Journal of Computational Chemistry

Core-shell potential-derived point charges.

Publication Date: 2012 Feb 3 PMID: 22302735
Authors: Tan, J. S. - Boerrigter, S. X. - Scaringe, R. P. - Morris, K. R.
Journal: J Comput Chem

The present work details the development of a core-shell model for the purposes of obtaining potential-derived point charges from the ab initio molecular electrostatic potential. In contrast to atomic point charge models, the core-shell model decomposes all atoms into a core with static charge located at a fixed atomic position and a shell with variable charge and position. The optimization of shell charges and positions is discussed. The core-shell model was found to significantly improve description of the ab initio electrostatic potential when compared to potential-derived net atomic point charge models as well as distributed multipoles with contributions up to atomic quadrupole moments. The core-shell model was found to produce similar results as the Weller-Williams lone-pair model and differences in the implementation of the models are discussed. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model.

Publication Date: 2012 Feb 1 PMID: 22298332
Authors: Kopitz, H. - Cashman, D. A. - Pfeiffer-Marek, S. - Gohlke, H.
Journal: J Comput Chem

The harmonic model is the most popular approximation for estimating the "configurational" entropy of a solute in molecular mechanics/Poisson-Boltzmann solvent accessible surface area (MM/PBSA)-type binding free energy calculations. Here, we investigate the influence of the solvent representation in the harmonic model by comparing estimates of changes in the vibrational entropies for 30 trypsin/ligand complexes on ligand binding. Second derivatives of Amber generalized Born (GB) solvation models are available in the nucleic acid builder code. They allow one to use these models for the calculation of vibrational entropies instead of using a simpler solvation model based on a distance-dependent dielectric (DDD) constant. Estimates of changes in the vibrational entropies obtained with a DDD model are systematically and significantly larger, by on average, 6 kcal mol(-1) (at T = 300 K), than estimates obtained with a GB model and so are more favorable for complex formation. The difference becomes larger the more the vibrational entropy contribution disfavors complex formation, that is, the larger the ligand is (for the complexes considered here). A structural decomposition of the estimates into per-residue contributions reveals polar interactions between the ligand and the surrounding protein, in particular involving charged nitrogens, as a main source of the differences. Snapshots minimized with the DDD model showed a structural deviation from snapshots minimized in explicit water that is larger by, on average, 0.5 A RMSD compared to snapshots that were minimized with GB(HCT) . As experimental vibrational entropies of biomacromolecules are elusive, there is no direct way to establish a solvent model's superiority. Thus, we can only recommend using the GB harmonic model for vibrational entropy calculations based on the reasoning that smaller structural deviations should point to the implicit solvent model that closer approximates the energy landscape of the solute in explicit solvent. (c) 2012 Wiley Periodicals, Inc.

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Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD.

Publication Date: 2012 Feb 1 PMID: 22298319
Authors: Balabin, I. A. - Hu, X. - Beratan, D. N.
Journal: J Comput Chem

We describe the new Pathways plugin for the molecular visualization program visual molecular dynamics. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules, and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU's Not Unix (GNU) public license. (c) 2012 Wiley Periodicals, Inc.

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Reply to comment on the paper "An efficient Algorithm for Energy Gradients and Orbital Optimization in Valence Bond Theory"

Publication Date: 2012 Feb 1 PMID: 22298305
Authors: Wu, W. - Mo, Y.
Journal: J Comput Chem

van Lenthe, Broer, and Rashid made comments on our 2009 paper [Song et al., J. Comput. Chem. 2009, 30, 399] by criticizing that we did not properly reference the work by Broer and Nieuwpoort in 1988 [Broer and Nieuwpoort, Theor. Chim. Acta. 1988, 73, 405], and we favorably compared our valence bond self-consistent field (VBSCF) algorithm with theirs. However, both criticisms are unjustified insignificant. The Broer-Nieuwpoort algorithm, properly cited in our paper, is for the evaluations of matrix elements between determinants of nonorthogonal orbitals. Stating that this algorithm "can be used for an orbital optimization" afterwards [van Lenthe et al., submitted] is not a plausible way to require more credits or even criticize others. While we stand by our statement that our algorithms scales at O(m(4) ) and van Lenthe et al.'s approximate Newton Raphson algorithm scales at O(mN(5) ) (here m and N are the numbers of basis functions and electrons), as we discussed in our original paper, it becomes obvious that any strict comparison among different algorithms is difficult, unproductive, and counteractive. (c) 2012 Wiley Periodicals, Inc.

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Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models.

Publication Date: 2012 Feb 1 PMID: 22298285
Authors: Bezkorovaynaya, O. - Lukyanov, A. - Kremer, K. - Peter, C.
Journal: J Comput Chem

A bottom-up coarse-graining procedure for peptides in aqueous solution is presented, where the interactions in the coarse-grained (CG) model are determined such that the CG peptide samples conformations according to a high-resolution (atomistic) model. It is shown that important aspects of conformational sampling, such as correlated degrees of freedom (DOF) which play an important role in secondary structure formation, can be reproduced in the CG description. In some cases, microscopic structural/conformational details are lost in the coarse-graining process. We show that these "lost" properties can be recovered in a backmapping procedure which reintroduces atomistic DOF into CG structures - as long as the overall conformational sampling of the molecule is correctly represented in the CG level of resolution. Thus, it is possible to link an existing all-atom model of a biomolecular system with a CG description such that after inverse mapping one can recover structures at high resolution with the correctly sampled (according to the atomistic model) conformational properties. (c) 2012 Wiley Periodicals, Inc.

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Fourier transform general formula for systematic potentials.

Publication Date: 2012 Feb 1 PMID: 22298234
Authors: Ishida, K.
Journal: J Comput Chem

For calculating molecular integrals of systematic potentials, a three-dimensional (3D) Fourier transform general formula can be derived, by the use of the Abel summation method. The present general formula contains all 3D Fourier transform formulas which are well known as Bethe-Salpeter formulas (Bethe and Salpeter, Handbuch der Physik, Bd. XXXV, 1957) as special cases. It is shown that, in several of the Bethe-Salpeter formulas, the integral does not converge in the meaning of the Riemann integral but converges in the meaning of a hyper function as the Schwartz distribution. For showing an effectiveness of the present general formula, the convergence condition of molecular integrals is derived generally for all of the present potentials. It is found that molecular integrals can be converged in the meaning of the Riemann integral for the present potentials, except for those for extra super singular potentials. It is also found that the convergence condition of molecular integrals over the Slater-type orbitals is exactly the same as that of the corresponding integrals over the Gaussian-type orbitals for the present systematic potentials. For showing more effectiveness, the molecular integral over the gauge-including atomic orbitals is derived for the magnetic dipole-same-dipole interaction. (c) 2012 Wiley Periodicals, Inc.

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Structural and electronic property responses to the arsenic/phosphorus exchange in GC-related DNA of the B-form.

Publication Date: 2012 Feb 1 PMID: 22298190
Authors: Gu, J. - Wang, J. - Xie, Y. - Leszczynski, J. - Schaefer, H. F. 3rd
Journal: J Comput Chem

The suggestion that phosphorus/arsenic replacement in DNA can play a role in living things has generated great controversy (Wolfe-Simon et al., Science 2011, 332, 1163). Examined here theoretically are substitution effects on Watson-Crick base pairing and base stacking patterns in realistic DNA subunits. Using duplex DNA models deoxyguanylyl-3',5'-deoxycytidine ([dGpdC](2) ) and deoxycytidyly-3',5'-deoxyguanosine ([dCpdG)](2) ), this research reveals that the geometric variations caused by the As/P exchange are small and are limited to the phosphate/arsenate groups. As/P replacement leads to alterations of approximately 0.15 A in P/AsO bond lengths and less than 1.5 degrees variations in OP/AsO angles. The Watson-Crick base pairing and base stacking patterns are independent of the As/P replacement. The vertical electron detachment energies are also largely unaffected. However, the electron capture ability of the DNA units is improved by the As substitution. The arsenate is found to be the main electron acceptor in As-DNA. The results are relevant to the possible existence of viable As-DNAs, at least in the guanine and cytosine (GC)-related B-form DNA. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Liquid properties of dimethyl ether from molecular dynamics simulations using Ab Initio force fields.

Publication Date: 2012 Jan 25 PMID: 22278976
Authors: Wang, S. B. - Li, A. H. - Chao, S. D.
Journal: J Comput Chem

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Moller-Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3-site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom-wise radial distribution functions, the self-diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori. (c) 2012 Wiley Periodicals, Inc.

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Computation of the binding affinities of catechol-O-methyltransferase inhibitors: Multisubstate relative free energy calculations.

Publication Date: 2012 Jan 25 PMID: 22278964
Authors: Nuno Palma, P. - Joao Bonifacio, M. - Isabel Loureiro, A. - Soares-da-Silva, P.
Journal: J Comput Chem

Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein-ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low-energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol-O-methyltransferase and BIA 9-1067, a newly developed tight-binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high-binding affinity (K(d) in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O-methylated product. By comparing the experimental catalytic rate (k(cat) ) and the estimated dissociation rate (k(off) ) constants of the enzyme-inhibitor complex, one can conclude that the observed inhibition potency (K(i) ) is primarily dependent on the catalytic rate constant of the inhibitor's O-methylation, rather than the rate constant of dissociation of the complex. (c) 2012 Wiley Periodicals, Inc.

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Mixed monte carlo/molecular dynamics simulations in explicit solvent.

Publication Date: 2012 Jan 25 PMID: 22278955
Authors: Ribeiro, A. A. - de Alencastro, R. B.
Journal: J Comput Chem

A mixed Monte Carlo/Molecular Dynamics method using the trial moves for peptide backbone sampling known as Concerted Rotations with Angles was implemented. The algorithm was used to study polyalanine systems. Equivalent results to conventional Molecular Dynamics were obtained for simulations of Ala(6) in implicit solvent. To test the efficiency of the implemented method, several 150 ns simulations of Ala(12) in explicit water were performed. The results show that the present method yields significantly faster formation of secondary structure than the conventional Molecular Dynamics simulations. This opens the possibility to selectively sample alanine-rich regions of larger peptides or proteins. It remains to be established whether hydrophilic amino acid residues can be successfully treated with the present methodology. (c) 2012 Wiley Periodicals, Inc.

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On the efficiency of VBSCF algorithms, a comment on "An efficient algorithm for energy gradients and orbital optimization in valence bond theory"

Publication Date: 2012 Jan 25 PMID: 22278948
Authors: van Lenthe, J. H. - Broer-Braam, H. B. - Rashid, Z.
Journal: J Comput Chem

We comment on the paper [Song et al., J. Comput. Chem. 2009, 30, 399]. and discuss the efficiency of the orbital optimization and gradient evaluation in the Valence Bond Self Consistent Field (VBSCF) method. We note that Song et al. neglect to properly reference Broer et al., who published an algorithm [Broer and Nieuwpoort, Theor. Chim. Acta 1988, 73, 405] to use a Fock matrix to compute a matrix element between two different determinants, which can be used for an orbital optimization. Further, Song et al. publish a misleading comparison with our VBSCF algorithm [Dijkstra and van Lenthe, J. Chem. Phys. 2000, 113, 2100; van Lenthe et al., Mol. Phys. 1991, 73, 1159] to enable them to favorably compare their algorithm with ours. We give detail timings in terms of different orbital types in the calculation and actual timings for the example cases. (c) 2012 Wiley Periodicals, Inc.

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GMCT : A Monte Carlo simulation package for macromolecular receptors.

Publication Date: 2012 Jan 25 PMID: 22278916
Authors: Ullmann, R. T. - Ullmann, G. M.
Journal: J Comput Chem

Generalized Monte Carlo titration (GMCT) is a versatile suite of computer programs for the efficient simulation of complex macromolecular receptor systems as for example proteins. The computational model of the system is based on a microstate description of the receptor and an average description of its surroundings in terms of chemical potentials. The receptor can be modeled in great detail including conformational flexibility and many binding sites with multiple different forms that can bind different ligand types. Membrane embedded systems can be modeled including electrochemical potential gradients. Overall properties of the receptor as well as properties of individual sites can be studied with a variety of different Monte Carlo (MC) simulation methods. Metropolis MC, Wang-Landau MC and efficient free energy calculation methods are included. GMCT is distributed as free open source software at www.bisb.uni-bayreuth.de under the terms of the GNU Affero General Public License. (c) 2012 Wiley Periodicals, Inc.

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thermocalc - A poor man's approach to computational thermochemistry.

Publication Date: 2012 Jan 25 PMID: 22278903
Authors: Hellweg, A. - Diedenhofen, M. - Huniar, U.
Journal: J Comput Chem

We present thermocalc, a Perl module to perform the automated calculation of atomization energies and heats of formation for lists of molecules. The methods used are based on density functional theory and second-order perturbation theory to ensure that data sets of medium sized to large molecules can be run at reasonable throughput rates. The quantum chemical calculations are performed using the program package TURBOMOLE in a three-step protocol. In a first step, a pre-optimization of the structure and a zero-point energy calculation are performed. As second step, a geometry optimization is being carried out, and the last step is a single point energy calculation. The level of theory used in the different steps can be modified by the user to allow for customized protocols. The performance of example protocols is investigated on different test sets of molecules. In the course of this work, a simple, but efficient one-parameter correction term based on the shared electron numbers has been developed, which reduces the error of calculated heats of formation significantly. (c) 2012 Wiley Periodicals, Inc.

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MoleculaRnetworks: An integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation.

Publication Date: 2012 Jan 25 PMID: 22278855
Authors: Mooney, B. L. - Corrales, L. R. - Clark, A. E.
Journal: J Comput Chem

This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations. (c) 2012 Wiley Periodicals, Inc.

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Potential of mean force of water-proton bath and molecular dynamic simulation of proteins at constant pH.

Publication Date: 2012 Jan 25 PMID: 22278814
Authors: Vorobjev, Y. N.
Journal: J Comput Chem

An advanced implicit solvent model of water-proton bath for protein simulations at constant pH is presented. The implicit water-proton bath model approximates the potential of mean force of a protein in water solvent in a presence of hydrogen ions. Accurate and fast computational implementation of the implicit water-proton bath model is developed using the continuum electrostatic Poisson equation model for calculation of ionization equilibrium and the corrected MSR6 generalized Born model for calculation of the electrostatic atom-atom interactions and forces. Molecular dynamics (MD) method for protein simulation in the potential of mean force of water-proton bath is developed and tested on three proteins. The model allows to run MD simulations of proteins at constant pH, to calculate pH-dependent properties and free energies of protein conformations. The obtained results indicate that the developed implicit model of water-proton bath provides an efficient way to study thermodynamics of biomolecular systems as a function of pH, pH-dependent ionization-conformation coupling, and proton transfer events. (c) 2012 Wiley Periodicals, Inc.

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Evaluation of the electron momentum density of crystalline systems from ab initio linear combination of atomic orbitals calculations.

Publication Date: 2012 Jan 25 PMID: 22278778
Authors: Erba, A. - Pisani, C.
Journal: J Comput Chem

Alternative techniques are presented for the evaluation of the electron momentum density (EMD) of crystalline systems from ab initio linear combination of atomic-orbitals calculations performed in the frame of one-electron self-consistent-field Hamiltonians. Their respective merits and drawbacks are analyzed with reference to two periodic systems with very different electronic features: the fully covalent crystalline silicon and the ionic lithium fluoride. Beyond one-electron Hamiltonians, a post-Hartree-Fock correction to the EMD of crystalline materials is also illustrated in the case of lithium fluoride. (c) 2012 Wiley Periodicals, Inc.

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Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks.

Publication Date: 2012 Jan 25 PMID: 22278759
Authors: Zhao, Y. - De Nicola, A. - Kawakatsu, T. - Milano, G.
Journal: J Comput Chem

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self-consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle-field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD-SCF program profiles, serial MD-SCF and parallel MD-SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. (c) 2012 Wiley Periodicals, Inc.

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Chemically modified fullerene derivatives as photosensitizers in photodynamic therapy: A first-principles study.

Publication Date: 2012 Jan 18 PMID: 22253075
Authors: Zhou, C. H. - Zhao, X.
Journal: J Comput Chem

The first-principles density functional theory (DFT) and its time-dependent approach (TD-DFT) are used to characterize the electronic structures and optical spectra properties of five chemically modified fullerenes. It is revealed that the metal fullerene derivatives possess not only stronger absorption bands in visible light regions than organically modified fullerene but also the large energy gaps (DeltaE(S-T) > 0.98 eV) between the singlet ground state and the triplet state, which imply their significant aspect of potential candidates as a photosensitizer. We have found that a new metal-containing bisfullerene complexes (Pt(C(60) )(2) ), with the extended conjugated pi-electrons, much degenerate orbitals and a uniform electrostatic potential surface, behave more pre-eminent photosensitizing properties than other examined fullerene derivatives. (c) 2012 Wiley Periodicals, Inc.

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Voids and necks in liquid ammonia and their roles in diffusion of ions of varying size.

Publication Date: 2012 Jan 18 PMID: 22253059
Authors: Chakraborty, D. - Chandra, A.
Journal: J Comput Chem

Voids in a medium are defined as the regions that are located outside an appropriately defined occupied space associated with molecules. Dynamical properties like diffusion can be related to the structure and distribution of voids present in the medium. This work deals with an analysis of voids and diffusion in liquid ammonia. The analysis of voids is done by the construction of Voronoi polyhedra and Delaunay tessellation. We have performed a series of molecular dynamics simulations of monovalent cations and anions of varying size in liquid ammonia at two different temperatures of 210 and 240 K to investigate the effects of ion size on the diffusion of ions and roles of voids in determining the observed diffusion behavior. It is found that with the increase of ion size, the diffusion coefficients first increase and then pass through a maximum similar to the behavior observed earlier for diffusion in water. The observed results are explained in terms of passage through voids and necks that are present in liquid ammonia. (c) 2012 Wiley Periodicals, Inc.

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"First-Principles" kinetic monte carlo simulations revisited: CO oxidation over RuO(2) (110).

Publication Date: 2012 Jan 18 PMID: 22253041
Authors: Hess, F. - Farkas, A. - Seitsonen, A. P. - Over, H.
Journal: J Comput Chem

First principles-based kinetic Monte Carlo (kMC) simulations are performed for the CO oxidation on RuO(2) (110) under steady-state reaction conditions. The simulations include a set of elementary reaction steps with activation energies taken from three different ab initio density functional theory studies. Critical comparison of the simulation results reveals that already small variations in the activation energies lead to distinctly different reaction scenarios on the surface, even to the point where the dominating elementary reaction step is substituted by another one. For a critical assessment of the chosen energy parameters, it is not sufficient to compare kMC simulations only to experimental turnover frequency (TOF) as a function of the reactant feed ratio. More appropriate benchmarks for kMC simulations are the actual distribution of reactants on the catalyst's surface during steady-state reaction, as determined by in situ infrared spectroscopy and in situ scanning tunneling microscopy, and the temperature dependence of TOF in the from of Arrhenius plots. (c) 2012 Wiley Periodicals, Inc.

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Electronic structure and thermochemical properties of silicon-doped lithium clusters Li(n) Si(0/+) , n = 1-8: New insights on their stability.

Publication Date: 2012 Jan 13 PMID: 22241620
Authors: Tai, T. B. - Nguyen, M. T.
Journal: J Comput Chem

A theoretical investigation on small silicon-doped lithium clusters Li(n) Si with n = 1-8, in both neutral and cationic states is performed using the high accuracy CCSD(T)/complete basis set (CBS) method. Location of the global minima is carried out using a stochastic search method and the growth pattern of the clusters emerges as follows: (i) the species Li(n) Si with n
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Theoretical investigation on the transportation behavior of molecular wires with redox reaction.

Publication Date: 2012 Jan 13 PMID: 22241601
Authors: Li, J. - Zhao, Z. - Yu, C. - Wang, H. - Zhao, J.
Journal: J Comput Chem

A series of model molecules [sequential quinone (Q) or hydroquinone (HQ) rings connected by triple bonds] as molecular wires have been investigated by using density functional theory combined with nonequilibrium Green's function method. The results show that the system has two discrete conductance states: a low-conductance state with Q form, and a high-conductance state with HQ form. The systematic investigations have suggested that more Q/HQ pairs in the system may improve the on/off ratio, though long molecule reduces the conductance of the molecular junction. The switch mechanism has been explained via molecular electronic structure as well as transmission spectra. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Highlighting and trying to overcome a serious drawback with qspr studies; data collection in different experimental conditions (mixed-QSPR).

Publication Date: 2012 Jan 13 PMID: 22241584
Authors: Beheshti, A. - Riahi, S. - Ganjali, M. R. - Norouzi, P.
Journal: J Comput Chem

The experimental conditions in quantitative structure-property relationship (QSPR) studies need to be the same for each dataset in case one wishes to relate the property, only to the structure. This major drawback limits QSPR studies due to two reasons: (1) Gathering of physicochemical data obtained under the same experimental condition is difficult. (2) The obtained model is just useful to predict the physicochemical properties under the specific experimental condition. In this article, we report an attempt to highlight the shortcoming of QSPR studies for a property that was measured under different experimental conditions. In addition, we reveal inadequacies that correlating the fluorescence properties and the descriptor of the solvent has. These defects are eventually removed by taking into account the solvent-solute interactions in descriptor calculations. Quantum chemical calculations (HF/6-31G*) were carried out to optimize geometry and calculate the structural descriptors. The genetic algorithm combined with multiple linear regression method was utilized to construct the linear QSPR models. Because of the better nonlinear relationship between the quantum yield of fluorescence and structural descriptors in comparison with those of a linear relationship, support vector machine was used to construct the nonlinear QSPR model. Result analyses demonstrated that the proposed models meet our goal. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Recent performance improvements to the DFT and TDDFT in GAMESS.

Publication Date: 2012 Jan 13 PMID: 22241553
Authors: Lasinski, M. E. - Romero, N. A. - Brown, S. T. - Blaudeau, J. P.
Journal: J Comput Chem

The general atomic and molecular electronic structure system (GAMESS) is a quantum chemistry package used in the first-principles modeling of complex molecular systems using density functional theory (DFT) as well as a number of other post-Hartree-Fock methods. Both DFT and time-dependent DFT (TDDFT) are of particular interest to the materials modeling community. Millions of CPU hours per year are expended by GAMESS calculations on high-performance computing systems; any substantial reduction in the time-to-solution for these calculations represents a significant saving in CPU hours. As part of this work, three areas for improvement were identified: (1) the exchange-correlation (XC) integration grid, (2) profiling and optimization of the DFT code, and (3) TDDFT parallelization. We summarize the work performed in these task areas and present the resulting performance improvement. These software enhancements are available in 12JAN2009R3 or later versions of GAMESS. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors.

Publication Date: 2012 Jan 13 PMID: 22241532
Authors: Barbault, F. - Maurel, F.
Journal: J Comput Chem

Urokinase plasminogen activator (uPA) is an enzyme involved in cancer growth and metastasis. Therefore, the design of inhibitors of uPA is of high therapeutic value, and several chemical families have been explored, even if none has still emerged, emphasizing the need of a rationalized approach. This work represents a complete computational study of uPA complexed with five inhibitors, which present weak similarities. Molecular dynamics simulations in explicit solvent were conducted, and structural analyses, along with molecular mechanics (MM)/Poisson-Boltzmann surface area free energies estimations, yield precious structure-activity relationships of these inhibitors. Besides, we realized supplemental QM/MM computations that improved drastically the quality of our models providing original information on the hydrogen bonds and charge transfer effects, which are, most often, neglected in other studies. We suggest that these simulations and analyses could be reproduced for other systems involving protein/ligand molecular recognitions. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Density functional study of S(N) 2 substitution reactions for CH(3) Cl + CX(1) X(2*-) (X(1) X(2) = HH, HF, HCl, HBr, HI, FF, ClCl, BrBr, and II).

Publication Date: 2012 Jan 13 PMID: 22241464
Authors: Liang, J. X. - Geng, Z. Y. - Wang, Y. C.
Journal: J Comput Chem

A systematic investigation on the S(N) 2 displacement reactions of nine carbene radical anions toward the substrate CH(3) Cl has been theoretically carried out using the popular density functional theory functional BHandHLYP level with different basis sets 6-31+G (d, p)/relativistic effective core potential (RECP), 6-311++G (d, p)/RECP, and aug-cc-pVTZ/RECP. The studied models are CX(1) X(2*-) + CH(3) Cl --> X(2) X(1) CH(3) C(*) + Cl(-) , with CX(1) X(2*-) = CH(2) (*-) , CHF(*-) , CHCl(*-) , CHBr(*-) , CHI(*-) , CF(2) (*-) , CCl(2) (*-) , CBr(2) (*-) , and CI(2) (*-) . The main results are proposed as follows: (a) Based on natural bond orbital (NBO), proton affinity (PA), and ionization energy (IE) analysis, reactant CH(2) (*-) should be a strongest base among the anion-containing species (CX(1) X(2*-) ) and so more favorable nucleophile. (b) Regardless of frontside attacking pathway or backside one, the S(N) 2 reaction starts at an identical precomplex whose formation with no barrier. (c) The back-S(N) 2 pathway is much more preferred than the front-S(N) 2 one in terms of the energy gaps [DeltaE cent not equal(front)-DeltaE cent not equal(back)], steric demand, NBO population analysis. Thus, the back-S(N) 2 reaction was discussed in detail. On the one hand, based on the energy barriers (DeltaE cent not equal and DeltaE ovr not equal) analysis, we have strongly affirmed that the stabilization of back attacking transition states (b-TSs) presents increase in the order: b-TS-CI(2) < b-TS-CBr(2) < b-TS-CCl(2) < b-TS-CHI < b-TS-CHBr < b-TS-CHCl < b-TS-CF(2) < b-TS-CHF < b-TS-CH(2) . On the other hand, depended on discussions of the correlations of DeltaE ovr not equal with influence factors (PA, IE, bond order, and DeltaE def not equal), we have explored how and to what extent they affect the reactions. Moreover, we have predicted that the less size of substitution (alpha-atom) required for the gas-phase reaction with alpha-nucleophile is related to the alpha-effect and estimated that the reaction with the stronger PA nucleophile, holding the lighter substituted atom, corresponds to the greater exothermicity given out from reactants to products. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Interactive quantum chemistry: A divide-and-conquer ASED-MO method.

Publication Date: 2012 Jan 7 PMID: 22228556
Authors: Bosson, M. - Richard, C. - Plet, A. - Grudinin, S. - Redon, S.
Journal: J Comput Chem

We present interactive quantum chemistry simulation at the atom superposition and electron delocalization molecular orbital (ASED-MO) level of theory. Our method is based on the divide-and-conquer (D&C) approach, which we show is accurate and efficient for this non-self-consistent semiempirical theory. The method has a linear complexity in the number of atoms, scales well with the number of cores, and has a small prefactor. The time cost is completely controllable, as all steps are performed with direct algorithms, i.e., no iterative schemes are used. We discuss the errors induced by the D&C approach, first empirically on a few examples, and then via a theoretical study of two toy models that can be analytically solved for any number of atoms. Thanks to the precision and speed of the D&C approach, we are able to demonstrate interactive quantum chemistry simulations for systems up to a few hundred atoms on a current multicore desktop computer. When drawing and editing molecular systems, interactive simulations provide immediate, intuitive feedback on chemical structures. As the number of cores on personal computers increases, and larger and larger systems can be dealt with, we believe such interactive simulations-even at lower levels of theory-should thus prove most useful to effectively understand, design and prototype molecules, devices and materials. (c) 2012 Wiley Periodicals, Inc.

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Seminumerical calculation of the Hartree-Fock exchange matrix: Application to two-component procedures and efficient evaluation of local hybrid density functionals.

Publication Date: 2012 Jan 7 PMID: 22228538
Authors: Plessow, P. - Weigend, F.
Journal: J Comput Chem

A two-component extension of the seminumerical procedure for the calculation of the Hartree-Fock (HF) exchange matrix recently presented by Neese et al. (Chem Phys 2009, 356, 98) was implemented into the program system TURBOMOLE. It is demonstrated that this allows for efficient self-consistent treatment of spin-orbit coupling at HF and hybrid density functional theory level. One-component HF calculations were performed to study the accuracy of integration grids and the exploitation of the molecular point group symmetry. The efficiency was tested, and for one-component calculations compared to the implementation realized by Neese. It was further demonstrated that local hybrid density functionals can be evaluated with this technique. The "prototype" of this class of functionals, Lh-BLYP, was applied to an organic molecule with more than 150 atoms. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Dispersive interactions in water bilayers at metallic surfaces: A comparison of the PBE and RPBE functional including semiempirical dispersion corrections.

Publication Date: 2012 Jan 7 PMID: 22228509
Authors: Tonigold, K. - Gross, A.
Journal: J Comput Chem

The accuracy and reliability of the density functional theory (DFT)-D approach to account for dispersion effects in first-principles studies of water-metal interfaces has been addressed by studying several water-metal systems. In addition to performing periodic DFT calculations for semi-infinite substrates using the popular PBE and RPBE functionals, the water dimer and water-metal atom systems have also been treated by coupled-cluster calculations. We show that indeed semiempirical dispersion correction schemes can be used to yield thermodynamically stable water bilayers at surfaces. However, the actual density functional needs to be chosen carefully. Whereas the dispersion-corrected RPBE functional yields a good description of both the water-water and the water-metal interaction, the dispersion-corrected PBE functional overestimates the energies of both systems. In contrast thereto, the adsorption distances predicted by the PBE functional is hardly changed due to the additional dispersion interaction, explaining the good performance of previous DFT-PBE studies of water-metal systems. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations.

Publication Date: 2012 Jan 7 PMID: 22228486
Authors: Kaukonen, M. - Gulans, A. - Havu, P. - Kauppinen, E.
Journal: J Comput Chem

Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution.

Publication Date: 2012 Jan 7 PMID: 22228455
Authors: Hansen, N. - Dolenc, J. - Knecht, M. - Riniker, S. - van Gunsteren, W. F.
Journal: J Comput Chem

The performance of enveloping distribution sampling (EDS) simulations to estimate free enthalpy differences associated with seven alchemical transformations of A-T into G-C base pairs at the netropsin binding site in the minor groove of a 13-base pair DNA duplex in aqueous solution is evaluated. It is demonstrated that sufficient sampling can be achieved with a two-state EDS Hamiltonian even for large perturbations such as the simultaneous transformation of up to three A-T into three G-C base pairs. The two parameters required to define the EDS reference state Hamiltonian are obtained automatically using a modified version of a scheme presented in earlier work. The sensitivity of the configurational sampling to a variation of these parameters is investigated in detail. Although for relatively small perturbations, that is, one base pair, the free enthalpy estimate depends only weakly on the EDS parameters, the sensitivity is stronger for the largest perturbation. Yet, EDS offers various convenient measures to evaluate the degree of sampling and thus the reliability of the free enthalpy estimate and appears to be an efficient alternative to the conventional thermodynamic integration methodology to obtain free energy differences for molecular systems. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias.

Publication Date: 2012 Jan 6 PMID: 22223194
Authors: Koppole, S. - Schaefer, M.
Journal: J Comput Chem

We introduce PMF*, a novel potential of mean force (PMF) for the Ramachandran varphi/Psi dihedral plot of the 20 standard amino acids and assess its relevance to the conformation of polypeptides by scoring structures in the protein data bank and decoy datasets. The new energy function is a linear combination of the conventional, unreferenced PMF and the DeltaPMF relative to the free energy of all amino acids in the parameterization set of structures, effectively removing their respective biases toward alpha-helix and beta-strand. It is shown that low-resolution crystal structures, NMR structures, and theoretical models have on average significantly higher energies than high-resolution crystal structures; also PMF* is more discriminative for structure quality than the individual PMF and DeltaPMF energy functions. PMF* may be well suited for use as a restraint energy term in the refinement of experimental structures and theoretical models. (c) 2012 Wiley Periodicals, Inc.

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Mechanisms of the cascade synthesis of substituted 4-amino-1,2,4-triazol-3-one from huisgen zwitterion and aldehyde hydrazone: A DFT study.

Publication Date: 2012 Jan 6 PMID: 22223156
Authors: Zhang, W. - Zhu, Y. - Wei, D. - Tang, M.
Journal: J Comput Chem

The detailed reaction mechanisms of the title reaction are shed light on by using the density functional theory (DFT). The calculated results have demonstrated that the whole reaction takes place via four processes (processes (I-IV)), among which, three possible reaction mechanisms are proposed for process (II) (channels 1-3) and two for process (IV) (channels 4-5). According to our calculated results, channel 3 and channel 5 are verified to be most energetically favorable. As interpreted in the text, in process (II), the proton transfer should be performed prior to the nucleophilic attack, and the AA-Type transfer strategy is more likely to occur. The global reactivity index (GRI) and frontier molecular orbital (FMO) analyses of the aldehyde hydrazone have further supported the AA-Type mechanism. In process (IV), however, the titled product has been demonstrated to be formed by the synergetic elimination of two protons via a six-membered ring transition state. Taking an integrated view, the highest energy barrier for the whole reaction along the most favorable pathway is 32.19 kcal/mol, which is consistent with the mild thermal experimental conditions. More interestingly, the qualified mechanisms in this work have given a perfect explanation to the optimal reactants molar ratio of highest yields (R1/R2/R3 = 2/1/1) employed in the experiment. (c) 2012 Wiley Periodicals, Inc.

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Ab initio calculation of structure and transport properties of He...X (X = Zn, Cd, Hg) van der Waals complexes.

Publication Date: 2012 Jan 6 PMID: 22223123
Authors: Sladek, V. - Lukes, V. - Ilcin, M. - Biskupic, S.
Journal: J Comput Chem

The ground state ab initio CCSD(T) potential curves using various basis sets (aug-cc-pVXZ-PP (X = D, T, Q, 5)) is obtained for the dimers of helium with IIb group metals. The effect of the position of the (mid) bond-functions on the interaction energy is discussed. A Symmetry Adapted Perturbation Theory decomposition of the interaction energy is provided and the trends in the dimer stabilizing and destabilizing contributions are depicted. The spline fitted potential curves are applied together with rigorous statistical formulae in order to obtain the transport coefficients (viscosity coefficients, diffusion coefficients) and the second virial coefficient both for pure constituents and mixtures. The obtained theoretical results are compared with available experimental data. Molecular dynamics is used to obtain reliable values of the diffusion coefficients for all the systems under study. (c) 2012 Wiley Periodicals, Inc.

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Two-step evaluation of binding energy and potential energy surface of van der Waals complexes.

Publication Date: 2012 Jan 6 PMID: 22223065
Authors: Deshmukh, M. M. - Sakaki, S.
Journal: J Comput Chem

Evaluation of intermolecular distance and binding energy (BE) of van der Waals complex/cluster at ab initio level of theory is computationally demanding when many monomers are involved. Starting from MP2 energy, we reached a two-step evaluation method of BE of van der Waals complex/cluster through reasonable approximations; $ {\rm BE} = {\rm BE(HF)} +\sum _{{{\rm M}{i}}>{{\rm M}j}}\{{\rm BE}_{{{\rm M}i}-{{\rm M}j}}({\rm MP2} \ {\rm or} \ {\rm MP}2.5)-{\rm BE}_{{{\rm M}i}-{{M}j}}({\rm HF})\} $ where HF represents the Hartree-Fock calculation, Mi, Mj, etc. are interacting monomers, and MP2.5 represents the arithmetic mean of MP2 and MP3. The first term is the usual BE of the complex/cluster evaluated at the HF level. The second term is the sum of the difference in two-body BE between the correlated and HF levels of theory. This equation was applied to various van der Waals complexes consisting of up-to-four monomers at MP2 and MP2.5 levels of theory. We found that this method is capable of providing precise estimate of the BE and reproducing well the potential energy surface of van der Waals complexes/clusters; the maximum error of the BE is less than 1 kcal/mol and 1% in most cases except for several limited cases. The origins of error in these cases are discussed in detail. (c) 2012 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Thermodynamics and kinetics of large-time-step molecular dynamics.

Publication Date: 2012 Feb 15 PMID: 22180257
Authors: Rao, F. - Spichty, M.
Journal: J Comput Chem

Molecular dynamics (MD) simulations provide essential information about the thermodynamics and kinetics of proteins. Technological advances in both hardware and algorithms have seen this method accessing timescales that used to be unreachable only few years ago. The quest to simulate slow, biologically relevant macromolecular conformational changes, is still open. Here, we present an approximate approach to increase the speed of MD simulations by a factor of approximately 4.5. This is achieved by using a large integration time step of 7 fs, in combination with frozen covalent bonds and look-up tables for nonbonded interactions of the solvent. Extensive atomistic MD simulations for a flexible peptide in water show that the approach reproduces the peptide's equilibrium conformational changes, preserving the essential properties of both thermodynamics and kinetics. Comparison of this approximate method with state-of-the-art implicit solvation simulations indicates that the former provides a better description of the underlying free-energy surface. Finally, simulations of a 33-residue peptide show that these fast MD settings are readily applicable to investigate biologically relevant systems. (c) 2011 Wiley Periodicals, Inc.

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On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations.

Publication Date: 2012 Feb 5 PMID: 22180225
Authors: Meier, K. - Thiel, W. - van Gunsteren, W. F.
Journal: J Comput Chem

During the past years, the use of combined quantum-classical, QM/MM, methods for the study of complex biomolecular processes, such as enzymatic reactions and photocycles, has increased considerably. The quality of the results obtained from QM/MM calculations is largely dependent on five aspects to be considered when setting up a molecular model: the QM Hamiltonian, the MM Hamiltonian or force field, the boundary and coupling between the QM and MM regions, the size of the QM region and the boundary condition for the MM region. In this study, we systematically investigate the influence of a variation of the molecular mechanics force field and the size of the QM region in QM/MM MD simulations on properties of the photoactive part of the blue light photoreceptor protein AppA. For comparison, we additionally performed classical MD simulations and studied the effect of a variation of the type of spatial boundary condition. The classical boundary conditions and the force field used in a QM/MM MD simulation are shown to have non-neglegible effects upon the structural and energetic properties of the protein which makes it advisable to minimize computational artifacts in QM/MM MD simulations by application of periodic boundary conditions and a thermodynamically calibrated force field. A comparison of the structural and energetic properties of MD simulations starting from two alternative, different X-ray structures for the blue light utilizing flavin protein in its dark state indicates a slight preference of the two force fields used for the so-called Anderson structure over the Jung structure. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory.

Publication Date: 2012 Feb 15 PMID: 22173959
Authors: Dong, H. - Chen, B. Z. - Huang, M. B. - Lindh, R.
Journal: J Comput Chem

The Bergman cyclizations of the enediyne and its four N-substituted analogs [(Z)-pent-2-en-4-ynenitrile, 3-azahex-3-en-1,5-diyne, malenotrile, and 3,4-azahex-3-en-1,5-diyne] have been studied using the complete active space self-consistent field and multiconfigurational second-order perturbation theory methods in conjunction with the atomic natural orbital basis sets. The geometries and energies of the reactants, transition states, and products along both the S(0) (the ground state) and T(1) (the lowest-lying triplet state) potential energy surfaces (PESs) were calculated. The calculated geometries are in good agreement with the available experimental data. The distance between two terminal carbons in enediyne, which was considered as an important parameter governing the Bergman cyclization, was predicted to be 4.319 A, in agreement with the experimental value of 4.321 A. Our calculations indicate that the replacements of the terminal C atom(s) or the middle C atom(s) in the CC bond by the N atom(s) increase or decrease the energy barrier values, respectively. There exist stable ring biradical products on the T(1) PESs for the five reactions. However, on the S(0) PESs the ring biradical products exist only for the reactions of enediyne, (Z)-pent-2-en-4-ynenitrile, and 3-azahex-3-en-1,5-diyne. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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A reliable and efficient first principles-based method for predicting pK(a) values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and pK(a) values predicted more accurately?

Publication Date: 2012 Feb 15 PMID: 22173939
Authors: Zhang, S.
Journal: J Comput Chem

A popular method for predicting pK(a) values for organic molecules in aqueous solution is to establish empirical linear least-squares fits between calculated deprotonation energies and known experimental pK(a) values. In virtually all such calculations, the empirically observed slope of the pK(a) vs. DeltaE fit is significantly less than the theoretical value, 1/(2.303RT) (which is 0.73 mol/kcal at room temperature). In our own continuum solvation calculations (Zhang et al., J Phys Chem A 2010, 114, 432), the empirical slope for carboxylic acids was only 0.23 mol/kcal, despite the excellent fit to the experimental pK(a) values. There has been much speculation about the reason for this phenomenon. Although the DeltaE - pK(a) relation neglects entropic effects, these are expected to largely cancel. The most likely cause for the strange behavior of the fitted slope is explicit solute-solvent (water) interactions, especially involving the ions, which cannot be described accurately by continuum solvation models. We used our previously developed pK(a) protocol (OLYP/6-311+G(d,p)//3-21G(d) with the COSMO solvation model) to investigate the effect of adding one or two explicit water molecules to the system. The slopes for organic acids (especially carboxylic acids) are much closer to the theoretical value when explicit water molecules are added to both the neutral molecule and the anion. However, explicit water molecules have almost no effect on the slopes for organic bases. Adding explicit water molecules to the ions only produces intermediate results. Unfortunately, linear fits involving explicit water molecules have much larger errors than with continuum solvation models alone and are also much more expensive. Consequently, they are not suitable for large-scale pK(a) calculations. The results compared with literature values showed that our predicted pK(a) s are more accurate. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Complex configuration interaction calculations of the cross section for the dissociative electron attachment process e(-) + F(2) --> F 2- --> F + F(-) using the complex basis function method.

Publication Date: 2012 Feb 5 PMID: 22173838
Authors: Honigmann, M. - Buenker, R. J. - Liebermann, H. P.
Journal: J Comput Chem

The F 2- molecule and the corresponding dynamic processes dealing with electron scattering on the neutral F(2) species have been the subject of many theoretical and experimental investigations in the past. In the context of the Born-Oppenheimer approximation, one of the best theoretical descriptions of the electronic states involves the use of complex basis functions together with configuration interaction (CI) methods. In this work, multireference CI calculations using the complex basis function method have been carried out for the autoionizing ground state of the F 2- molecule. Potential curves and vibrational levels have been obtained for the ground and various excited states of both F(2) and F 2-, as well as the variation of the line width of the anionic ground state for the bond distance region in which it is metastable. Cross sections for the dissociative electron attachment process e(-) + F(2) --> F 2- --> F + F(-) have also been computed within the framework of the boomerang model, and good agreement with available experimental data has been found. In addition, some calculations for the process of vibrational excitation are included which also give good agreement with experiment. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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In Silico screening for agonists and blockers of the beta(2) adrenergic receptor: Implications of inactive and activated state structures.

Publication Date: 2012 Feb 15 PMID: 22170280
Authors: Costanzi, S. - Vilar, S.
Journal: J Comput Chem

Ten crystal structures of the beta(2) adrenergic receptor have been published, reflecting different signaling states. Here, through controlled-docking experiments, we examined the implications of using inactive or activated structures on the in silico screening for agonists and blockers of the receptor. Specifically, we targeted the crystal structures solved in complex with carazolol (2RH1), the neutral antagonist alprenalol, the irreversible agonist FAUC50 (3PDS), and the full agonist BI-167017 (3P0G). Our results indicate that activated structures favor agonists over blockers, whereas inactive structures favor blockers over agonists. This tendency is more marked for activated than for inactive structures. Additionally, agonists tend to receive more favorable docking scores when docked at activated rather than inactive structures, while blockers do the opposite. Hence, the difference between the docking scores attained with an activated and an inactive structure is an excellent means for the classification of ligands into agonists and blockers as we determined through receiver operating characteristic curves and linear discriminant analysis. With respect to virtual screening, all structures prioritized well agonists and blockers over nonbinders. However, inactive structures worked better for blockers and activated structures worked better for agonists, respectively. Notably, the combination of individual docking experiments through receptor ensemble docking resulted in an excellent performance in the retrieval of both agonists and blockers. Finally, we demonstrated that the induced-fit docking of agonists is a viable way of modifying an inactive crystal structure and bias it toward the in silico recognition of agonists rather than blockers. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Interaction and protection mechanism between li@C(60) and nucleic acid bases (NABs): Performance of PM6-DH2 on noncovalent interaction of NABs-Li@C60.

Publication Date: 2012 Feb 15 PMID: 22170247
Authors: Sun, W. - Bu, Y. - Wang, Y.
Journal: J Comput Chem

To discuss the protection mechanism of DNA from radiation as well as assess the performance of PM6-DH2 on noncovalent interactions, the interaction of four nucleic acid bases (NABs) such as adenine (A), cytosine (C), guanine (G), and thymine (T), with Li@C(60) was extensively investigated with the-state-of-art theoretical methods describing noncovalent systems, like M06-2x, PBE-D, and PM6-DH2 methods. In the gas phase, the binding strength of NABs to Li@C(60) from M06-2x decreases in the sequence, G>C>A>T. As dispersion was explicitly included, PBE-D relatively enhances the binding of A and T and corrects the sequence to, G>A>C approximately T. PM6-DH2 predicted similar binding energies to those from PBE-D within 0.5 kcal/mol and the same binding sequence, suggesting that the PM6-DH2 method is promising for nano-scale systems. In the aqueous solution, binding of NABs-Li@C(60) is considerably decreased, and the M06-2X and PM6-D methods yield a different sequence from the gas phase, G>A>T>C. The encapsulation of Li atom results in a lower IP for Li@C(60) than those of NABs, and the dominant localization of single-occupied molecular orbital on Li@C(60) moiety of the complexes NABs-Li@C(60) further indicates that an electron would be ejected from Li@C(60) upon radiation and Li@C(60) is therefore able to protect DNA bases from radiation. In addition, it was revealed that Li prefers coordination with the hexagonal ring at Li@C(60) , which clarifies the existing controversy in this respect. Finally, Yang's reduced density gradient approach clearly shows that the weak and strong noncovalent interaction regions in the complexes, NABs-Li@C(60) and (NABs-Li@C(60) )(+) . (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system.

Publication Date: 2012 Feb 5 PMID: 22170234
Authors: Liu, C. - Zhao, D. X. - Yang, Z. Z.
Journal: J Comput Chem

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMsigmapi H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMsigmapi HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Theoretical investigations of the reactivities of four-membered N-heterocyclic carbene analogues of the group 13 elements.

Publication Date: 2012 Jan 5 PMID: 22167870
Authors: Wu, C. S. - Su, M. D.
Journal: J Comput Chem

The potential energy surfaces for the chemical reactions of four-membered N-heterocyclic group 13 heavy carbeneoid species have been studied using density functional theory (Becke, 3-parameter, Lee-Yang-Parr (B3LYP)/Los Alamos National Laboratory 2-Double-Zeta (LANL2DZ)). Five four-membered group 13 heavy carbeneoid species, iPr2NC(NAr)2E:, where E (1/4) B, Al, Ga, In, and Tl, have been chosen as model reactants in this work. Also, three kinds of chemical reactions, CAH bond insertion, alkene cycloaddition, and dimerization, have been used to study the chemical reactivities of these group 13 fourmembered N-heterocyclic carbeneoid species. In principle, our present theoretical work predicts that the larger the ffNEN bond angle of the four-membered group 13 iPr2NC(NAr)2E: species, the smaller the singlet-triplet splitting, the lower the activation barrier, and, in turn, the more rapid its chemical reactions to various chemical species. Moreover, our theoretical investigations suggest that the relative carbenic reactivity decreases in the following order: B > Al > Ga > In > Tl. That is, the heavier the group 13 atom (E), the more stable its fourmembered carbeneoid toward chemical reactions is. As a result, our computations predict that the four-membered heavy group 13 iPr2NC(NAr)2E: species (E (1/4) Al, Ga, In, and Tl) should be both kinetically and thermodynamically stable, and can be readily synthesized and isolated at room temperature. Furthermore, the singlet-triplet energy splitting of the four-membered group 13 iPr2NC(NAr)2E: species, as described in the configuration mixing model attributed to the work of Pross and Shaik, can be used as a diagnostic tool to predict their reactivities. The results obtained allow a number of predictions to be made.

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Virtual screening for compounds that mimic protein-protein interface epitopes.

Publication Date: 2012 Feb 15 PMID: 22162049
Authors: Geppert, T. - Reisen, F. - Pillong, M. - Hahnke, V. - Tanrikulu, Y. - Koch, C. P. - Perna, A. M. - Perez, T. B. - Schneider, P. - Schneider, G.
Journal: J Comput Chem

Modulation of protein-protein interactions (PPI) has emerged as a new concept in rational drug design. Here, we present a computational protocol for identifying potential PPI inhibitors. Relevant regions of interfaces (epitopes) are predicted for three-dimensional protein models and serve as queries for virtual compound screening. We present a computational screening protocol that incorporates two different pharmacophore models. One model is based on the mathematical concept of autocorrelation vectors and the other utilizes fuzzy labeled graphs. In a proof-of-concept study, we were able to identify serine protease inhibitors using a predicted trypsin epitope as query. Our virtual screening framework may be suited for rapid identification of PPI inhibitors and suggesting bioactive tool compounds. Copyright for JCC Journal: (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Evaluation of protein-ligand binding free energy focused on its entropic components.

Publication Date: 2012 Feb 15 PMID: 22162031
Authors: Chiba, S. - Harano, Y. - Roth, R. - Kinoshita, M. - Sakurai, M.
Journal: J Comput Chem

The binding free energy for FK506-binding protein-ligand systems is evaluated as a sum of two entropic components, the water-entropy gain, and the configurational-entropy loss for the protein and ligand molecules upon the binding. The two entropic components are calculated using morphometric thermodynamics combined with a statistical-mechanical theory for molecular liquids and the normal mode analysis, respectively. We find that there is an excellent correlation between the calculated and experimental values of the binding free energy. This result is compared with those of several other binding-free energy calculation methods, including MM-PB/SA. The binding can well be elucidated by competition of the two entropic components. Upon the protein-ligand binding, the total volume available to the translational displacement of the coexisting water molecules increases, leading to an increase in the number of accessible configurations of the water. The water-entropy gain, by which the binding is driven, originates primarily from this effect. This study sheds new light on the theoretical prediction of the protein-ligand binding free energy. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Multiwfn: A multifunctional wavefunction analyzer.

Publication Date: 2012 Feb 15 PMID: 22162017
Authors: Lu, T. - Chen, F.
Journal: J Comput Chem

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Identifying clusters as low-lying mimina-efficiency of stochastic and genetic algorithms using inexpensive electronic structure levels.

Publication Date: 2012 Feb 15 PMID: 22162002
Authors: Avaltroni, F. - Corminboeuf, C.
Journal: J Comput Chem

Molecular candidates possessing unconventional chemical bonding paradigms (e.g., boron wheels, molecular stars, and multicenter bonding) have attracted a great deal of attention by the computational community. The viability of such systems is necessarily assessed through the identification of the lowest lying energy forms of a given chemical composition on the potential energy surface (PES). Although dozens of search algorithms have been developed, only a few are general and simple enough to become standard everyday procedures for this purpose. The simple random search and genetic algorithm (GA) are among these: but how do these approaches perform on typical isomeric searches? The performance of three specific variants for the ab initio exploration of the PES of prototype planar tetracoordinated and hypercoordinated carbon-containing systems C(2) Al(4) and CB(6) (2-) are compared. The advantages of preoptimizing with a low-cost semiempirical method (e.g., PM6) together with the most cost-efficient GA-based variant are discussed, and the trends verified by the isomer search of the larger Si(5) Li(7) (+) clusters. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Modeling nonlinear optics of nanosystems with sum-over-states model.

Publication Date: 2012 Feb 5 PMID: 22147416
Authors: Tian, W. Q.
Journal: J Comput Chem

Three-stage strategies (ladder rule, few state model (FSM), and parallelization) were proposed to improve the computational efficiency of the sum-over-states (SOS) model in nonlinear optics (NLO) modeling. Ladder rule decomposes NLO coefficients of the nth state into the (n-1)th term and the contribution from the (n-1)th to the nth state without loss of rigor in theory. FSM singles out the states with substantial contribution to NLO. Those strategies are universal to all (including revised and simplified) SOS models. The computing cost reduces roughly to C/(n(i-1) ) (C is a constant and i is the rank (order) of the NLO coefficients). (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective.

Publication Date: 2012 Feb 15 PMID: 22144113
Authors: Xue, W. - Liu, H. - Yao, X.
Journal: J Comput Chem

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme for splicing a viral DNA (vDNA) replica of its genome into host cell chromosomal DNA (hDNA) and has been recently recognized as a promising therapeutic target for developing anti-AIDS agents. The interaction between HIV-1 IN and vDNA plays an important role in the integration process of the virus. However, a detailed understanding about the mechanism of this interactions as well as the action of the anti-HIV drug raltegravir (RAL, approved by FDA in 2007) targeting HIV-1 IN in the inhibition of the vDNA strand transfer is still absent. In the present work, a molecular modeling study by combining homology modeling, molecular dynamics (MD) simulations with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and molecular mechanics Generalized-Born surface area (MM-GBSA) calculations was performed to investigate the molecular mechanism of HIV-1 IN-vDNA interactions and the inhibition action of vDNA strand transfer inhibitor (INSTI) RAL. The structural analysis showed that RAL did not influence the interaction between vDNA and HIV-1 IN, but rather targeted a special conformation of HIV-1 IN to compete with host DNA and block the function of HIV-1 IN by forcing the 3'-OH of the terminal A17 nucleotide away from the three catalytic residues (Asp64, Asp116, and Glu152) and two Mg(2+) ions. Thus, the obtained results could be helpful for understanding of the integration process of the HIV-1 virus and provide some new clues for the rational design and discovery of potential compounds that would specifically block HIV-1 virus replication. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Alder-ene reaction: Aromaticity and activation-strain analysis.

Publication Date: 2012 Feb 15 PMID: 22144106
Authors: Fernandez, I. - Bickelhaupt, F. M.
Journal: J Comput Chem

We have computationally explored the trend in reactivity of the Alder-ene reactions between propene and a series of seven enophiles using density functional theory at M06-2X/def2-TZVPP. The reaction barrier decreases along the enophiles in the order H(2) CCH(2) > HCCH > H(2) CNH > H(2) CCH(COOCH(3) ) > H(2) CO > H(2) CPH > H(2) CS. Thus, barriers drop in particular, if third-period atoms become involved in the double bond of the enophile. Activation-strain analyses show that this trend in reactivity correlates with the activation strain associated with deforming reactants from their equilibrium structure to the geometry they adopt in the transition state. We discuss the origin of this trend and its relationship with the extent of synchronicity between H transfer from ene to enophile and the formation of the new CC bond. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges.

Publication Date: 2012 Feb 5 PMID: 22131287
Authors: Marques, J. M. - Pais, A. A. - Abreu, P. E.
Journal: J Comput Chem

The efficiency of the so-called big-bang method for the optimization of atomic clusters is analysed in detail for Morse pair potentials with different ranges; here, we have used Morse potentials with four different ranges, from long- rho = 3) to short-ranged rho = 14) interactions. Specifically, we study the efficacy of the method in discovering low-energy structures, including the putative global minimum, as a function of the potential range and the cluster size. A new global minimum structure for long-ranged rho = 3) Morse potential at the cluster size of n= 240 is reported. The present results are useful to assess the maximum cluster size for each type of interaction where the global minimum can be discovered with a limited number of big-bang trials. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Path-integral calculations of heavy atom kinetic isotope effects in condensed phase reactions using higher-order trotter factorizations.

Publication Date: 2012 Feb 5 PMID: 22121039
Authors: Vardi-Kilshtain, A. - Azuri, A. - Major, D. T.
Journal: J Comput Chem

A convenient approach to compute kinetic isotope effects (KIEs) in condensed phase chemical reactions is via path integrals (PIs). Usually, the primitive approximation is used in PI simulations, although such quantum simulations are computationally demanding. The efficiency of PI simulations may be greatly improved, if higher-order Trotter factorizations of the density matrix operator are used. In this study, we use a higher-order PI method, in conjunction with mass-perturbation, to compute heavy-atom KIE in the decarboxylation of orotic acid in explicit sulfolane solvent. The results are in good agreement with experiment and show that the mass-perturbation higher-order Trotter factorization provides a practical approach for computing condensed phase heavy-atom KIE. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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A computational study on the hydrogen adsorption capacity of various lithium-Doped boron hydrides.

Publication Date: 2012 Feb 5 PMID: 22121031
Authors: Pan, S. - Giri, S. - Chattaraj, P. K.
Journal: J Comput Chem

An aromatic boron hydride B(3) H(3) (2-) and its various Li/Li(+) doped isomers have been studied at the B3LYP/6-311+G(d) and M06/6-311+G(d) levels of theory to assess their hydrogen storage potential. Different types of interaction energies, reaction enthalpies and reaction electrophilicities associated with the hydrogen adsorption process suggest that B(3) H(3) (2-) itself and some of its Li-decorated analogues may turn out to be effective hydrogen storage material. Nucleus independent chemical shift and conceptual density functional theory based reactivity descriptors lend additional support. The temperature-pressure phase diagram identifies the temperature-pressure zone where the reaction Gibbs free energy for the hydrogen adsorption is negative making it a thermodynamically feasible process. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Structure and properties of the aluminum borates Al(BO(2) )(n) and Al(BO(2) )(n) (-) , (n = 1-4).

Publication Date: 2012 Feb 5 PMID: 22121015
Authors: Gutsev, G. L. - Weatherford, C. A. - Johnson, L. E. - Jena, P.
Journal: J Comput Chem

The geometrical and electronic structures of Al(BO(2) )(n) and Al(BO(2) )(n) (-) (n = 1-4) clusters are computed at different levels of theory including density functional theory (DFT), hybrid DFT, double-hybrid DFT, and second-order perturbation theory. All aluminum borates are found to be quite stable toward the BO(2) and BO(2) (-) loss in the neutral and anion series, respectively. Al(BO(2) )(4) belongs to the class of hyperhalogens composed of smaller superhalogens, and should possess a large adiabatic electron affinity (EA(ad) ) larger than that of its superhalogen building block BO(2) . Indeed, the aluminum tetraborate possesses the EA(ad) of 5.6 eV, which, however, is smaller than the EA(ad) of 7.8 eV of the AlF(4) supehalogen despite BO(2) is more electronegative than F. The EA(ad) decrease in Al(BO(2) )(4) is due to the higher thermodynamic stability of Al(BO(2) )(4) compared to that of AlF(4) . Because of its high EA and thermodynamic stability, Al(BO(2) )(4) should be capable of forming salts with electropositive counter ions. We optimized KAl(BO(2) )(4) as corresponding to a unit cell of a hypothetical KAl(BO(2) )(4) salt and found that specific energy and energy density of such a salt are competitive with those of trinitrotoluol (TNT). (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Ab Initio direct classical trajectory investigation on the S(N) 2 reaction of F(-) with NH(2) F: Nonstatistical central barrier recrossing dynamics.

Publication Date: 2012 Feb 5 PMID: 22121003
Authors: Yu, F.
Journal: J Comput Chem

The bimolecular nucleophilic substitution (S(N) 2) reaction of F(a) (-) with NH(2) F(b) has been investigated with the ab initio direct classical trajectory method. According to our trajectory calculations, a dynamic behavior of nonstatistical central barrier recrossing is revealed. Among the 64 trajectories calculated in this work, 45 trajectories follow the dynamic reaction pathways as assumed by statistical theory and other 19 trajectories with central barrier recrossings are nonstatistical. For the nonstatistical trajectories, the central barrier recrossings may originate from the inefficient kinetic energy transfer from the intramolecular modes of the NH(2) F(a) moiety in the dynamic F(b) (-) ...HNHF(a) complex to the intermolecular modes of the dynamic F(b) (-) ...HNHF(a) complex on the exit-channel potential energy surface. With respect to the dynamic behavior of the nonstatistical central barrier recrossing, the statistical theories such as the Rice-Ramsperger-Kassel-Marcus and transition state theories without further corrections cannot be used to model the reaction kinetics for this S(N) 2 reaction. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Development and optimization of a novel genetic algorithm for identifying nanoclusters from scanning transmission electron microscopy images.

Publication Date: 2012 Feb 5 PMID: 22120989
Authors: Logsdail, A. J. - Li, Z. Y. - Johnston, R. L.
Journal: J Comput Chem

Whilst technological advancements have allowed imaging at atomic resolution using scanning transmission electron microscopy (STEM), identification of nanocluster structures has proven difficult due to their low thermal stability, and often resultant low-symmetry. In this work, we look at a novel solution to this problem using a genetic algorithm (GA). GAs are search methods for the minimization of statistical problems based on natural evolution. We develop a STEM model first described by Curley et al. (2007) and, using high-symmetry cluster structures as test subjects, look at the effectiveness and efficiency of the GA at optimizing orientation parameters for a cluster when compared to a model solution. We find for a 309-atom icosahedron that a random minimizing search would prove more efficient than a GA; however, for a 309-atom decahedron the GA becomes more effective and efficient than a random search. We predict that as we continue to lower symmetry of our test cases, we will find the GA becomes even more efficient at optimizing this otherwise computationally expensive problem. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models.

Publication Date: 2012 Jan 30 PMID: 22120971
Authors: Lettieri, S. - Zuckerman, D. M.
Journal: J Comput Chem

Typically, the most time consuming part of any atomistic molecular simulation is the repeated calculation of distances, energies, and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed-up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (precalculation) of distance- and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic-but rigid-benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table, which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary ("exact") Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications, greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules.

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Theoretical calculation about the valence and rydberg excited states of hydrogen cyanide.

Publication Date: 2012 Feb 15 PMID: 22120208
Authors: Li, B. T. - Li, L. L. - Wu, H. S.
Journal: J Comput Chem

The singlet and triplet excited states of hydrogen cyanide have been computed by using the complete active space self-consistent field and completed active space second order perturbation methods with the atomic natural orbital (ANO-L) basis set. Through calculations of vertical excitation energies, we have probed the transitions from ground state to valence excited states, and further extensions to the Rydberg states are achieved by adding 1s1p1d Rydberg orbitals into the ANO-L basis set. Four singlet and nine triplet excited states have been optimized. The computed adiabatic energies and the vertical transition energies agree well with the available experimental data and the inconsistencies with the available theoretical reports are discussed in detail. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2011.

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Durandal: Fast exact clustering of protein decoys.

Publication Date: 2012 Feb 5 PMID: 22120171
Authors: Berenger, F. - Shrestha, R. - Zhou, Y. - Simoncini, D. - Zhang, K. Y.
Journal: J Comput Chem

In protein folding, clustering is commonly used as one way to identify the best decoy produced. Initializing the pairwise distance matrix for a large decoy set is computationally expensive. We have proposed a fast method that works even on large decoy sets. This method is implemented in a software called Durandal. Durandal has been shown to be consistently faster than other software performing fast exact clustering. In some cases, Durandal can even outperform the speed of an approximate method. Durandal uses the triangular inequality to accelerate exact clustering, without compromising the distance function. Recently, we have further enhanced the performance of Durandal by incorporating a Quaternion-based characteristic polynomial method that has increased the speed of Durandal between 13% and 27% compared with the previous version. Durandal source code is available under the GNU General Public License at http://www.riken.jp/zhangiru/software/durandal_released_qcp.tgz. Alternatively, a compiled version of Durandal is also distributed with the nightly builds of the Phenix (http://www.phenix-online.org/) crystallographic software suite (Adams et al., Acta Crystallogr Sect D 2010, 66, 213). (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Convergence and error estimation in free energy calculations using the weighted histogram analysis method.

Publication Date: 2012 Feb 5 PMID: 22109354
Authors: Zhu, F. - Hummer, G.
Journal: J Comput Chem

The weighted histogram analysis method (WHAM) has become the standard technique for the analysis of umbrella sampling simulations. In this article, we address the challenges (1) of obtaining fast and accurate solutions of the coupled nonlinear WHAM equations, (2) of quantifying the statistical errors of the resulting free energies, (3) of diagnosing possible systematic errors, and (4) of optimally allocating of the computational resources. Traditionally, the WHAM equations are solved by a fixed-point direct iteration method, despite poor convergence and possible numerical inaccuracies in the solutions. Here, we instead solve the mathematically equivalent problem of maximizing a target likelihood function, by using superlinear numerical optimization algorithms with a significantly faster convergence rate. To estimate the statistical errors in one-dimensional free energy profiles obtained from WHAM, we note that for densely spaced umbrella windows with harmonic biasing potentials, the WHAM free energy profile can be approximated by a coarse-grained free energy obtained by integrating the mean restraining forces. The statistical errors of the coarse-grained free energies can be estimated straightforwardly and then used for the WHAM results. A generalization to multidimensional WHAM is described. We also propose two simple statistical criteria to test the consistency between the histograms of adjacent umbrella windows, which help identify inadequate sampling and hysteresis in the degrees of freedom orthogonal to the reaction coordinate. Together, the estimates of the statistical errors and the diagnostics of inconsistencies in the potentials of mean force provide a basis for the efficient allocation of computational resources in free energy simulations. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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Understanding cross-boundary events in ONIOM QM:QM' calculations.

Publication Date: 2012 Feb 5 PMID: 22109102
Authors: Lundberg, M.
Journal: J Comput Chem

QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard quantum mechanics: molecular mechanics (QM:MM) models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, that is, when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, for example, Hartree-Fock versus B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, that is, when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, for example, by choosing a proper model system. Importantly, an accurate description of cross-boundary reactions would open up possibilities to simulate chemical reactions without a priori limiting the reactivity in the design of the computational model. Challenges to implement a simulation scheme (ONIOM-XR) that can automatically handle chemical reactions between different layers are briefly discussed. (c) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012.

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The stability of small helical gold nanorods: a relativistic density functional study.

Publication Date: 2012 Jan 30 PMID: 22108955
Authors: Liu, X. J. - Hamilton, I. - Krawczyk, R. P. - Schwerdtfeger, P.
Journal: J Comput Chem

Multistrand 7-1 helical Au(24), Au(32), and Au(40) structures with three, four, and five gold atoms in the central strand and 21, 28, and 35 gold atoms in the coaxial tube are investigated using relativistic density functional theory. We demonstrate that these helical gold nanorods are stable structures with a rather large HOMO-LUMO gap, a large binding energy per atom, a very large vertical dissociation energy, and an extremely large electron affinity. On the basis of the atomic charges and the nature of the frontier orbitals, they are also expected to have strong selective reactivity toward electrophiles and nucleophiles. Furthermore, we show that these helical Au(n) structures and, in particular, the helical Au(40) structure are competitive energetically and chemically with respect to alternate cage and compact Au(n) structures. We consider two fragmentations of the helical Au(40) structure and perform a density of states analysis to examine both charge transfer and electronic polarization.

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QM/MM refinement and analysis of protein bound retinoic acid.

Publication Date: 2012 Jan 30 PMID: 22108894
Authors: Li, X. - Fu, Z. - Merz, K. M. Jr
Journal: J Comput Chem

Retinoic acid (RA) is a vitamin A derivative, which modifies the appearance of fine wrinkles and roughness of facial skin and treats acne and activates gene transcription by binding to heterodimers of the retinoic acid receptor (RAR) and the retinoic X receptor (RXR). There are series of protein bound RA complexes available in the protein databank (PDB), which provides a broad range of information about the different bioactive conformations of RA. To gain further insights into the observed bioactive RA conformations we applied quantum mechanic (QM)/molecular mechanic (MM) approaches to re-refine the available RA protein-ligand complexes. MP2 complete basis set (CBS) extrapolations single energy calculations are also carried out for both the experimental conformations and QM optimized geometries of RA in the gas as well as solution phase. The results demonstrate that the re-refined structures show better geometries for RA than seen in the originally deposited PDB structures through the use of QMs for the ligand in the X-ray refinement procedure. QM/MM re-refined conformations also reduced the computed strain energies found in the deposited crystal conformations for RA. Finally, the dependence of ligand strain on resolution is analyzed. It is shown that ligand strain is not converged in our calculations and is likely an artifact of the typical resolutions employed to study protein-ligand complexes.

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A new approximate method for the stochastic simulation of chemical systems: the representative reaction approach.

Publication Date: 2012 Jan 30 PMID: 22108838
Authors: Kadam, S. - Vanka, K.
Journal: J Comput Chem

We have developed two new approximate methods for stochastically simulating chemical systems. The methods are based on the idea of representing all the reactions in the chemical system by a single reaction, i.e., by the "representative reaction approach" (RRA). Discussed in the article are the concepts underlying the new methods along with flowchart with all the steps required for their implementation. It is shown that the two RRA methods {with the reaction 2A -> B as the representative reaction (RR)} perform creditably with regard to accuracy and computational efficiency, in comparison to the exact stochastic simulation algorithm (SSA) developed by Gillespie and are able to successfully reproduce at least the first two moments of the probability distribution of each species in the systems studied. As such, the RRA methods represent a promising new approach for stochastically simulating chemical systems.

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Theoretical investigation of the ethylene dimer: interaction energy and dipole moment.

Publication Date: 2012 Jan 30 PMID: 22102329
Authors: Kalugina, Y. N. - Cherepanov, V. N. - Buldakov, M. A. - Zvereva-Loete, N. - Boudon, V.
Journal: J Comput Chem

The interaction potential energy and the interaction-induced dipole moment surfaces of the van der Waals C(2)H(4)-C(2)H(4) complex has been calculated for a broad range of intermolecular separations and configurations in the approximation of rigid interacting molecules. The calculations have been carried out using high-level ab initio theory with the aug-cc-pVTZ basis set and within the framework of the analytical description of long-range interactions between ethylene molecules. Binding energy for the most stable configuration of the C(2)H(4)-C(2)H(4) complex was calculated at the CCSD(T)/CBS level of theory. The harmonic fundamental vibrational frequencies for this complex were calculated at the MP2 level of theory.

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Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods.

Publication Date: 2012 Jan 30 PMID: 22102317
Authors: Mori, T. - Ogushi, F. - Sugita, Y.
Journal: J Comput Chem

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.

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A computational chemist approach to gas sensors: modeling the response of SnO2 to CO, O2, and H2O gases.

Publication Date: 2012 Jan 30 PMID: 22102259
Authors: Ducere, J. M. - Hemeryck, A. - Esteve, A. - Rouhani, M. D. - Landa, G. - Menini, P. - Tropis, C. - Maisonnat, A. - Fau, P. - Chaudret, B.
Journal: J Comput Chem

A general bottom-up modeling strategy for gas sensor response to CO, O(2), H(2)O, and related mixtures exposure is demonstrated. In a first stage, we present first principles calculations that aimed at giving an unprecedented review of basic chemical mechanisms taking place at the sensor surface. Then, simulations of an operating gas sensor are performed via a mesoscopic model derived from calculated density functional theory data into a set of differential equations. Significant presence of catalytic oxidation reaction is highlighted.

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Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.

Publication Date: 2012 Jan 30 PMID: 22102176
Authors: Lee, K. I. - Jo, S. - Rui, H. - Egwolf, B. - Roux, B. - Pastor, R. W. - Im, W.
Journal: J Comput Chem

Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), alpha-Hemolysin (alpha-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and alpha-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10-20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5-7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.

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New functionalities in the GROMOS biomolecular simulation software.

Publication Date: 2012 Jan 30 PMID: 22076815
Authors: Kunz, A. P. - Allison, J. R. - Geerke, D. P. - Horta, B. A. - Hunenberger, P. H. - Riniker, S. - Schmid, N. - van Gunsteren, W. F.
Journal: J Comput Chem

Since the most recent description of the functionalities of the GROMOS software for biomolecular simulation in 2005 many new functions have been implemented. In this article, the new functionalities that involve modified forces in a molecular dynamics (MD) simulation are described: the treatment of electronic polarizability, an implicit surface area and internal volume solvation term to calculate interatomic forces, functions for the GROMOS coarse-grained supramolecular force field, a multiplicative switching function for nonbonded interactions, adiabatic decoupling of a number of degrees of freedom with temperature or force scaling to enhance sampling, and nonequilibrium MD to calculate the dielectric permittivity or viscosity. Examples that illustrate the use of these functionalities are given.

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Rigid-CLL: avoiding constant-distance computations in cell linked-lists algorithms.

Publication Date: 2012 Jan 30 PMID: 22072568
Authors: de Angulo, V. R. - Cortes, J. - Porta, J. M.
Journal: J Comput Chem

Many of the existing molecular simulation tools require the efficient identification of the set of nonbonded interacting atoms. This is necessary, for instance, to compute the energy values or the steric contacts between atoms. Cell linked-lists can be used to determine the pairs of atoms closer than a given cutoff distance in asymptotically optimal time. Despite this long-term optimality, many spurious distances are anyway computed with this method. Therefore, several improvements have been proposed, most of them aiming to refine the volume of influence for each atom. Here, we suggest a different improvement strategy based on avoiding to fill cells with those atoms that are always at a constant distance of a given atom. This technique is particularly effective when large groups of the particles in the simulation behave as rigid bodies as it is the case in simplified models considering only few of the degrees of freedom of the molecule. In these cases, the proposed technique can reduce the number of distance computations by more than one order of magnitude, as compared with the standard cell linked-list technique. The benefits of this technique are obtained without incurring in additional computation costs, because it carries out the same operations as the standard cell linked-list algorithm, although in a different order. Since the focus of the technique is the order of the operations, it might be combined with existing improvements based on bounding the volume of influence for each atom.

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A possible overestimation of the effect of acetylation on lysine residues in KQ mutant analysis.

Publication Date: 2012 Jan 30 PMID: 22072565
Authors: Fujimoto, H. - Higuchi, M. - Koike, M. - Ode, H. - Pinak, M. - Bunta, J. K. - Nemoto, T. - Sakudoh, T. - Honda, N. - Maekawa, H. - Saito, K. - Tsuchida, K.
Journal: J Comput Chem

Acetylation of lysine residues, one of the most common protein post-transcriptional modifications, is thought to regulate protein affinity with other proteins or nucleotides. Experimentally, the effects of acetylation have been studied using recombinant mutants in which lysine residues (K) are substituted with glutamine (Q) as a mimic of acetyl lysine (KQ mutant), or with arginine (R) as a mimic of nonacetylated lysine (KR mutant). These substitutions, however, have not been properly validated. The effects lysine acetylation on Ku, a multifunctional protein that has been primarily implicated in DNA repair and cell survival, are characterized herein using a series of computer simulations. The binding free energy was reduced in the KQ mutant, while the KR mutant had no effect, which is consistent with previous experimental results. Unexpectedly, the binding energy between Ku and DNA was maintained at almost the same level as in the wild type protein despite full acetylation of the lysine residues. These results suggest that the effects of acetylation may be overestimated when the KQ mutant is used as a mimic of the acetylated protein.

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An effective method for accurate prediction of the first hyperpolarizability of alkalides.

Publication Date: 2012 Jan 15 PMID: 22045548
Authors: Wang, J. N. - Xu, H. L. - Sun, S. L. - Gao, T. - Li, H. Z. - Li, H. - Su, Z. M.
Journal: J Comput Chem

The proper theoretical calculation method for nonlinear optical (NLO) properties is a key factor to design the excellent NLO materials. Yet it is a difficult task to obatin the accurate NLO property of large scale molecule. In present work, an effective intelligent computing method, as called extreme learning machine-neural network (ELM-NN), is proposed to predict accurately the first hyperpolarizability (beta(0)) of alkalides from low-accuracy first hyperpolarizability. Compared with neural network (NN) and genetic algorithm neural network (GANN), the root-mean-square deviations of the predicted values obtained by ELM-NN, GANN, and NN with their MP2 counterpart are 0.02, 0.08, and 0.17 a.u., respectively. It suggests that the predicted values obtained by ELM-NN are more accurate than those calculated by NN and GANN methods. Another excellent point of ELM-NN is the ability to obtain the high accuracy level calculated values with less computing cost. Experimental results show that the computing time of MP2 is 2.4-4 times of the computing time of ELM-NN. Thus, the proposed method is a potentially powerful tool in computational chemistry, and it may predict beta(0) of the large scale molecules, which is difficult to obtain by high-accuracy theoretical method due to dramatic increasing computational cost.

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SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles.

Publication Date: 2012 Jan 30 PMID: 22045506
Authors: Faraggi, E. - Zhang, T. - Yang, Y. - Kurgan, L. - Zhou, Y.
Journal: J Comput Chem

Accurate prediction of protein secondary structure is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. The accuracy of ab initio secondary structure prediction from sequence, however, has only increased from around 77 to 80% over the past decade. Here, we developed a multistep neural-network algorithm by coupling secondary structure prediction with prediction of solvent accessibility and backbone torsion angles in an iterative manner. Our method called SPINE X was applied to a dataset of 2640 proteins (25% sequence identity cutoff) previously built for the first version of SPINE and achieved a 82.0% accuracy based on 10-fold cross validation (Q(3)). Surpassing 81% accuracy by SPINE X is further confirmed by employing an independently built test dataset of 1833 protein chains, a recently built dataset of 1975 proteins and 117 CASP 9 targets (critical assessment of structure prediction techniques) with an accuracy of 81.3%, 82.3% and 81.8%, respectively. The prediction accuracy is further improved to 83.8% for the dataset of 2640 proteins if the DSSP assignment used above is replaced by a more consistent consensus secondary structure assignment method. Comparison to the popular PSIPRED and CASP-winning structure-prediction techniques is made. SPINE X predicts number of helices and sheets correctly for 21.0% of 1833 proteins, compared to 17.6% by PSIPRED. It further shows that SPINE X consistently makes more accurate prediction in helical residues (6%) without over prediction while PSIPRED makes more accurate prediction in coil residues (3-5%) and over predicts them by 7%. SPINE X Server and its training/test datasets are available at http://sparks.informatics.iupui.edu/

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Mechanism for the reaction of 2-naphthol with N-methyl-N-phenyl-hydrazine suggested by the density functional theory investigations.

Publication Date: 2012 Jan 15 PMID: 22042734
Authors: Gao, J. Y. - Zhang, C. H. - Luo, M. M. - Kim, C. K. - Chu, W. - Xue, Y.
Journal: J Comput Chem

For the first time the computed mechanisms for the novel reaction of 2-naphthol with N-methyl-N-phenylhydrazine, leading to 1-amino-2-naphthol (Tang et al., J Am Chem Soc 2008, 130, 5840), have been investigated using the density functional theory. Four distinct possible pathways were evaluated: two amination mechanisms with the attack of NH(2) group respectively at the alpha-position C1 and beta-position C3 atoms of 2-naphthol (pathways 1 and 2) as well as two rearrangement processes with displacement of the phenolic hydroxyl group followed by the benzidine-like rearrangement at the alpha-position C1 and beta-position C3 atoms of 2-naphthol, respectively (pathways 3 and 4). Solvent effect has been tested based on the optimized geometries of the stationary points in solution at the B3LYP/PCM/6-31+G(d,p) level of theory with an averaged dielectric constant of binary solvent. Single-point energies of the optimized structures have been calculated using three hybrid density functionals, B3LYP, MPW3LYP, and B3PW91 with the 6-311++G(3df,2p) basis set. Our computed results clearly manifest that pathway 1 (alpha-amination) has the highest possibility to occur, with the Gibbs free energies being lower by 6 to 20 kcal/mol compared with the other three pathways, which leads to 1-amino-2-naphthol and N-methylaniline as products. It is in excellent agreement with the experimental observation.

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Theoretical investigation on redox-switchable second-order nonlinear optical responses of push-pull Cp*CoEt2C2B4H3-expanded (metallo)porphyrins.

Publication Date: 2012 Jan 15 PMID: 22042719
Authors: Ma, N. - Liu, C. - Qiu, Y. - Sun, S. - Su, Z.
Journal: J Comput Chem

The second-order nonlinear optical (NLO) properties of the Cp*Co(C(2)H(5))(2)C(2)B(4)H(3)-expanded (metallo)porphyrins (Cp* = C(5)Me(5)) have been investigated by using ab inito RHF and density functional theory (DFT) methods. The investigation shows that the compound with expand porphyrin possesses remarkable large molecular hyperpolarizability beta(tot) value, ~414.1 x 10(-30) esu (at LC-omegaPBE level), and might be an excellent second-order NLO material. From the character of charge transfer (CT) transition, it indicates that the -Cp*Co(C(2)H(5))(2)C(2)B(4)H(3) acts as an electron donor in this kind of systems. As a result of the redox behavior on expanded (metallo)porphyrin, the redox switching character of the NLO responses for the systems 2a-4a has also been studied. The results show that the beta(tot) values of reduced forms are larger than that of neutral ones. Furthermore, the time-dependent DFT calculation illustrates that reduced forms have a significant difference on the CT patterns versus neutral ones. The present investigation provides insight into the comparison with DFT results on estimating first hyperpolarizability and the NLO properties of the series of push-pull compounds.

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Theoretical study on the reaction CX3 + SiH(CH3)3 (X = H, F).

Publication Date: 2012 Jan 15 PMID: 22042710
Authors: Zhang, H. - Yang, L. - Liu, J. Y. - Li, Z. S.
Journal: J Comput Chem

Theoretical investigations are carried out on the multiple-channel reactions, CH(3) + SiH(CH(3))(3) --> products and CF(3) + SiH(CH(3))(3) --> products. The minimum energy paths (MEP) are calculated at the MP2/6-311 + G(d,p) level, and energetic information is further refined by the MC-QCISD (single point) method. The rate constants for major reaction channels are calculated by the canonical variational transition state theory (CVT) with small-curvature tunneling (SCT) correction over the temperature range 200-1500 K. The theoretical rate constants are in good agreement with the available experimental data and are found to be k(1a)(T) = 1.93 x 10(-24) T(3.15) exp(-1214.59/T) and k(2a)(T) = 1.33 x 10(-25) T(4.13) exp(-397.94/T) (in unit of cm(3) molecule(-1) s(-1)). Our calculations indicate that hydrogen abstraction channel from SiH group is the major channel due to the smaller barrier height among five channels considered.

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MATCH: an atom-typing toolset for molecular mechanics force fields.

Publication Date: 2012 Jan 15 PMID: 22042689
Authors: Yesselman, J. D. - Price, D. J. - Knight, J. L. - Brooks, C. L. 3rd
Journal: J Comput Chem

We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized.

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Comment on the paper "indexing molecules with chemical graph identifiers" by Elisabeth Gregori-Puigjane, Rut Garriga-Sust, and Jordi Mestres.

Publication Date: 2012 Jan 15 PMID: 22042650
Authors: Ihlenfeldt, W. D.
Journal: J Comput Chem

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A topological method for global optimization of clusters: application to (TiO2)n (n = 1-6).

Publication Date: 2012 Jan 15 PMID: 22038735
Authors: Tang, L. - Sai, L. - Zhao, J. - Qiu, R.
Journal: J Comput Chem

A new topological method is presented to generate the isomer structures of compound clusters with well defined covalent bonds. This method, combined with density functional theory, has been used to perform global optimization of (TiO(2))(n) (n = 1-6) clusters. Our comprehensive search not only reproduces all of the known lowest-energy structures reported in previous works but also reveals some new low-energy structures. Some energetically unfavorable motifs that induce energy penalties are obtained and discussed. Based on the ground state structures of the anionic (TiO(2))(n). clusters, the electron affinities and photoelectron spectra are simulated and compared with available experimental data.

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Dynamics and mechanism of structural diffusion in linear hydrogen bond.

Publication Date: 2012 Jan 15 PMID: 22009491
Authors: Chaiwongwattana, S. - Phonyiem, M. - Vchirawongkwin, V. - Prueksaaroon, S. - Sagarik, K.
Journal: J Comput Chem

Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n >/= 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state.

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Verification of DFT-predicted hydrogen storage capacity of VC3H3 complex using molecular dynamics simulations.

Publication Date: 2012 Jan 15 PMID: 21997892
Authors: Wadnerkar, N. - Kalamse, V. - Lee, S. L. - Chaudhari, A.
Journal: J Comput Chem

Density functional theory (DFT) and Fourth-order Moller-Plesset (MP4) perturbation theory calculations are performed to examine the possibility of hydrogen storage in V-capped VC(3)H(3) complex. Stability of bare and H(2) molecules adsorbed V-capped VC(3)H(3) complex is verified using DFT and MP4 method. Thermo-chemistry calculations are carried out to estimate the Gibbs free corrected averaged H(2) adsorption energy which reveals whether H(2) adsorption on V-capped VC(3)H(3) complex is energetically favorable, at different temperatures. We use different exchange and correlation functionals employed in DFT to see their effect on H(2) adsorption energy. Molecular dynamic (MD) simulations are performed to confirm whether this complex adsorbs H(2) molecules at a finite temperature. We elucidate the correlation between H(2) adsorption energy obtained from density functional calculations and retaining number of H(2) molecules on VC(3)H(3) complex during MDs simulations at various temperatures.

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Empirical formulation and parameterization of cation-pi interactions for protein modeling.

Publication Date: 2012 Jan 15 PMID: 21997880
Authors: Du, Q. S. - Long, S. Y. - Meng, J. Z. - Huang, R. B.
Journal: J Comput Chem

Cation-pi interaction is comparable and as important as other main molecular interaction types, such as hydrogen bond, electrostatic interaction, van der Waals interaction, and hydrophobic interaction. Cation-pi interactions frequently occur in protein structures, because six (Phe, Tyr, Trp, Arg, Lys, and His) of 20 natural amino acids and all metallic cations could be involved in cation-pi interaction. Cation-pi interactions arise from complex physicochemical nature and possess unique interaction behaviors, which cannot be modeled and evaluated by existing empirical equations and force field parameters that are widely used in the molecular dynamics. In this study, the authors present an empirical approach for cation-pi interaction energy calculations in protein interactions. The accurate cation-pi interaction energies of aromatic amino acids (Phe, Tyr, and Try) with protonated amino acids (Arg and Lys) and metallic cations (Li(+), Na(+), K(+), and Ca(2+)) are calculated using B3LYP/6-311+G(d,p) method as the benchmark for the empirical formulization and parameterization. Then, the empirical equations are built and the parameters are optimized based on the benchmark calculations. The cation-pi interactions are distance and orientation dependent. Correspondingly, the empirical equations of cation-pi interactions are functions of two variables, the distance r and the orientation angle theta. Two types of empirical equations of cation-pi interactions are proposed. One is a modified distance and orientation dependent Lennard-Jones equation. The second is a polynomial function of two variables r and theta. The amino acid-based empirical equations and parameters provide simple and useful tools for evaluations of cation-pi interaction energies in protein interactions.

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Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields.

Publication Date: 2012 Jan 15 PMID: 21997857
Authors: Lucas, T. R. - Bauer, B. A. - Davis, J. E. - Patel, S.
Journal: J Comput Chem

We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields, which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 +/-1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 +/-1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 +/-0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. As the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.

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Similarity recognition of molecular structures by optimal atomic matching and rotational superposition.

Publication Date: 2012 Jan 15 PMID: 21997798
Authors: Helmich, B. - Sierka, M.
Journal: J Comput Chem

An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.

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Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle.

Publication Date: 2012 Jan 15 PMID: 21997754
Authors: Shahrokh, K. - Orendt, A. - Yost, G. S. - Cheatham, T. E. 3rd
Journal: J Comput Chem

Molecular mechanics (MM) methods are computationally affordable tools for screening chemical libraries of novel compounds for sites of P450 metabolism. One challenge for MM methods has been the absence of a consistent and transferable set of parameters for the heme within the P450 active site. Experimental data indicate that mammalian P450 enzymes vary greatly in the size, architecture, and plasticity of their active sites. Thus, obtaining X-ray-based geometries for the development of accurate MM parameters for the major classes of hepatic P450 remains a daunting task. Our previous work with preliminary gas-phase quantum mechanics (QM)-derived atomic partial charges greatly improved the accuracy of docking studies of raloxifene to CYP3A4. We have therefore developed and tested a consistent set of transferable MM parameters based on gas-phase QM calculations of two model systems of the heme-a truncated (T-HM) and a full (F-HM) for four states of the P450 catalytic cycle. Our results indicate that the use of the atomic partial charges from the F-HM further improves the accuracy of docked predictions for raloxifene to CYP3A4. Different patterns for substrate docking are also observed depending on the choice of heme model and state. Newly parameterized heme models are tested in implicit and explicitly solvated MD simulations in the absence and presence of enzyme structures, for CYP3A4, and appear to be stable on the nanosecond simulation timescale. The new force field for the various heme states may aid the community for simulations of P450 enzymes and other heme-containing enzymes.

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Ab initio characterization of size dependence of electronic spectra for linear anionic carbon clusters C(n) (-) (n = 4-17).

Publication Date: 2012 Jan 5 PMID: 21968891
Authors: Guo, X. G. - Zhang, J. L. - Zhao, Y.
Journal: J Comput Chem

In this article, we determine the ground-state equilibrium geometries of the linear anionic carbon clusters C n- (n = 4-17) by means of the density functional theory B3LYP, CAM-B3LYP, and coupled cluster CCSD(T) calculations, as well as their electronic spectra obtained by the multireference second-order perturbation theory CASPT2 method. These studies indicate that these linear anions possess doublet (2) product operator(g) or (2) product operator(u) ground state, and the even-numbered clusters are generally acetylenic, whereas the odd-numbered ones are essentially cumulenic. The energy differences, electron affinities, and incremental binding energies of C n- chains all exhibit a notable tread of parity alternation, with n-even chains being more stable than n-odd ones. In addition, the predicted vertical excitation energies from the ground state to four low-lying excited states are in reasonably good agreement with the available experimental observations, and the calculations for the higher excited electronic transitions can provide accurate information for the experimentalists and spectroscopists. Interestingly, the absorption wavelengths of the 1(2) product operator(u/g) <-- X(2) product operator(g/u) transitions of the n-even clusters show a nonlinear trend of exponential growth, whereas those of the n-odd counterparts are found to obey a linear relationship as a function of the chain size, as shown experimentally. Moreover, the absorption wavelengths of the transitions to the higher excited states of C n- series have the similar linear size dependence as well.

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First-principle investigation of magnetic coupling mechanism in hypothesized a-site-ordered perovskite YMnScO.

Publication Date: 2012 Jan 5 PMID: 21968825
Authors: Li, H. - Lv, S. - Bai, Y. - Xia, Y. - Liu, X. - Meng, J.
Journal: J Comput Chem

We have systematically investigated the electronic and magnetic properties of hypothesized A-site-ordered perovskite YMnScO using first-principle calculation based on the density functional theory. Our calculated results predict that YMnScO is both thermodynamically and mechanically stable and its ground state is antiferromagnetic insulator. The Mn(3+) is in the high-spin state. More importantly, by comparison to YMnScO, we point out that the empty Sc 3d orbital provides the Mn--O--Sc--O--Mn superexchange interaction, which is similar to its isostructural perovskite CaCuTiO, and enhances the antiferromagnetic interaction between Mn ions. From these calculations, we can clearly see that the empty 3d orbital plays an important role to realize superexchange interaction.

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Oxygen versus sulfur: Structure and reactivity of substituted arsine oxides and arsine sulfides.

Publication Date: 2012 Jan 5 PMID: 21960430
Authors: Orthaber, A. - Sax, A. F. - Francesconi, K. A.
Journal: J Comput Chem

Although arsenic in its inorganic forms is a well know toxic agent, biotransformations in the environment and in the human body can produce organoarsenic compounds that are generally of much lower toxicity. Foremost among these products is a range of dimethylated arsine oxides and their analogous sulfides, which are crucial to the arsenic detoxification process. We have investigated the formation and interconversion of substituted and unsubstituted arsenicals (R(2)As(=Z)R(1), R(2) = CH, R(1) = CHCHOH, CHCOOH; Z = S or O) with density functional theory (DFT)/B3LYP. Formation of isomers including a cyclic hydrogen bonded conformer is observed for the ethanol and acetate derivatives. Furthermore, investigating the reaction of arsine oxide with hydrogen sulfide revealed the formation of arsine sulfide via pentacoordinated trigonal bipyramidal intermediates. A tetragonal pyramidal transition state was located enabling exchange of equatorial and axial positions in the trigonal bipyramidal species. The reaction was proven exothermic for all studied substituents (DeltaE(rxn) -50 to -80 kJ/mol). This fundamental study shows that HS easily leads to the formation of thio-organoarsenicals. Conversion of arsine sulfides into their corresponding arsine oxides is experimentally accomplished with hydrogen peroxide, which could also be rationalized by means of ab initio calculations showing high exothermicity (DeltaE(rxn) ca. -550 kJ/mol). Reactions are considered at different levels of theory (i.e., DFT, second and fourth order Moller-Plesset (MP) perturbation theory) including two solvation models for DFT, which show good agreement for resulting geometries and reaction energies. Hence, the widely used B3LYP/6-31G** combination is a suitable method for the description of molecular organoarsenicals.

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Ab initio molecular dynamics approach to tunneling splitting in polyatomic molecules.

Publication Date: 2012 Jan 5 PMID: 21956595
Authors: Ootani, Y. - Taketsugu, T.
Journal: J Comput Chem

An ab initio molecular dynamics approach is combined with the semiclassical tunneling method of Makri and Miller, which is applied to estimations of tunneling splitting in the umbrella inversion of ammonia and the intramolecular hydrogen transfer in malonaldehyde. In the application to malonaldehyde, effects of multidimensionality are examined by assigning quantum zero-point energies only to significant vibrational modes and changing the amount of energy given to other degrees of freedom. The calculated tunneling splitting values are in good agreement with the corresponding experimental values for both molecules.

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A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions of L-phenylalanine.

Publication Date: 2012 Jan 5 PMID: 21956539
Authors: Purushotham, U. - Vijay, D. - Narahari Sastry, G.
Journal: J Comput Chem

The structure and stability of various conformations of L-phenylalanine (PheN) and its zwitterions (PheZ), along with their ionized counterparts, cation (PheC) and anion (PheA), generated by adding and removing a proton respectively, have been investigated using first principle calculations in vacuum and in solution. This is followed by an extensive study on various possible dimer (PheD) conformations, which are noncovalently bound units without a peptide bond. This study results in 52, 31, 12, 9, and 11 minimum energy structures on the potential energy surfaces of PheD, PheN, PheC, PheA, and PheZ, respectively. Several important nonbonded interactions such as hydrogen bonds, NH-pi, CH-pi, OH-pi, and pi-pi interactions, which impart stability to the monomeric and dimeric units, have been analyzed. The capability and strength of the nonbonded interactions drastically changing the conformational orientations of monomeric units has been illustrated.

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Implementation of renormalized excitonic method at ab initio level.

Publication Date: 2012 Jan 5 PMID: 21956437
Authors: Zhang, H. - Malrieu, J. P. - Ma, H. - Ma, J.
Journal: J Comput Chem

The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.

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Linear-scaling soft-core scheme for alchemical free energy calculations.

Publication Date: 2012 Jan 5 PMID: 21953650
Authors: Buelens, F. P. - Grubmuller, H.
Journal: J Comput Chem

Alchemical free energy calculations involving the removal or insertion of atoms into condensed phase systems generally make use of soft-core scaling of nonbonded interactions, designed to circumvent numerical instabilities that arise from weakly interacting "hard" atoms in close proximity. Current methods model soft-core atoms by introducing a nonlinear dependence between the shape of the interaction potential and the strength of the interaction. In this article, we propose a soft-core method that avoids introducing such a nonlinear dependence, through the application of a smooth flattening of the potential energy only in a region that is energetically accessible under normal conditions. We discuss the benefits that this entails and explore a selection of applications, including enhanced methods for the estimation of free energy differences and for the automated optimization of the placement of intermediate states in multistage alchemical calculations.

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The effect of structure and phase transformation on the mechanical properties of ReN and the stability of MnN.

Publication Date: 2012 Jan 5 PMID: 21953596
Authors: Du, X. P. - Lo, V. C. - Wang, Y. X.
Journal: J Comput Chem

First-principles calculations were carried out on recently synthesized ReN and ReN as well as hypothetical Tc and Mn nitrides. It is found that structure and covalent bonds play an important role in determining mechanical properties. Under a large strain along (0001)<1010> direction, ReN undergoes a phase transformation with a slight increase in ideal shear strength. On the other hand, it is transformed into a phase with weaker mechanical properties, if the strain is along Re <1210> direction. MnN can be synthesized under moderate conditions due to its more negative formation energy. ReN, ReN, and Mn N show structure-related mechanical property under larger strains to ReB but exhibit much lower ideal strengths, which is attributed to the larger ionicity of cation-anion bond. Three-dimensional framework of strong covalent bonds is thus highly recommended to design superhard materials.

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Electronic structure and low temperature thermoelectric properties of InMO (M = Ge(4+), Sn(4+), Ti(4+), and Zr(4+)).

Publication Date: 2012 Jan 5 PMID: 21952977
Authors: Yan, Y. L. - Wang, Y. X.
Journal: J Comput Chem

The electronic structure and transport properties of InMO (M = Ge(4+), Sn(4+), Ti(4+), and Zr(4+)) have been studied by using the full-potential linearized augmented plane-wave method and the semiclassical Boltzmann theory, respectively. It is found that the magnitude of powerfactor with respect to relation time follows the order of InSnO > InZrO > InGeO > InTiO. The largest powerfactor is 2.7 x 10(1)(2) W/K(2) ms for InSnO at 60 K, which is nearly thirty times larger than those of conventional n-type thermoelectric materials. The origin of the different thermoelectric behavior for these compounds is discussed from the electronic structure level. It is found that, at low temperature, the dopant strongly affect the bands near the Fermi level, which consequently leads to their different thermoelectric properties. The electronic configuration and the difference in atomic number between the dopant and the host atom also play an important role on the thermoelectric properties of InMO. Our calculations give a valuable insight on how to enhance the thermoelectric performance of InO.

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Pairwise verlet lists: combining cell lists and verlet lists to improve memory locality and parallelism.

Publication Date: 2012 Jan 5 PMID: 21952937
Authors: Gonnet, P.
Journal: J Comput Chem

Verlet lists, which are commonly used in many particle-based simulations, are not suited for modern, shared-memory parallel multicore architectures. In this article, we introduce pairwise Verlet lists: local Verlet lists containing only interacting particle pairs between a pair of neighboring computational cells. We show that these pairwise Verlet lists are more efficient and scale much better than the traditional global Verlet list, both on a single processor as well as on multiple shared-memory cores. The improved performance on a single core makes them an interesting option for distributed-memory simulations as well.

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Hydrogen abstraction reactions of OH radicals with CHCHCHCl and CHCHClCH: a mechanistic and kinetic study.

Publication Date: 2012 Jan 5 PMID: 21952915
Authors: Wang, L. - Li, Y. - He, H. - Zhang, J.
Journal: J Comput Chem

The hydrogen abstraction reactions of OH radicals with CHCHCHCl and CHCHClCH (R2) have been investigated theoretically by a dual-level direct dynamics method. The optimized geometries and frequencies of the stationary points are calculated at the B3LYP/6-311G(d,p) level. To improve the reaction enthalpy and potential barrier of each reaction channel, the single point energy calculation is performed by the BMC-CCSD method. Using canonical variational transition-state theory (CVT) with the small-curvature tunneling correction, the rate constants are evaluated over a wide temperature range of 200-2000 K at the BMC-CCSD//B3LYP/6-311G(d,p) level. For the reaction channels with the negative barrier heights, the rate constants are calculated by using the CVT. The calculated total rate constants are consistent with available experimental data. The results show that at lower temperatures, the tunneling correction has an important contribution in the calculation of rate constants for all the reaction channels with the positive barrier heights, while the variational effect is found negligible for some reaction channels. For reactions OH radicals with CHCHCHCl (R1) and CHCHClCH (R2), the channels of H-abstraction from -CH - and -CHCl groups are the major reaction channels, respectively, at lower temperatures. With temperature increasing, contributions from other channels should be taken into account. Finally, the total rate constants are fitted by two models, i.e., three-parameter and four-parameter expressions. The enthalpies of formation of the species CHCHClCH, CHCHCHCl, and CHCHCHCl are evaluated by isodesmic reactions.

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A sequence-based computational model for the prediction of the solvent accessible surface area for alpha-helix and beta-barrel transmembrane residues.

Publication Date: 2012 Jan 5 PMID: 21935968
Authors: Wang, C. - Xi, L. - Li, S. - Liu, H. - Yao, X.
Journal: J Comput Chem

Predicting the solvent accessible surface area (ASA) of transmembrane (TM) residues is of great importance for experimental researchers to elucidate diverse physiological processes. TM residues fall into two major structural classes (alpha-helix membrane protein and beta-barrel membrane protein). The reported solvent ASA prediction models were developed for these two types of TM residues respectively. However, this prevents the general use of these methods because one cannot determine which model is suitable for a given TM residue without information of its type. To conquer this limitation, we developed a new computational model that can be used for predicting the ASA of both TM alpha-helix and beta-barrel residues. The model was developed from 78 alpha-helix membrane protein chains and 24 beta-barrel membrane protein. Its prediction ability was evaluated by cross validation method and its prediction result on an independent test set of 20 membrane protein chains. The results show that our model performs well for both types of TM residues and outperforms other prediction model which was developed for the specific type of TM residues. The prediction results also proved that the random forest model incorporating conservation score is an effective sequence-based computational approach for predicting the solvent ASA of TM residues.

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Tight-binding molecular dynamics simulation of ZnSe liquid within the local environment dependence.

Publication Date: 2012 Jan 5 PMID: 21935967
Authors: Laref, A.
Journal: J Comput Chem

We investigate the structural, electronic and dynamical properties of ZnSe liquid using tight-binding molecular dynamics (TBMD) simulations. We report the TBMD calculations for the solid and liquid forms of the ZnSe compound. To produce more realistic results the TB model includes the local environment dependence in the Hamiltonian matrix at finite temperature for ZnSe. To further demonstrate the efficiency of the TBMD approach, we present results for finite temperature physical properties of ZnSe liquid. We are able to show good agreement with experiment for the atomic mean-squared displacement and melting point.

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