We present structural, electronic, bonding and vibrational properties of new type hydrogen storage material calcium amidoborane by first principles density functional theory using plane wave pseudopotential method. The calculated ground state properties are in good agreement with experiments. The computed Bulk modulus of is found to be 28.7 GPa which is slightly higher than that of indicating that the material is hard over . From the band structure calculations, the compound is found to be a direct band gap insulator with a band gap of 3.27 eV at the Γ point. The calculated bandstructure shows that the top of the valance band is from the p states of N and the bottom of the conduction band is from d states of Ca. The Mulliken bond populations, Born effective charges and charge density distributions are used to analyze the bonding nature of the compound. It is found that the N-H and B-H bonds are covalent in nature. Further we also compared the phonon density of states and vibrational frequencies of with . The study reveals that in both the cases the heavier mass atoms Ca, N, B are involved in the low frequency vibrations whereas the higher frequency vibrations are from H atoms. It is also observed that the vibrational frequencies of B-H bonds are soft in when compared to and thereby concluded that is a potential hydrogen storage material for fuel cell applications when compared to . © 2012 Wiley Periodicals, Inc.

We present a stochastic model for the kinetics of photoinduced anisotropy in a sample of molecular chromophores that may undergo photoisomerization. It is assumed that the chromo-phores do not interact among them, but are embedded in a medium that slows down the rotational diffusion. The model makes use of data about the photoinduced reorientation of the single chromophore, its photoisomerization and its rotational diffusion, that are made available by molecular dynamics simulations. For the first time such molecular scale processes are computationally connected to the development of anisotropy in a large sample and on a long time scale. A test on azobenzene shows the potentiality of the method and the interplay between photoinduced anisotropy and photoisomerization. © 2012 Wiley Periodicals, Inc.

Non-equilibrium molecular dynamics simulations of a solvated 21-residue polyalanine (A21) peptide, featuring a high propensity for helix formation, have been performed at 300 K and 1 bar in the presence of external electromagnetic (e/m) fields in the microwave region (2.45 GHz) and an r.m.s. electric field intensity range of 0.01–0.05 V/Å. To investigate how the field presence affects transitions between the conformational states of a protein, we report 16 independent 40 ns-trajectories of A21 starting from both extended and fully folded states. We observe folding-behavior of the peptide consistent with prior simulation and experimental studies. The peptide displays a natural tendency to form stable elements of secondary structure which are stabilized by tertiary interactions with proximate regions of the peptide. Consistent with our earlier work, the presence of external e/m fields disrupts this behavior, involving a mechanism of localized dipolar alignment which serves to enhance intra-protein perturbations in hydrogen bonds (English, et al., J. Chem. Phys.2010, 133, 091105), leading to more frequent transitions between shorter-lifetime states. © 2012 Wiley Periodicals, Inc.

The viability of making [Fe(CB₆)L] (L = H₂, N₂, O₂, nitric oxide [NO⁻, NO, and NO⁺], CO₂, and hydrocarbons [CH₄, C₂H₆, C₂H₄, and C₆H₆]) has been investigated by density functional theory (DFT) calculations. The complexes 2–18 are thermodynamically stable and may be synthesized. The small molecules are activated to some extent after complexation. Molecular orbital and ΔG calculation revealed that the molecular hydrogen and hydrocarbons can be chemically adsorbed and desorbed on [Fe(CB₆)] without any significant chemical modification and therefore [Fe(CB₆)] may serve as a storage material. The N₂, O₂, and nitric oxide (NO⁻, NO, and NO⁺) can be activated using [Fe(CB₆)]. Proton, carbon, boron, and nitrogen NMR chemical shift calculation predicts drastic chemical shift difference before and after the complexation of [Fe(CB₆)] with small molecules. This new findings suggest that the CB₆²⁻ ligand-based complex may provide several applications in the future. © 2012 Wiley Periodicals, Inc.

By sulfurization of phosphaalkenes (a) either (σ³,λ⁵)-phosphoranes (b) or (σ³,λ³)-thiaphosphiranes (c) are formed. In this study, Density Functional Theory (DFT) and coupled cluster (CCSD(T)) calculations have been carried out for model and experimental structures of (σ³,λ⁵)-phosphoranes and (σ³,λ³)-thiaphosphiranes to elucidate the factors influencing relative stabilities of b and c. According to the results of quantum chemical calculations, sterically bulky substituents make the phosphorane form more favored. Conversely, electronic effects of the most substituents provide higher stability for thiaphosphirane isomers. The only exception has been found in the cases where the substituent at the phosphorus atom possesses π-donor and σ-acceptor properties (e.g., in the case of amino group) and the substituents at carbon atom exhibit σ-donor/π-acceptor effects (e.g., silyl groups). The stability of the cyclic form c decreases further, if the substituents at the carbon atom are amino groups. In this case, a quite unusual structure has been theoretically predicted, which is considerably different from those of the hitherto known phosphoranes. It indicates a pyramidal configuration at the phosphorus atom and can be conventionally presented as a donor–acceptor adduct of diaminocarbene with thioxophosphine. © 2012 Wiley Periodicals, Inc.

Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro-drug approach, Pro-Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6-311+G** level of theory for the plausible mechanisms of action considered. In the five-membered ring case, transition state theory demonstrated how the overall, gas-phase, mechanism of action could be split into two in-line addition–elimination (A–E) steps separated by a penta-coordinate phosphorane intermediate. The difference between five-membered and six-membered ring first A–E was also explored, revealing a single step, unimolecular reaction for the six-membered ring A–E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A–E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro-Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate. © 2012 Wiley Periodicals, Inc.

In this article, we advance the foundations of a strategy to develop a molecular mechanics method based not on classical mechanics and force fields but entirely on quantum mechanics and localized electron-pair orbitals, which we call quantum molecular mechanics (QMM). Accordingly, we introduce a new manner of calculating Hartree–Fock ab initio wavefunctions of closed shell systems based on variationally preoptimized nonorthogonal electron pair orbitals constructed by linear combinations of basis functions centered on the atoms. QMM is noniterative and requires only one extremely fast inversion of a single sparse matrix to arrive to the one-particle density matrix, to the electron density, and consequently, to the ab initio electrostatic potential around the molecular system, or cluster of molecules. Although QMM neglects the smaller polarization effects due to intermolecular interactions, it fully takes into consideration polarization effects due to the much stronger intramolecular geometry distortions. For the case of methane, we show that QMM was able to reproduce satisfactorily the energetics and polarization effects of all distortions of the molecule along the nine normal modes of vibration, well beyond the harmonic region. We present the first practical applications of the QMM method by examining, in detail, the cases of clusters of helium atoms, hydrogen molecules, methane molecules, as well as one molecule of HeH⁺ surrounded by several methane molecules. We finally advance and discuss the potentialities of an exact formula to compute the QMM total energy, in which only two center integrals are involved, provided that the fully optimized electron-pair orbitals are known. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012

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. © 2012 Wiley Periodicals, Inc.

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 ∼0.15 Å in P/AsO bond lengths and less than 1.5° 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. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012

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. © 2012 Wiley Periodicals, Inc.

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(m⁴) and van Lenthe et al.'s approximate Newton Raphson algorithm scales at O(mN⁵) (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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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 Å 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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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 Møller-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. © 2012 Wiley Periodicals, Inc.

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 Ala₆ in implicit solvent. To test the efficiency of the implemented method, several 150 ns simulations of Ala₁₂ 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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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 (ΔE_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(C₆₀)₂), with the extended conjugated π-electrons, much degenerate orbitals and a uniform electrostatic potential surface, behave more pre-eminent photosensitizing properties than other examined fullerene derivatives. © 2012 Wiley Periodicals, Inc.

Posttranslational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role in modifying the end product of gene expression and contributes toward biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are not only costly but also time consuming. Hence, computational methods are highly desired. In this article, a novel encoding method PSDP (position-specific dipeptide propensity), which is a modified version of position-specific amino acid propensity, is developed. Then, a support vector machine SVM with the kernel matrix computed by PSDP is applied to predict the PTM sites related to serine (S) and threonine (T) residues. The numerical results indicate that the performance of new method is better than the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. As the application, a software PTMPred is developed for predicting phosphorylation and O-glycosylation sites, and available at http://www.aporc.org/doc/wiki/PTMPred. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012

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. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012

We analyze the behavior of the energy profile of the ring-closure process for the transformation of (3Z,5Z)-octa-1,3,5,7-tetraene 5 to (1Z,3Z,5Z)-cycloocta-1,3,5-triene 6 through a combination of electron localization function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1C8) = 2.342 Å, where all bonds have topological signature of single bonds (CC). The “new” C1C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1C8) ≈ 1.97 Å, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1C8 bond in the Lewis formula. In cycloocta-1,3,5-triene 6 the single C1C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

First principles-based kinetic Monte Carlo (kMC) simulations are performed for the CO oxidation on RuO₂(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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc.

We introduce PMF*, a novel potential of mean force (PMF) for the Ramachandran ϕ/Ψ 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 ΔPMF relative to the free energy of all amino acids in the parameterization set of structures, effectively removing their respective biases toward α-helix and β-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 ΔPMF energy functions. PMF* may be well suited for use as a restraint energy term in the refinement of experimental structures and theoretical models. © 2012 Wiley Periodicals, Inc.

A theoretical investigation on small silicon-doped lithium clusters Li_nSi 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_nSi with n ≤ 6 are formed by directly binding one Li to a Si of the smaller cluster Li_n−1Si, (ii) the structures tend to have an as high as possible symmetry and to maximize the coordination number of silicon. The first three-dimensional global minimum is found for Li₄Si, and (iii) for Li₇Si and Li₈Si, the global minima are formed by capping Li atoms on triangular faces of Li₆Si (O_h). A maximum coordination number of silicon is found to be 6 for the global minima, and structures with higher coordination of silicon exist but are less stable. Heats of formation at 0 K (Δ_fH⁰) and 298 K (Δ_fH²⁹⁸), average binding energies (E_b), adiabatic (AIE) and vertical (VIE) ionization energies, dissociation energies (D_e), and second-order difference in total energy (Δ²E) of the clusters in both neutral and cationic states are calculated from the CCSD(T)/CBS energies and used to evaluate the relative stability of clusters. The species Li₄Si, Li₆Si, and Li₅Si⁺ are the more stable systems with large HOMO–LUMO gaps, E_b, and Δ²E. Their enhanced stability can be rationalized using a modified phenomenological shell model, which includes the effects of additional factors such as geometrical symmetry and coordination number of the dopant. The new model is subsequently applied with consistency to other impure clusters Li_nX with X = B, Al, C, Si, Ge, and Sn. © 2012 Wiley Periodicals, Inc.

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. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012