Journal of Computational Chemistry

The cover image shows the structure of methane hydrate, a form of water ice containing a large amount of methane within a crystal structure of water. Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates. On page 121, Yuan Liu, Jijun Zhao, Fengyu Li, and Zhongfang Chen assess the performance of a variety of exchange-correlation functionals and various basis sets in describing the non-covalent interactions in methane hydrates.

As presented on page 149 by Kenta Yamada and Nobuaki Koga, a method to analyze intramolecular interaction energy is applied to an analysis of the P—O bonding in phosphine oxide in conjunction with a newly developed technique to interpret change in electronic structure upon the interaction. The inside cover picture demonstrates, as a result of the analysis, electron-transfer processes in sigma and pi spaces that reorganize the electronic structure with localized three lone pair orbitals on the O atom into the genuine electronic state and that play critical roles in the P—O bond formation.

Nucleotide sequential labels recorded in nucleotide adjacency matrix are used to find local similarities of DNA sequences.

QMC electronic structure calculations are accelerated using GPGPU applied to solids [N = 216 (Si/2 × 2 × 2), 648 (TiO₂/3 × 3 × 3), and 1536 (TiO₂/4 × 4 × 4)]. 30.7 times faster evaluation is achieved by GPU compared with CPU, with a new quasisimultaneous scheme for Monte Carlo updating. The plot shows the computational time (ms) per a Monte Carlo step and corresponding acceleration factors depending on the system size. PbP stands for the conventional particle-by-particle updating scheme.

A GPU-powered parallel k-centers algorithm is able to speedup the clustering of molecular dynamics simulation conformations by up to two orders of magnitude compared to the CPU implementation. For example, it is capable of grouping 250,000 conformations of the Maltose Binding Protein (∼370 residues) into 4000 clusters within 40 s. To achieve this, the code on the GPU is effectively parallelized and the triangle inequality of metric spaces is utilized.

The theory behind Ballcontact, a new program that measures analytically interatomic surface contacts between atoms in a biomolecule, is described. The performance of an environment free energy computed from these contact areas is assessed against a standard solvation free energy. The former outperforms the latter, thereby emphasizing the importance of taking into account the nonpolar contact areas as they complement the information represented by the accessible surface areas.

M06-2X and ωB97X-D combined with aug-cc-pVQZ basis set (either with or without BSSE correction) give rather accurate description of the E_HB and E_vdW in methane hydrate. However, using 6-311++G(2d, 2p) basis set, B97-D without BSSE correction, M06-2X and ωB97X-D with or without BSSE correction are sufficient for describing the E_HB and E_vdW in methane hydrate. Considering both computational cost and accuracy, the recommendations are B97-D, M06-2X and ωB97X-D combined with 6-311++G(2d,2p) basis set without BSSE correction.

Replica-exchange is a powerful simulation method for sampling protein energy landscapes. However, when tackling severely frustrated systems, this method might take a long time to reach equilibrium and find all free energy basins. Here, a simple modification of the exchange method is presented, in which one of the replicas steadily raises or lowers its temperature, while maintaining the correct equilibrium distributions. Results show that the proposed method is twice as fast as the standard method.

The performance of a range of DFT functionals combined in a QM/MM approach is investigated in their ability to reliably provide geometries, electronic distributions and relative energies of a multi-centered open-shell mechanistic intermediate in the mechanism 8R–LOX. While the complex involves three open shell centers, the catalytically relevant arrangement of these electrons leads to the possibility of only having a quartet or sextet state.

The nature of the PO bond in phosphine oxides, which has been extensively studied, is reinvestigated with a recently developed method for analyzing various types of intramolecular interactions. This method provides a more suitable reference state with a target interaction deactivated than existing analysis methods. The results suggest two types of descriptions of the bond, depending on whether the dative PO single bond is present or absent in the reference state.