Journal of Computational Chemistry

doi: 10.1002/jcc.23959pmid: N/A

On page 1349 (DOI: 10.1002/jcc.23922), Wei Li, Yanli Zeng, Xiaoyan Li, Zheng Sun, and Lingpeng Meng designed the complexes OPH3•••NCX, NCY•••OPH3•••NCX, and OPH3•••NCX•••NCY (X, Y = F, Cl, Br) to investigate the enhancing effects of Y•••O and X•••N halogen bonds on the P•••N Group V σ‐hole interaction. The Y•••O halogen bonds affect the σ‐hole region (decreased density region) outside the phosphorus atom more than the P•••N internuclear region (increased density region outside the nitrogen atom), while it is contrary for the X•••N halogen bonds.

doi: 10.1002/jcc.23960pmid: N/A

The image implies efficient computing with quite high precision for a set of neutral amino acid side‐chain analogues, as well as for 504 small organic molecules. Tomonari Sumi, Ayori Mitsutake, and Yutaka Maruyama estimate the SFE values for several conformations of chignolin protein using the RMDFT functional on page 1359 (DOI: 10.1002/jcc.23942). The background image of HA‐PACS was provided by Center for Computational Sciences, University of Tsukuba

Li, Wei; Zeng, Yanli; Li, Xiaoyan; Sun, Zheng; Meng, Lingpeng

doi: 10.1002/jcc.23922pmid: 25916886

The positive electrostatic potentials (ESP) outside the σ‐hole along the extension of OP bond in OPH3 and the negative ESP outside the nitrogen atom along the extension of the CN bond in NCX could form the Group V σ‐hole interaction OPH3⋯NCX. In this work, the complexes NCY⋯OPH3⋯NCX and OPH3⋯NCX⋯NCY (X, YF, Cl, Br) were designed to investigate the enhancing effects of Y⋯O and X⋯N halogen bonds on the P⋯N Group V σ‐hole interaction. With the addition of Y⋯O halogen bond, the VS, max values outside the σ‐hole region of OPH3 becomes increasingly positive resulting in a stronger and more polarizable P⋯N interaction. With the addition of X⋯N halogen bond, the VS, min values outside the nitrogen atom of NCX becomes increasingly negative, also resulting in a stronger and more polarizable P⋯N interaction. The Y⋯O halogen bonds affect the σ‐hole region (decreased density region) outside the phosphorus atom more than the P⋯N internuclear region (increased density region outside the nitrogen atom), while it is contrary for the X⋯N halogen bonds. © 2015 Wiley Periodicals, Inc.

Sumi, Tomonari; Mitsutake, Ayori; Maruyama, Yutaka

doi: 10.1002/jcc.23942pmid: 26032201

The three‐dimensional reference interaction site model (3D‐RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation‐free‐energy (SFE) for large solute molecules in water. To improve the free‐energy density functional for the SFE of solute molecules, we propose a reference‐modified density functional theory (RMDFT) that is a general theoretical approach to construct the free‐energy density functional systematically. In the RMDFT formulation, hard‐sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction‐site‐model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side‐chain analogues as well as for 504 small organic molecules. © 2015 Wiley Periodicals, Inc.

Huang, Ming; Giese, Timothy J.; York, Darrin M.

doi: 10.1002/jcc.23933pmid: 25943338

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.

Weiss, Alexander K. H.; Ochsenfeld, Christian

doi: 10.1002/jcc.23935pmid: 25974205

This work is focused on the efficient evaluation of the Boys function located at the heart of Coulomb and exchange type electron integrals. Different evaluation strategies for individual orders and arguments of the Boys function are used to achieve a minimal number of floating‐point operations. Based on previous work of other groups, two similar algorithms are derived that are compared based on both accuracy and efficiency: The first algorithm combines the work of Gill et al. (Int. J. Quantum Chem. 1991, 40, 745) and Kazuhiro Ishida (Int. J. Quantum Chem. 1996, 59, 209 and following work), amplifying the benefits of the two strategies. © 2015 Wiley Periodicals, Inc.

Fernandes, Kyle D.; Renison, C. Alicia; Naidoo, Kevin J.

doi: 10.1002/jcc.23936pmid: 25975763

We present here a set of algorithms that completely rewrites the Hartree–Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS‐US, GAMESS‐UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6‐31G Self‐Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one‐ and two‐electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc.

Renison, C. Alicia; Fernandes, Kyle D.; Naidoo, Kevin J.

doi: 10.1002/jcc.23938pmid: 25975864

This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two‐electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one‐ and two‐electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree–Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS‐UK, which uses the efficient Schlegel method for s‐ and l‐orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6‐31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.

Müller, Carsten; Spångberg, Daniel

doi: 10.1002/jcc.23939pmid: 25976008

Combining classical force fields for the Hartree–Fock (HF) part and the method of increments for post‐HF contributions, we calculate the cohesive energy of the ordered and randomly disordered nitrous oxide (N2O) solid. At 0 K, ordered N2O is most favorable with a cohesive energy of −27.7 kJ/mol. At temperatures above 60 K, more disordered structures become compatible and a phase transition to completely disordered N2O is predicted. Comparison with experiment in literature suggests that experimentally prepared N2O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes. © 2015 Wiley Periodicals, Inc.