Journal of Computational Chemistry
© Wiley Periodicals, Inc.
Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner
Impact Factor: 3.648
ISI Journal Citation Reports © Ranking: 2015: 41/163 (Chemistry Multidisciplinary)
Online ISSN: 1096-987X
Recently Published Articles
- Regularized regression analysis of digitized molecular structures in organic reactions for quantification of steric effects
Shigeru Yamaguchi, Takahiro Nishimura, Yuta Hibe, Masaki Nagai, Hirofumi Sato and Ian Johnston
Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24791
The performance of a regularized regression method, LASSO/Elastic Net, in obtaining information about the steric effects in organic reactions is examined. Important partial structures for the reactions are extracted and visualized from high-dimensional digitized molecular structures (the indicator field) using regularized regression. We compare the performance of the regularized regression analyses with those of classical PLS regression. Regularized regressions provide highly interpretable models that include less noise than those from PLS regression.
- Phage-like packing structures with mean field sequence dependence
Christopher G. Myers and B. Montgomery Pettitt
Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24727
DNA sequence determines the response to packing stress in some phages. Left is a purely elastic model and right is a mean field sequence model with structural defects determined by the nonlinear elastic response to sequence thermodynamics.
- Evaluation of the restricted virtual space approximation in the algebraic-diagrammatic construction scheme for the polarization propagator to speed-up excited-state calculations
Chong Yang and Andreas Dreuw
Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24794
Within the reduced virtual space (RVS) approximation a significant amount of energetically high-lying virtual orbitals are discarded speeding up excited-state calculations substantially. The applicability and limitations of the RVS approximation within the algebraic-diagrammatic construction (ADC) for the polarization propagator at second and third order are discussed. While RVS-ADC(2) turns out to be useful for ππ* excited states only, RVS-ADC(3) is more robust and applicable also for nπ* excited states.
- Photo absorption of p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach
Kenji Hirano, Hiroshi Nakano, Yoshihide Nakao, Hirofumi Sato and Shigeyoshi Sakaki
Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24784
Photo absorption properties of p-coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated based on a hybrid method of quantum chemistry and statistical mechanics for molecular liquids. The electronic structure and excited energy of the solvated chromophore are significantly changed from the isolated one.
- GPU accelerated implementation of NCI calculations using promolecular density
Gaëtan Rubez, Jean-Matthieu Etancelin, Xavier Vigouroux, Michael Krajecki, Jean-Charles Boisson and Eric Hénon
Version of Record online: 25 MAR 2017 | DOI: 10.1002/jcc.24786
Molecular interactions (noncovalent interactions [NCI]) are forces, either attractive or repulsive, between molecules. They are involved in important processes like boiling or crystallization or drug action. The NCI methodology provides a visual picture of these interactions from grid-based calculations relying on the electron density knowledge. A graphics processing unit (GPU) accelerated NCI algorithm is described that leads to a 39-fold speedup compared to an OpenMP parallel run with 16 CPU cores. The NCI GPU implementation is attractive in terms of runtime and energy efficiency.