Journal of Computational Chemistry

doi: 10.1002/jcc.23203pmid: N/A

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.

doi: 10.1002/jcc.23202pmid: N/A

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.

Randić, Milan

doi: 10.1002/jcc.23105pmid: 22949371

We describe a very efficient search for nucleotide alignments, which is analogous to the novel very efficient search for protein alignment. Just as it has been the case with the alignment of proteins, based on 20 × 20 adjacency matrices for amino acids, obtained from a superposition of labeled amino acids adjacency matrices for the proteins considered, one can construct labeled matrices of size 4 × 4, listing adjacencies of nucleotides in DNA sequence. The matrix elements correspond to 16 pairs of adjacent nucleotides. To obtain DNA alignments, one combines information in the corresponding matrices for a pair of DNA nucleotides. Matrices are obtained by insertion of the sequential labels for pairs of nucleotides in the corresponding cells of the 4 × 4 tables. When two such matrices are superimposed, one can identify all segments in two DNA sequences, which are shifted relative to one another by the same amount in either direction, without using trial‐and‐error displacements of the two sequences one relative to the other to find local nucleotide alignments. © 2012 Wiley Periodicals, Inc.

Uejima, Yutaka; Maezono, Ryo

doi: 10.1002/jcc.23106pmid: 22941835

We have accelerated an ab initio quantum Monte Carlo electronic structure calculation using general purpose computing on graphical processing units (GPGPU). The part of the code causing the bottleneck for extended systems is replaced by Compute Unified Device Architecture‐GPGPU subroutine kernels which build up spline basis set expansions of electronic orbital functions at each Monte Carlo step. We have achieved a speedup of a factor of 30 for the bottleneck for a simulation of solid TiO2 with 1536 electrons. To improve the performance with GPGPU we propose a new updating scheme for Monte Carlo sampling, quasi‐simultaneous updating, which is intermediate between configuration‐by‐configuration updating and the widely used particle‐by‐particle updating. The error in the energy due to by the single precision treatment and the new updating scheme is found to be within the required accuracy of ∼10−3 hartree per primitive cell. © 2012 Wiley Periodicals, Inc.

Zhao, Yutong; Sheong, Fu Kit; Sun, Jian; Sander, Pedro; Huang, Xuhui

doi: 10.1002/jcc.23110pmid: 22996151

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.

Mach, Paul; Koehl, Patrice

doi: 10.1002/jcc.23111pmid: 22965816

We propose a new analytical method for detecting and computing contacts between atoms in biomolecules. It is based on the alpha shape theory and proceeds in three steps. First, we compute the weighted Delaunay triangulation of the union of spheres representing the molecule. In the second step, the Delaunay complex is filtered to derive the dual complex. Finally, contacts between spheres are collected. In this approach, two atoms i and j are defined to be in contact if their centers are connected by an edge in the dual complex. The contact areas between atom i and its neighbors are computed based on the caps formed by these neighbors on the surface of i; the total area of all these caps is partitioned according to their spherical Laguerre Voronoi diagram on the surface of i. This method is analytical and its implementation in a new program BallContact is fast and robust. We have used BallContact to study contacts in a database of 1551 high resolution protein structures. We show that with this new definition of atomic contacts, we generate realistic representations of the environments of atoms and residues within a protein. In particular, we establish the importance of nonpolar contact areas that complement the information represented by the accessible surface areas. This new method bears similarity to the tessellation methods used to quantify atomic volumes and contacts, with the advantage that it does not require the presence of explicit solvent molecules if the surface of the protein is to be considered. © 2012 Wiley Periodicals, Inc.

Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

doi: 10.1002/jcc.23112pmid: 22949382

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 (MHs). Using high‐level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange–correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta‐GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long‐range corrected functionals (ωB97X, ωB97, LC‐ωPBE, CAM‐B3LYP, and LC‐TPSS), the newly developed Minnesota class functionals (M06‐L, M06‐HF, M06, and M06‐2X), and the dispersion‐corrected density functional theory (DFT) (DFT‐D) methods (B97‐D, ωB97X‐D, PBE‐TS, PBE‐Grimme, and PW91‐OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH4 and (H2O)6 cluster. M06‐2X is the best among the M06‐Class functionals. The ωB97X‐D outperforms the other DFT‐D methods and is recommended for accurate first‐principles calculations of MH. B97‐D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97‐D, ωB97X‐D, and M06‐2X functional with 6‐311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug‐cc‐pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6‐311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first‐principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc.

Spill, Yannick G.; Bouvier, Guillaume; Nilges, Michael

doi: 10.1002/jcc.23113pmid: 22961200

Replica‐exchange is a powerful simulation method for sampling the basins of a rugged energy landscape. The replica‐exchange method's sampling is efficient because it allows replicas to perform round trips in temperature space, thereby visiting both low and high temperatures in the same simulation. However, replicas have a diffusive walk in temperature space, and the round trip rate decreases significantly with the system size. These drawbacks make convergence of the simulation even more difficult than it already is when bigger systems are tackled. Here, we present a simple modification of the exchange method. In this method, one of the replicas steadily raises or lowers its temperature. We tested the convective replica‐exchange method on three systems of varying complexity: the alanine dipeptide in implicit solvent, the GB1 β‐hairpin in explicit solvent and the Aβ25–35 homotrimer in a coarse grained representation. For the highly frustrated Aβ25–35 homotrimer, the proposed “convective” replica‐exchange method is twice as fast as the standard method. It discovered 24 out of 27 free‐energy basins in less than 500 ns. It also prevented the formation of groups of replicas that usually form on either side of an exchange bottleneck, leading to a more efficient sampling of new energy basins than in the standard method. © 2012 Wiley Periodicals, Inc.

Bushnell, Eric A. C.; Gauld, James W.

doi: 10.1002/jcc.23114pmid: 22949391

The performance of a range density functional theory functionals combined in a quantum mechanical (QM)/molecular mechanical (MM) approach was investigated in their ability to reliably provide geometries, electronic distributions, and relative energies of a multicentered open‐shell mechanistic intermediate in the mechanism 8R–Lipoxygenase. With the use of large QM/MM active site chemical models, the smallest average differences in geometries between the catalytically relevant quartet and sextet complexes were obtained with the B3LYP* functional. Moreover, in the case of the relative energies between 4II and 6II, the use of the B3LYP* functional provided a difference of 0.0 kcal mol–1. However, B3LYP± and B3LYP also predicted differences in energies of less than 1 kcal mol–1. In the case of describing the electronic distribution (i.e., spin density), the B3LYP*, B3LYP, or M06‐L functionals appeared to be the most suitable. Overall, the results obtained suggest that for systems with multiple centers having unpaired electrons, the B3LYP* appears most well rounded to provide reliable geometries, electronic structures, and relative energies. © 2012 Wiley Periodicals, Inc.

Yamada, Kenta; Koga, Nobuaki

doi: 10.1002/jcc.23118pmid: 22987752

We have developed a space‐restricted wave function (SRW) method for the analysis of various types of intramolecular interactions. In this study, we demonstrate the applicability of our SRW method to the analysis of the nature of the PO bond in phosphine oxide (R3PO), one of the hypervalent molecules. An interesting character of this bond has been extensively studied by focusing on the negative hyperconjugation of the O lone pair (nO) with the R3P group. We reinvestigated the nature of the bond in terms of a change in total energy to produce evidence for the validity of our method. The electronic states without the interaction involving three nO orbitals (R3P+−O−) produced by the method were used as reference states in the assessment of the effects of this nO–R3P interaction. The result confirms that this interaction plays an essential role in the nature of the bond and occurs between the nO orbitals and the PR antibonding orbitals, in agreement with previous studies. A molecular orbital (MO)‐pair analysis technique shows that the nO–R3P interaction is decomposed into the negative hyperconjugation and the Pauli repulsion. Considering a reference state where the PO bond is completely broken (R3P2+···O2−) at an interacting distance, PO bond formation is attributed to one σ bond plus two 0.5 π bonds. This is equivalent to three banana bonds highly polarized to the O atom. Consequently, the SRW method suggested improved explanations of the nature of the PO bond. © 2012 Wiley Periodicals, Inc.