc.24452

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      With the aid of computer image processing technology, an electrostatic potential-based image segmentation methodology is implemented to evaluate the relative binding strength of [2]rotaxane and other more complicated interlocked systems. The size and electrostatic compatibility criteria are demonstrated to be useful in the rational design and construction of novel interlocked architectures.

    6. Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid

      Sunghwan Choi, Oh-Kyoung Kwon, Jaewook Kim and Woo Youn Kim

      Version of Record online: 19 JUL 2016 | DOI: 10.1002/jcc.24443

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      Grid-based electronic structure calculations can be maximally accelerated on a modern computer architecture that combines between graphics processing units (GPUs) and central processing units. We compare the performance of heterogeneous computing between GPUs and many integrated cores for Hartree potential evaluations for silver nanoparticles with various sizes (3.1 to 6.9 nm). In particular, we use the work stealing scheduler for dynamically balanced task distribution between processors with different computing powers.

    7. Stability of functionalized corannulene cations [R-C20H10]+: An influence of the nature of R-Group

      Jingbai Li, Giovana da Silva Ramos and Andrey Yu Rogachev

      Version of Record online: 18 JUL 2016 | DOI: 10.1002/jcc.24444

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      Increasing the length of the R-group results in decrease of the stability of the functionalized corannulene cations [R-C20H10]+. Different attractive components of the bonding between R-group and C20H10-bowl show opposite trends in series.

    8. Structure, stability, and nature of bonding in carbon monoxide bound EX3+ complexes (E = group 14 element; X = H, F, Cl, Br, I)

      Manas Ghara, Sudip Pan, Anand Kumar, Gabriel Merino and Pratim K. Chattaraj

      Version of Record online: 18 JUL 2016 | DOI: 10.1002/jcc.24446

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      The structures and stability of carbon monoxide (CO) bound inline image (E = C, Si, Ge, Sn, Pb; X = H, F, Cl, Br, I) complexes are analyzed. In comparison to free CO, a red shift in C[BOND]O stretching frequency is observed in O-side binding whereas a blue shift occurs in C-side binding. The observed change can be explained by the change in polarization in the σ- and π-orbitals and the relative strength of C[RIGHTWARDS ARROW]E or O[RIGHTWARDS ARROW]E σ-donation and E[RIGHTWARDS ARROW]C or E[RIGHTWARDS ARROW]O π-back-donation.

    9. Thermodynamic compatibility of actives encapsulated into PEG-PLA nanoparticles: In Silico predictions and experimental verification

      Andreas Erlebach, Timm Ott, Christoph Otzen, Stephanie Schubert, Justyna Czaplewska, Ulrich S. Schubert and Marek Sierka

      Version of Record online: 18 JUL 2016 | DOI: 10.1002/jcc.24449

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      A theoretical approach based on atomistic simulations and the Flory–Huggins theory for rapid prediction of drug loading efficiencies of copolymers comprising hydrophilic and hydrophobic blocks is reported. The results of the simulations are directly verified by comparison with observed encapsulation efficiency of PEG-PLA nanoparticles prepared by nanoprecipitation.

  2. Software News and Updates

    1. GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments

      Lynn Groß and Carmen Herrmann

      Version of Record online: 15 JUL 2016 | DOI: 10.1002/jcc.24420

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      Dipole moments of molecular subsystems are important for understanding chemical gating, solvent effects, and atomic force microscopy. Due to partial charges on the subsystems, a unique definition of such local dipole moments is not straightforward. We present a new implementation of a modified version of Bader's and Laidig's approach to origin-independent local dipole moments which can be used in a very flexible way, e.g. for both covalently and non-covalently bound systems.

  3. Full Papers

    1. Efficient implementation of constant pH molecular dynamics on modern graphics processors

      Evan J. Arthur and Charles L. Brooks III

      Version of Record online: 12 JUL 2016 | DOI: 10.1002/jcc.24435

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      Novel implementation of constant pH molecular dynamics on GPUs utilizing GPU-based Generalized Born with a Simple sWitching function implicit solvent enables fast constant pH simulations of proteins.

    2. Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12

      Kaori Ueno-Noto and Keiko Takano

      Version of Record online: 8 JUL 2016 | DOI: 10.1002/jcc.24447

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      HIV-1 neutralizing antibody 2G12 binds to d-fructose stronger than to d-mannose. Classical molecular dynamics and quantum chemical simulations using a model describing inner water molecules of a protein have enough accuracy to model ligand's affinity and dynamics. The results indicate that d-fructose's strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligand's conformation and relative position in the active site

    3. Theoretical study on photooxidation mechanism of ruthenium complex [Ru(II)-(bpy)2(TMBiimH2)]2+ with molecular oxygen

      Li-Hong Liu, Dan Wu, Shu-Hua Xia and Ganglong Cui

      Version of Record online: 7 JUL 2016 | DOI: 10.1002/jcc.24448

      Thumbnail image of graphical abstract

      DFT electronic structure calculations shed important light on the visible-light induced photooxidation mechanism of ruthenium complexes with molecular oxygen.

    4. Optical response of the Cu2S2 diamond core in Cu2II(NGuaS)2Cl2

      Matthias Witte, Benjamin Grimm-Lebsanft, Arne Goos, Stephan Binder, Michael Rübhausen, Martin Bernard, Adam Neuba, Serge Gorelsky, Uwe Gerstmann, Gerald Henkel, Wolf Gero Schmidt and Sonja Herres-Pawlis

      Version of Record online: 30 JUN 2016 | DOI: 10.1002/jcc.24439

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      The structural CuA model complex inline image(NGuaS)2Cl2 is analyzed using density functional theory. We discuss the molecular orbitals and their relation to other CuA model complexes. Another focus is set on the optical response in UV/Vis spectroscopy and Raman excitations. For comparison, resonant Raman spectra are determined for two excitation wavelengths and analyzed. The experimental spectra are in good agreement with the theoretical predictions and reveal striking similarities with other CuA model complexes.

  4. Corrigendum

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