Journal of Computational Chemistry

Conformational behavior of simple furanosides studied by optical rotation.

Publication Date: 2010 Feb 23 PMID: 20186863
Authors: Kaminsky, J. - Raich, I. - Tomcakova, K. - Bour, P.
Journal: J Comput Chem

Experimental and theoretical specific optical rotations (OR) of anhydro, epithio, and epiminoderivatives of methyl tetrofuranosides in chloroform solutions have been compared and used as a tool for exploring their conformational behavior. The potential energy surfaces of these saccharides with reduced flexibility were examined with the density functional theory and the MP2 and CCSD(T) wavefunctions methods. Theoretical ORs were obtained by Boltzmann averaging of values calculated for local minima. Resultant rotations could be used to assess the quality of the DFT and MP2 relative conformer energies. OR values calculated for equilibrium geometries in vacuum were significantly improved when the solvent was accounted for by a polarizable continuum model and first and diagonal second OR derivatives were used for an anharmonic vibrational averaging. The DFT used as a default method reproduced the experimental data fairly well. A modified B3LYP functional containing 70% of HF exchange further improved the results. Because of the strong dependence of OR on the conformation, not only the absolute configuration could be determined, but also the conformational populations were estimated. Likewise, the predicted dependence of OR on the light wavelength well agreed with experiment. The increasing precision of the contemporary computational methods thus makes it possible to relate the specific rotation to more detailed features in molecular structure. (c) 2010 Wiley Periodicals, Inc. J Comput Chem 2010.

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Mechanisms of norbornadiene dimerization to Binor-S using cationic Co(I), Rh,(I) and Ir(I) catalysts.

Publication Date: 2010 Feb 23 PMID: 20186862
Authors: Wu, Y. - Jin, L. - Xue, Y. - Lee, I. M. - Kim, C. K.
Journal: J Comput Chem

We investigated the transition metal-catalyzed reaction mechanisms of NBD dimerization to Binor-S using cationic Co(I), Rh(I), and Ir(I) catalysts, using mPW1PW91, mPW1K, and B3LYP density functional methods. Our results indicate that the monomeric metal center has the ability to bind with four double bonds of two NBD molecules with a syn spatial geometry to form a penta-coordinated complex. We designed three possible pathways, but found two of them blocked. The favored pathway involves three steps from the reactant precursor to the product precursor: the first step is the formation of a single bond to connect two NBD units, the second is the alkene insertion leading to the formation of the three-membered ring structure, and the final step is the formation of the final product precursor. Orbital analysis showed metal...C--C sigma agostic interaction in the product precursor, which is in agreement with the previous experimental findings. In addition, we found that the solvent and counter-ions had significant effects on the dimerization reactions. (c) 2010 Wiley Periodicals, Inc. J Comput Chem 2010.

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Molecular design of a "molecular syringe" mimic for metal cations using a 1,3-alternate calix[4]arene cavity.

Publication Date: 2010 Feb 23 PMID: 20186861
Authors: Zheng, X. - Wang, X. - Shen, K. - Wang, N. - Peng, Y.
Journal: J Comput Chem

The chemically switchable actions well imitate the function of a "molecular syringe," has been studied in theory using the 1,3-alternate calix [4]arene bearing a nitrogen-containing crown cap at one side and a bis(ethoxyethoxy) group at another side by the pi-basic calixtube as a pipette and the crown ring as a rubber cap. The model is characterized by geometry optimization using density functional theory (DFT) at B3LYP/6-31G level. The obtained optimized structures are used to perform natural bond orbital (NBO) and frequency analysis. The electron-donating heteroatoms: O and N offer lone pair electrons to the contacting RY* (1-center Rydberg) or LP* (1-center valence antibond lone pair) orbitals of K(+), Ag(+). The results indicate that when the nitrogen atom in the crown ring is protonated, K(+) and Ag(+) will be pushed out to the bis(ethoxyethoxy) side through a pi-basic calixtube. When the nitrogen.H(+) in the crown ring is deprotonated, K(+) and Ag(+) are sucked back to the crown-capped side again. In the course of the coordination, both the intermolecular electrostatic interactions and the cation-pi interactions between the metal ion and pi-orbitals of the two pairs facing inverted benzene rings play a significant role. It is believed that this prototype of a "molecular syringe" is a novel molecular architecture for the action of metal cations. (c) 2010 Wiley Periodicals, Inc. J Comput Chem 2010.

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A gradient-directed Monte Carlo approach for protein design.

Publication Date: 2010 Feb 23 PMID: 20186860
Authors: Hu, X. - Hu, H. - Beratan, D. N. - Yang, W.
Journal: J Comput Chem

We develop a new global optimization strategy, gradient-directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design. (c) 2010 Wiley Periodicals, Inc. J Comput Chem 2010.

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Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids.

Publication Date: 2010 Feb 19 PMID: 20175215
Authors: Zhu, X. - Koenig, P. - Hoffmann, M. - Yethiraj, A. - Cui, Q.
Journal: J Comput Chem

All-atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic beta-amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using beta(3)-homo-Alanine (beta(3)-hAla) diamide in water with SCC-DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the beta(3)-hAla diamide in water. The MM model is further applied to a beta-hepta-peptide in methanol solution. The calculated NOE values and (3)J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non-natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of beta amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that beta-amino-acid based random copolymers can develop a high degree of amphiphilicity without regular three-dimensional structure. (c) 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.

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Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence.

Publication Date: 2010 Feb 19 PMID: 20175214
Authors: Yu, J. F. - Sun, X.
Journal: J Comput Chem

Over annotation of protein coding genes is common phenomenon in microbial genomes, the genome of Amsacta moorei entomopoxvirus (AmEPV) is a typical case, because more than 63% of its annotated ORFs are hypothetical. In this article, we propose an improved graphical representation titled I-TN (improved curve based on trinucleotides) curve, which allows direct inspection of composition and distribution of codons and asymmetric gene structure. This improved graphical representation can also provide convenient tools for genome analysis. From this presentation, 18 variables are exploited as numerical descriptors to represent the specific features of protein coding genes quantitatively, with which we reannotate the protein coding genes in several viral genomes. Using the parameters trained on the experimentally validated genes, all of the 30 experimentally validated genes and 63 putative genes in AmEPV genome are recognized correctly as protein coding, the accuracies of the present method for self-test and cross-validation are 100%, respectively. Twenty-eight annotated hypothetical genes are predicted as noncoding, and then the number of reannotated protein coding genes in AmEPV should be 266 instead of 294 reported in the original annotations. Extending the present method trained in AmEPV to other entomopoxvirus genomes directly, such as Melanoplus sanguinipes entomopoxvirus (MsEPV), all of the 123 annotated function-known and putative genes are recognized correctly as protein coding, and 17 hypothetical genes are recognized as noncoding. The present method could also be extended to other genomes with or without adaptation of training sets with high accuracy. (c) 2010 Wiley Periodicals, Inc. J Comput Chem 2010.

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Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein.

Publication Date: 2010 Feb 17 PMID: 20166125
Authors: Li, H. - Li, C.
Journal: J Comput Chem

Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively. (c) 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.

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The QM-MM interface for CHARMM-deMon.

Publication Date: 2010 Apr 15 PMID: 20027641
Authors: Lev, B. - Zhang, R. - de la Lande, A. - Salahub, D. - Noskov, S. Y.
Journal: J Comput Chem

We present a new QM/MM interface for fast and efficient simulations of organic and biological molecules. The CHARMM/deMon interface has been developed and tested to perform minimization and atomistic simulations for multi-particle systems. The current features of this QM/MM interface include readability for molecular dynamics, tested compatibility with Free Energy Perturbation simulations (FEP) using the dual topology/single coordinate method. The current coupling scheme uses link atoms, but further extensions of the code to incorporate other available schemes are planned. We report the performance of different levels of theory for the treatment of the QM region, while the MM region was represented by a classical force-field (CHARMM27) or a polarizable force-field based on a simple Drude model. The current QM/MM implementation can be coupled to the dual-thermostat method and the VV2 integrator to run molecular dynamics simulations.

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Assessment of quantum-chemical methods for electronic properties and geometry of signaling biomolecules.

Publication Date: 2010 Apr 15 PMID: 19899146
Authors: Ferro, N. - Bredow, T.
Journal: J Comput Chem

A reasonable balance between accuracy and feasibility of quantum-chemical methods depends on the complexity of the molecular system and the scientific goals. Six series of indole-, naphthalene-, phenol-, benzoic-, phenoxy-, other auxin-derivatives, and a test set of similar organic molecules have been chosen for an assessment of 13 density functional and semi-empirical molecular orbital methods with respect to electronic and structural properties. The accuracy and precision of HOMO/LUMO calculations are determined by comparison with experimental ionization potentials and electron affinities. Further comparison was performed at atomic level by covariance analysis. The methods KMLYP, MSINDO, and PM3 are precise and accurate for the whole set of molecules. The method AM1 offers comparable accuracy with the exception of electron affinities of indole derivatives, where significant deviations from experiment were observed. Geometrical properties were best reproduced with the semi-empirical method MSINDO.

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A compound QM/MM procedure: comparative performance on a pyruvate formate-lyase model system.

Publication Date: 2010 Apr 15 PMID: 19847785
Authors: Condic-Jurkic, K. - Zipse, H. - Smith, D. M.
Journal: J Comput Chem

We present an ONIOM(G3:MM) method as an example of a technique capable of producing chemical accuracy in the quantum mechanical (QM) treatment with a molecular mechanical description context. By applying the method to small model systems, in which we are also able to calculate the pure QM G3-type results, it is possible to establish the reliability of the method as it applies to evaluating reaction mechanisms. By choosing small model systems that are relevant to the substrate mechanism of pyruvate formate-lyase, we are also able to discuss the inhibitory effect of oxamate and the relevance of an alternative H-abstraction mechanism in that context.

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Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

Publication Date: 2010 Apr 15 PMID: 19827144
Authors: Brylinski, M. - Skolnick, J.
Journal: J Comput Chem

The success of ligand docking calculations typically depends on the quality of the receptor structure. Given improvements in protein structure prediction approaches, approximate protein models now can be routinely obtained for the majority of gene products in a given proteome. Structure-based virtual screening of large combinatorial libraries of lead candidates against theoretically modeled receptor structures requires fast and reliable docking techniques capable of dealing with structural inaccuracies in protein models. Here, we present Q-Dock(LHM), a method for low-resolution refinement of binding poses provided by FINDSITE(LHM), a ligand homology modeling approach. We compare its performance to that of classical ligand docking approaches in ligand docking against a representative set of experimental (both holo and apo) as well as theoretically modeled receptor structures. Docking benchmarks reveal that unlike all-atom docking, Q-Dock(LHM) exhibits the desired tolerance to the receptor's structure deformation. Our results suggest that the use of an evolution-based approach to ligand homology modeling followed by fast low-resolution refinement is capable of achieving satisfactory performance in ligand-binding pose prediction with promising applicability to proteome-scale applications.

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ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

Publication Date: 2010 Apr 15 PMID: 19824035
Authors: Marsili, S. - Signorini, G. F. - Chelli, R. - Marchi, M. - Procacci, P.
Journal: J Comput Chem

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.

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Investigation on the individual contributions of N-H...O=C and C-H...O=C interactions to the binding energies of beta-sheet models.

Publication Date: 2010 Apr 15 PMID: 19821516
Authors: Wang, C. S. - Sun, C. L.
Journal: J Comput Chem

In this article, the binding energies of 16 antiparallel and parallel beta-sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for beta-sheet models. Further comparisons suggest that the binding energy of the beta-sheet models might come mainly from dipole-dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole-dipole attractive and repulsive interactions are further obtained in this article. The total of N-H...H-N and C=O...O=C dipole-dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel beta-sheet models is estimated to be about 6.0 kcal/mol. The individual N-H...O=C dipole-dipole attractive interaction is predicted to be -6.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -5.2 +/- 0.6 kcal/mol in the parallel beta-sheet models. The individual C(alpha)-H...O=C attractive interaction is -1.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -1.5 +/- 0.2 kcal/mol in the parallel beta-sheet models. These values are important in understanding the interactions at protein-protein interfaces and developing a more accurate force field for peptides and proteins.

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How the choice of a computational model could rule the chemical interpretation: the Ni(II) catalyzed ethylene dimerization as a case study.

Publication Date: 2010 Apr 15 PMID: 19821515
Authors: Tognetti, V. - Le Floch, P. - Adamo, C.
Journal: J Comput Chem

In this article, we present a critical study of the theoretical protocol used for the determination of the nickel(II) catalyzed ethylene dimerization mechanism, considered as a representative example of the various problems related to the modeling a catalytic cycle. The choice of an appropriate computational procedure is indeed crucial for the validity of the conclusions that will be drawn from the computational process. The influence of the exchange-correlation functional on energetic profiles and geometries, the role of the basis set describing the metal atom, as well as the importance of the chosen molecular model, have been thus examined in details. From the obtained results, some general conclusions and guidelines are presented, which could constitute useful warnings in modeling homogenous catalysis. Besides, the database constituted by our high-level calculations can be used within benchmarking procedures to assess the performances of new computational methods based on density functional theory.

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Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization.

Publication Date: 2010 Apr 15 PMID: 19821514
Authors: Vorobjev, Y. N.
Journal: J Comput Chem

This study describes the development of a new blind hierarchical docking method, bhDock, its implementation, and accuracy assessment. The bhDock method uses two-step algorithm. First, a comprehensive set of low-resolution binding sites is determined by analyzing entire protein surface and ranked by a simple score function. Second, ligand position is determined via a molecular dynamics-based method of global optimization starting from a small set of high ranked low-resolution binding sites. The refinement of the ligand binding pose starts from uniformly distributed multiple initial ligand orientations and uses simulated annealing molecular dynamics coupled with guided force-field deformation of protein-ligand interactions to find the global minimum. Assessment of the bhDock method on the set of 37 protein-ligand complexes has shown the success rate of predictions of 78%, which is better than the rate reported for the most cited docking methods, such as AutoDock, DOCK, GOLD, and FlexX, on the same set of complexes.

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Comparative study of various normal mode analysis techniques based on partial Hessians.

Publication Date: 2010 Apr 15 PMID: 19813181
Authors: Ghysels, A. - Van Speybroeck, V. - Pauwels, E. - Catak, S. - Brooks, B. R. - Van Neck, D. - Waroquier, M.
Journal: J Comput Chem

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein.

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Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation.

Publication Date: 2010 Apr 15 PMID: 19777597
Authors: Yao, Y. H. - Dai, Q. - Li, L. - Nan, X. Y. - He, P. A. - Zhang, Y. Z.
Journal: J Comput Chem

A (two-dimensional) 2D graphical representation of protein sequences based on six physicochemical properties of amino acids is outlined. The numerical characterization of protein graphs is given as descriptors of protein sequences. It is not only useful for comparative study of proteins but also for encoding innate information about the structure of proteins. The coefficient of determination is proposed as a new similarity/dissimilarity measure. Finally, a simple example is taken to highlight the behavior of the new similarity/dissimilarity measure on protein sequences taken from the ND6 (NADH dehydrogenase subunit 6) proteins for eight different species. The results demonstrate the approach is convenient, fast, and efficient.

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Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes.

Publication Date: 2010 Apr 15 PMID: 19777596
Authors: Holland, J. P. - Green, J. C.
Journal: J Comput Chem

The electronic absorption spectra of a range of copper and zinc complexes have been simulated by using time-dependent density functional theory (TD-DFT) calculations implemented in Gaussian03. In total, 41 exchange-correlation (XC) functionals including first-, second-, and third-generation (meta-generalized gradient approximation) DFT methods were compared in their ability to predict the experimental electronic absorption spectra. Both pure and hybrid DFT methods were tested and differences between restricted and unrestricted calculations were also investigated by comparison of analogous neutral zinc(II) and copper(II) complexes. TD-DFT calculated spectra were optimized with respect to the experimental electronic absorption spectra by use of a Matlab script. Direct comparison of the performance of each XC functional was achieved both qualitatively and quantitatively by comparison of optimized half-band widths, root-mean-squared errors (RMSE), energy scaling factors (epsilon(SF)), and overall quality-of-fit (Q(F)) parameters. Hybrid DFT methods were found to outperform all pure DFT functionals with B1LYP, B97-2, B97-1, X3LYP, and B98 functionals providing the highest quantitative and qualitative accuracy in both restricted and unrestricted systems. Of the functionals tested, B1LYP gave the most accurate results with both average RMSE and overall Q(F) < 3.5% and epsilon(SF) values close to unity (>0.990) for the copper complexes. The XC functional performance in spin-restricted TD-DFT calculations on the zinc complexes was found to be slightly worse. PBE1PBE, mPW1PW91 and B1LYP gave the most accurate results with typical RMSE and Q(F) values between 5.3 and 7.3%, and epsilon(SF) around 0.930. These studies illustrate the power of modern TD-DFT calculations for exploring excited state transitions of metal complexes.

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A new strategy to improve the predictive ability of the local lazy regression and its application to the QSAR study of melanin-concentrating hormone receptor 1 antagonists.

Publication Date: 2010 Apr 15 PMID: 19670228
Authors: Li, J. - Li, S. - Lei, B. - Liu, H. - Yao, X. - Liu, M. - Gramatica, P.
Journal: J Comput Chem

In the quantitative structure-activity relationship (QSAR) study, local lazy regression (LLR) can predict the activity of a query molecule by using the information of its local neighborhood without need to produce QSAR models a priori. When a prediction is required for a query compound, a set of local models including different number of nearest neighbors are identified. The leave-one-out cross-validation (LOO-CV) procedure is usually used to assess the prediction ability of each model, and the model giving the lowest LOO-CV error or highest LOO-CV correlation coefficient is chosen as the best model. However, it has been proved that the good statistical value from LOO cross-validation appears to be the necessary, but not the sufficient condition for the model to have a high predictive power. In this work, a new strategy is proposed to improve the predictive ability of LLR models and to access the accuracy of a query prediction. The bandwidth of k neighbor value for LLR is optimized by considering the predictive ability of local models using an external validation set. This approach was applied to the QSAR study of a series of thienopyrimidinone antagonists of melanin-concentrating hormone receptor 1. The obtained results from the new strategy shows evident improvement compared with the commonly used LOO-CV LLR methods and the traditional global linear model.

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An ab initio potential energy surface and vibrational energy levels of ZnH2.

Publication Date: 2010 Apr 15 PMID: 19670227
Authors: Huang, Z. G. - Yu, L. - Dai, Y. M.
Journal: J Comput Chem

A three-dimensional potential energy surface of the electronic ground state of ZnH(2) (X1 Sigma(g)+) molecule is constructed from more than 7500 ab initio points calculated at the internally contracted multireference configuration interaction with the Davidson correction (icMRCI+Q) level employing large basis sets. The calculated relative energies of various dissociation reactions are in good agreement with the previous theoretical/experimental values. Low-lying vibrational energy levels of ZnH(2), ZnD(2), and HZnD are calculated on the three-dimensional potential energy surface using the Lanczos algorithm, and found to be in good agreement with the available experimental band origins and the previous theoretical values.

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Interaction energy and the shift in OH stretch frequency on hydrogen bonding for the H2O --> H2O, CH3OH --> H2O, and H2O --> CH3OH dimers.

Publication Date: 2010 Apr 15 PMID: 19655308
Authors: Campen, R. K. - Kubicki, J. D.
Journal: J Comput Chem

The ability to use calculated OH frequencies to assign experimentally observed peaks in hydrogen bonded systems hinges on the accuracy of the calculation. Here we test the ability of several commonly employed model chemistries--HF, MP2, and several density functionals paired with the 6-31+G(d) and 6-311++G(d,p) basis sets--to calculate the interaction energy (D(e)) and shift in OH stretch fundamental frequency on dimerization (delta(nu)) for the H(2)O --> H(2)O, CH(3)OH --> H(2)O, and H(2)O --> CH(3)OH dimers (where for X --> Y, X is the hydrogen bond donor and Y the acceptor). We quantify the error in D(e) and delta(nu) by comparison to experiment and high level calculation and, using a simple model, evaluate how error in D(e) propagates to delta(nu). We find that B3LYP and MPWB1K perform best of the density functional methods studied, that their accuracy in calculating delta(nu) is approximately 30-50 cm(-1) and that correcting for error in D(e) does little to heighten agreement between the calculated and experimental delta(nu). Accuracy of calculated delta(nu) is also shown to vary as a function of hydrogen bond donor: while the PBE and TPSS functionals perform best in the calculation of delta(nu) for the CH(3)OH --> H(2)O dimer their performance is relatively poor in describing H(2)O --> H(2)O and H(2)O --> CH(3)OH.

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Theoretical study on the gas-phase reaction mechanism between rhodium monoxide and methane for methanol production.

Publication Date: 2010 Apr 15 PMID: 19655307
Authors: Gao, C. - Yang, H. Q. - Xu, J. - Qin, S. - Hu, C. W.
Journal: J Comput Chem

The gas-phase reaction mechanism between methane and rhodium monoxide for the formation of methanol, syngas, formaldehyde, water, and methyl radical have been studied in detail on the doublet and quartet state potential energy surfaces at the CCSD(T)/6-311+G(2d, 2p), SDD//B3LYP/6-311+G(2d, 2p), SDD level. Over the 300-1100 K temperature range, the branching ratio for the Rh((4)F) + CH(3)OH channel is 97.5-100%, whereas the branching ratio for the D-CH(2)ORh + H(2) channel is 0.0-2.5%, and the branching ratio for the D-CH(2)ORh + H(2) channel is so small to be ruled out. The minimum energy reaction pathway for the main product methanol formation involving two spin inversions prefers to both start and terminate on the ground quartet state, where the ground doublet intermediate CH(3)RhOH is energetically preferred, and its formation rate constant over the 300-1100 K temperature range is fitted by k(CH3RhOH) = 7.03 x 10(6) exp(-69.484/RT) dm(3) mol(-1) s(-1). On the other hand, the main products shall be Rh + CH(3)OH in the reactions of RhO + CH(4), CH(2)ORh + H(2), Rh + CO +2H(2), and RhCH(2) + H(2)O, whereas the main products shall be CH(2)ORh + H(2) in the reaction of Rh + CH(3)OH. Meanwhile, the doublet intermediates H(2)RhOCH(2) and CH(3)RhOH are predicted to be energetically favored in the reactions of Rh + CH(3)OH and CH(2)ORh + H(2) and in the reaction of RhCH(2) + H(2)O, respectively.

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Electronic properties for small tin clusters Sn(n) (n < or = 20) from density functional theory and the convergence toward the solid state.

Publication Date: 2010 Apr 15 PMID: 19655306
Authors: Assadollahzadeh, B. - Schafer, S. - Schwerdtfeger, P.
Journal: J Comput Chem

Global minimum structures of neutral tin clusters with up to 20 atoms obtained recently from genetic algorithm simulations within a density-functional approach (Schafer et al., J Phys Chem A 2008, 112, 12312) were used to evaluate the corresponding electronic properties. The evolution of these properties with increasing cluster size is discussed in detail and compared with the lighter silicon and germanium clusters. We also discuss the extrapolation of these properties to the bulk limit.

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Electronic structures of heme a of cytochrome c oxidase in the redox states--charge density migration to the propionate groups of heme a.

Publication Date: 2010 Apr 15 PMID: 19645053
Authors: Takano, Y. - Nakamura, H.
Journal: J Comput Chem

The electronic structures of heme a of cytochrome c oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe ion are determined by the orbital interactions of the d orbitals of the Fe ion with the pi orbitals of the porphyrin ring and the His residues. The redox reaction of the Fe ion influences the charge density on the formyl group through the pi conjugation of the porphyrin ring. In addition, we found the charge transfer from the Fe ion to the propionate group of heme a in the redox change despite the lack of the pi-conjugation. We elucidated that the charge propagation originates from the heme a structure itself and that the origin of the charge delocalization to the heme propionate is the orbital interactions between the d orbital of the Fe ion and the p orbitals of the carboxylate part of the heme propionate via the pi conjugation of the porphyrin ring and the sigma* orbital of the C-C bond of the propionate group. The electrostatic effect by surrounding proteins enhances the charge transfer from the Fe ion to the propionate group. These results indicate that heme propionate groups serve electron mediators in electron transfer as well as electrostatic anchors, and that proteins surrounding the active site reinforce the congenital abilities of the cofactors.

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A universal scale of aromaticity for pi-organic compounds.

Publication Date: 2010 Apr 15 PMID: 19637212
Authors: Alonso, M. - Herradon, B.
Journal: J Comput Chem

Aromaticity is an essential concept in chemistry, invented to account for the stability, reactivity, molecular structure, and properties of many organic and inorganic compounds. In recent years, numerous methods to quantify aromaticity based on the energetic, magnetic, structural, and electronic properties of molecules have been proposed but none of them is universal. The inability of establishing a universal scale of aromaticity based on a single parameter is due to the multidimensional character of this phenomenon. Consequently, aromaticity analyses should be carried out by employing a set of aromaticity descriptors on the basis of different physical manifestations of aromaticity. Here, we report a universal scale of aromaticity for pi-organic compounds based on the Euclidean distance between neurons in a self-organizing map. The most widely used aromaticity indicators have been used as molecular descriptors, and so our approach provides the first scale of aromaticity which contains the energetic, magnetic, and structural aspects of this property. The method is applicable to a wide variety of unsaturated organic compounds and allows quantification of both aromaticity and antiaromaticity. Additionally, the position of a compound on the bidimensional map determinates immediately the following: (a) the group (aromatic, nonaromatic, or antiaromatic) to which the system belongs, (b) their degree of pi-electronic delocalization, and (c) the similarity in aromaticity/antiaromaticity between different compounds. This new scale of aromaticity is able to indicate the expected order of aromaticity of analogues of fulvene and heptafulvene, heteroaromatic species, substituted benzenes, and functionalized cyclopentadienyl compounds.

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An efficient algorithm for multistate protein design based on FASTER.

Publication Date: 2010 Apr 15 PMID: 19637210
Authors: Allen, B. D. - Mayo, S. L.
Journal: J Comput Chem

Most of the methods that have been developed for computational protein design involve the selection of side-chain conformations in the context of a single, fixed main-chain structure. In contrast, multistate design (MSD) methods allow sequence selection to be driven by the energetic contributions of multiple structural or chemical states simultaneously. This methodology is expected to be useful when the design target is an ensemble of related states rather than a single structure, or when a protein sequence must assume several distinct conformations to function. MSD can also be used with explicit negative design to suggest sequences with altered structural, binding, or catalytic specificity. We report implementation details of an efficient multistate design optimization algorithm based on FASTER (MSD-FASTER). We subjected the algorithm to a battery of computational tests and found it to be generally applicable to various multistate design problems; designs with a large number of states and many designed positions are completely feasible. A direct comparison of MSD-FASTER and multistate design Monte Carlo indicated that MSD-FASTER discovers low-energy sequences much more consistently. MSD-FASTER likely performs better because amino acid substitutions are chosen on an energetic basis rather than randomly, and because multiple substitutions are applied together. Through its greater efficiency, MSD-FASTER should allow protein designers to test experimentally better-scoring sequences, and thus accelerate progress in the development of improved scoring functions and models for computational protein design.

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Density functional theory study of the free and tetraprotonated spheroidal macrotricyclic ligands and the complexes with halide anions: F(-), Cl(-), Br(-).

Publication Date: 2010 Mar PMID: 19618416
Authors: Zheng, X. - Wang, X. - Yi, S. - Wang, N. - Peng, Y.
Journal: J Comput Chem

Theoretical studies of the macrotricyclic tetramine hexaether (SC), its tetraprotonated form SC-4H(+), and the corresponding complexes X(-) subsetSC-4H(+) (This expression represents the structural properties of the halide inclusion complex formed though the free ligand SC-4H(+) and the halide anion X(-): the spherical halide anion X(-) is held by a tetrahedral array of (+)N--H...X(-) hydrogen bonds inside the intramolecular cavity of the tetraprotonated form SC-4H(+)) of SC-4H(+) with the halide anions: F(-), Cl(-), and Br(-) have been performed using density functional theory (DFT) with B3LYP/6-31G method implemented in the Gaussian 03 program package. The optimized geometric structures obtained from DFT calculations are used to perform Natural Bond Orbital (NBO) analysis. The three main types of hydrogen bonds (+)N--H...F(-), (+)N--H...Cl(-), and (+)N--H...Br(-) are investigated. The results indicate that hydrogen bonding interactions are dominant and the halide anions: F(-), Cl(-), and Br(-) offer lone pair electrons to the contacting sigma* (N--H) antibond orbital of SC-4H(+). For all the structures, the most pronounced changes in geometric parameters upon interaction are observed in the proton-donor molecule. The intermolecular interaction energies are predicted by using B3LYP/6-31G methods with basis set superposition error (BSSE) and zero-point energy (ZPE) correction.

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New angle-dependent potential energy function for backbone-backbone hydrogen bond in protein-protein interactions.

Publication Date: 2010 Apr 15 PMID: 19618414
Authors: Choi, H. - Kang, H. - Park, H.
Journal: J Comput Chem

Backbone-backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein-protein complex. Here, we propose an angle-dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy function is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard-Jones 12-10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge-based potential derived by applying Boltzmann statistics for a variety of protein-protein complexes in protein data bank.

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Designing novel antitrypanosomal agents from a mixed graph-theoretical substructural approach.

Publication Date: 2010 Mar PMID: 19618411
Authors: Planche, A. S. - Scotti, M. T. - Emerenciano Vde, P. - Lopez, A. G. - Perez, E. M. - Uriarte, E.
Journal: J Comput Chem

Chagas disease is nowadays the most serious parasitic health problem. This disease is caused by Trypanosoma cruzi. The great number of deaths and the insufficient effectiveness of drugs against this parasite have alarmed the scientific community worldwide. In an attempt to overcome this problem, a model for the design and prediction of new antitrypanosomal agents was obtained. This used a mixed approach, containing simple descriptors based on fragments and topological substructural molecular design descriptors. A data set was made up of 188 compounds, 99 of them characterized an antitrypanosomal activity and 88 compounds that belong to other pharmaceutical categories. The model showed sensitivity, specificity and accuracy values above 85%. Quantitative fragmental contributions were also calculated. Then, and to confirm the quality of the model, 15 structures of molecules tested as antitrypanosomal compounds (that we did not include in this study) were predicted, taking into account the information on the abovementioned calculated fragmental contributions. The model showed an accuracy of 100% which means that the "in silico" methodology developed by our team is promising for the rational design of new antitrypanosomal drugs.

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On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

Publication Date: 2010 Mar PMID: 19603502
Authors: Noel, Y. - D'arco, P. - Demichelis, R. - Zicovich-Wilson, C. M. - Dovesi, R.
Journal: J Comput Chem

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented.

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Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.

Publication Date: 2010 Mar PMID: 19603501
Authors: Wang, L. - Stumm, B. - Helms, V.
Journal: J Comput Chem

Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction.

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Theoretical study on nonlinear optical properties of the Li(+)[calix[4]pyrrole]Li(-)dimer, trimer and its polymer with diffuse excess electrons.

Publication Date: 2010 Mar PMID: 19603500
Authors: Yu, G. T. - Chen, W. - Gu, F. L. - Aoki, Y.
Journal: J Comput Chem

The static (hyper)polarizabilities of the dimer and trimer with diffuse excess electrons, [Li(+)[calix[4]pyrrole]Li(-)](n), are firstly investigated by the DFT(B3LYP) method in detail. For the dimer and trimer, a Li atom inside each calix[4]pyrrole unit is ionized to form a diffuse excess electron. The results show that the dimer and trimer containing two and three excess electrons, respectively, have very large first hyperpolarizablities as 2.3 x 10(4) and 4.0 x 10(4) au, which are 30 and 40 times larger than that of the corresponding [calix[4]pyrrole](n) (n = 2, 3) without Li atom. Also, beta values of dimer and trimer are twice and four times as large as that of monomer containing one excess electron. Obviously, not only excess electron but also the number of excess electron plays an important role in increasing the first hyperpolarizability. Moreover, the (hyper)polarizabilities of the [Li(+)[calix[4]pyrrole]Li(-)](n) polymer are investigated at ab initio level by using the elongation finite-field (elongation FF) method. All the oligomers of the [Li(+)[calix[4]pyrrole]Li(-)](n) with many excess electrons exhibit very large first hyperpolarizability and large second hyperpolarizability. The present investigation shows that by introducing several and more excess electrons into the nonlinear optical (NLO) materials will be an important strategy for improving their NLO properties, which will be helpful for design of NLO materials.

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Absorption and fluorescence emission spectroscopic characters of naphtho-homologated yy-DNA bases and effect of methanol solution and base pairing.

Publication Date: 2010 Mar PMID: 19598267
Authors: Zhang, L. - Li, H. - Li, J. - Chen, X. - Bu, Y.
Journal: J Comput Chem

A comprehensive theoretical study of electronic transitions of naphtho-homologated base analogs, namely, yy-T, yy-C, yy-A, and yy-G, was performed. The nature of the low-lying excited states is discussed, and the results are compared with those from experiment and also with those of y-bases. Geometrical characteristics of the lowest excited singlet pipi* and npi* states were explored using the CIS method, and the effects of methanol solution and paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were examined. The calculated excitation and emission energies agree well with the measured data, where experimental results are available. In methanol solution, the fluorescence from yy-A and yy-G would be expected to occur around 539 and 562 nm, respectively, suggesting that yy-A is a green-colored fluorophore, whereas yy-G is a yellow-colored fluorophore. The methanol solution was found to red-shift both the absorption and emission maxima of yy-A, yy-T, and yy-C, but blue-shift those for yy-G. Generally, though base pairing has no significant effects on the absorption and fluorescence maxima of yy-A, yy-C, and yy-T, it blue-shifts those for yy-G.

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Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions.

Publication Date: 2010 Mar PMID: 19598266
Authors: Truchon, J. F. - Nicholl's, A. - Grant, J. A. - Iftimie, R. I. - Roux, B. - Bayly, C. I.
Journal: J Comput Chem

Recently, the vacuum-phase molecular polarizability tensor of various molecules has been accurately modeled (Truchon et al., J Chem Theory Comput 2008, 4, 1480) with an intramolecular continuum dielectric model. This preliminary study showed that electronic polarization can be accurately modeled when combined with appropriate dielectric constants and atomic radii. In this article, using the parameters developed to reproduce ab initio quantum mechanical (QM) molecular polarizability tensors, we extend the application of the "electronic polarization from internal continuu" (EPIC) approach to intermolecular interactions. We first derive a dielectric-adapted least-square-fit procedure similar to RESP, called DRESP, to generate atomic partial charges based on a fit to a QM abinitio electrostatic potential (ESP). We also outline a procedure to adapt any existing charge model to EPIC. The ability of this to reproduce local polarization, as opposed to uniform polarization, is also examined leading to an induced ESP relative root mean square deviation of 1%, relative to ab initio, when averaged over 37 molecules including aromatics and alkanes. The advantage of using a continuum model as opposed to an atom-centered polarizable potential is illustrated with a symmetrically perturbed atom and benzene. We apply EPIC to a cation-pi binding system formed by an atomic cation and benzene and show that the EPIC approach can accurately account for the induction energy. Finally, this article shows that the ab initio electrostatic component in the difficult case of the H-bonded 4-pyridone dimer, a highly polar and polarized interaction, is well reproduced without adjusting the vacuum-phase parameters.

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How to obtain statistically converged MM/GBSA results.

Publication Date: 2010 Mar PMID: 19598265
Authors: Genheden, S. - Ryde, U.
Journal: J Comput Chem

The molecular mechanics/generalized Born surface area (MM/GBSA) method has been investigated with the aim of achieving a statistical precision of 1 kJ/mol for the results. We studied the binding of seven biotin analogues to avidin, taking advantage of the fact that the protein is a tetramer with four independent binding sites, which should give the same estimated binding affinities. We show that it is not enough to use a single long simulation (10 ns), because the standard error of such a calculation underestimates the difference between the four binding sites. Instead, it is better to run several independent simulations and average the results. With such an approach, we obtain the same results for the four binding sites, and any desired precision can be obtained by running a proper number of simulations. We discuss how the simulations should be performed to optimize the use of computer time. The correlation time between the MM/GBSA energies is approximately 5 ps and an equilibration time of 100 ps is needed. For MM/GBSA, we recommend a sampling time of 20-200 ps for each separate simulation, depending on the protein. With 200 ps production time, 5-50 separate simulations are required to reach a statistical precision of 1 kJ/mol (800-8000 energy calculations or 1.5-15 ns total simulation time per ligand) for the seven avidin ligands. This is an order of magnitude more than what is normally used, but such a number of simulations is needed to obtain statistically valid results for the MM/GBSA method.

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CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Publication Date: 2010 Mar PMID: 19575467
Authors: Vanommeslaeghe, K. - Hatcher, E. - Acharya, C. - Kundu, S. - Zhong, S. - Shim, J. - Darian, E. - Guvench, O. - Lopes, P. - Vorobyov, I. - Mackerell, A. D. Jr
Journal: J Comput Chem

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

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Covalent hydration energies for purine analogs by quantum chemical methods.

Publication Date: 2010 Mar PMID: 19569207
Authors: Wang, S. C. - Beal, P. A. - Tantillo, D. J.
Journal: J Comput Chem

In this work, covalent hydration energies for a variety of azanaphthalenes and purine analogs have been calculated using a variety of quantum chemical methods. On the basis of these results, we recommend the CPCM(UA0)-B3LYP/6-31+G(d,p) level for rapid prediction of covalent hydration energies. However, we caution the use of this methodology for computing covalent hydration energies for fluorine-containing compounds.

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Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.

Publication Date: 2010 Mar PMID: 19569205
Authors: Rastelli, G. - Del Rio, A. - Degliesposti, G. - Sgobba, M.
Journal: J Comput Chem

In the drug discovery process, accurate methods of computing the affinity of small molecules with a biological target are strongly needed. This is particularly true for molecular docking and virtual screening methods, which use approximated scoring functions and struggle in estimating binding energies in correlation with experimental values. Among the various methods, MM-PBSA and MM-GBSA are emerging as useful and effective approaches. Although these methods are typically applied to large collections of equilibrated structures of protein-ligand complexes sampled during molecular dynamics in water, the possibility to reliably estimate ligand affinity using a single energy-minimized structure and implicit solvation models has not been explored in sufficient detail. Herein, we thoroughly investigate this hypothesis by comparing different methods for the generation of protein-ligand complexes and diverse methods for free energy prediction for their ability to correlate with experimental values. The methods were tested on a series of structurally diverse inhibitors of Plasmodium falciparum DHFR with known binding mode and measured affinities. The results showed that correlations between MM-PBSA or MM-GBSA binding free energies with experimental affinities were in most cases excellent. Importantly, we found that correlations obtained with the use of a single protein-ligand minimized structure and with implicit solvation models were similar to those obtained after averaging over multiple MD snapshots with explicit water molecules, with consequent save of computing time without loss of accuracy. When applied to a virtual screening experiment, such an approach proved to discriminate between true binders and decoy molecules and yielded significantly better enrichment curves.

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Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: Development and application to the beta(2)-adrenergic receptor.

Publication Date: 2010 Mar PMID: 19569204
Authors: Vilar, S. - Karpiak, J. - Costanzi, S.
Journal: J Comput Chem

In this study, we evaluated the applicability of ligand-based and structure-based models to quantitative affinity predictions and virtual screenings for ligands of the beta(2)-adrenergic receptor, a G protein-coupled receptor (GPCR). We also devised and evaluated a number of consensus models obtained through partial least square regressions, to combine the strengths of the individual components. In all cases, the bioactive conformation of each ligand was derived from molecular docking at the crystal structure of the receptor. We identified the most effective models applicable to the different scenarios, in the presence or in the absence of a training set. For ranking the affinity of closely related analogs when a training set is available, a ligand-based consensus model (LI-CM) seems to be the best choice, while the structure-based MM-GBSA score seems the best alternative in the absence of a training set. For virtual screening purposes, the structure-based MM-GBSA score was found to be the method of choice. Consensus models consistently had performances superior or close to those of the best individual components, and were endowed with a significantly increased robustness. Given multiple models with no a priori knowledge of their predictive capabilities, constructing a consensus model ensures results very close to those that the best model alone would have yielded.

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Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity.

Publication Date: 2010 Mar PMID: 19569203
Authors: Tawari, N. R. - Degani, M. S.
Journal: J Comput Chem

A five point pharmacophore was generated using PHASE for a series of nitroaromatic compounds and their congeners as antitubercular agents. The generated pharmacophore yielded significant 3D-QSAR model with r(2) of 0.890 for a training set of 92 molecules. The model also showed excellent predictive power with correlation coefficient Q(2) of 0.857 for a test set of 31 compounds. The pharmacophore indicated that presence of a nitro group, a piperazine moiety, one aromatic ring feature and two acceptor features are necessary for potent antitubercular activity. The pharmacophore was supported by electronic property analysis using density functional theory (DFT) at B3LYP/3-21*G level. Molecular electrostatic profile of the compounds was consistent with the generated pharmacophore model, particularly appearance of localized negative potential regions near both the oxygen atoms of nitro group extending laterally to the isoxazole ring system/amide bond in the most active compounds. Calculated data further revealed that all active compounds have smaller LUMO energies located over the nitro group, furan ring, and isoxazole ring/amide bond attached to it. Higher negative values of LUMO energies concentrated over the nitro group are indicative of the electron acceptor capacity of the compounds, suggesting that these compounds are prodrugs and must be activated by TB-nitroreductase. The results obtained from this study should aid in efficient design and development of nitroaromatic compounds as antitubercular agents.

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Identification of small molecule aggregators from large compound libraries by support vector machines.

Publication Date: 2010 Mar PMID: 19569201
Authors: Rao, H. - Li, Z. - Li, X. - Ma, X. - Ung, C. - Li, H. - Liu, X. - Chen, Y.
Journal: J Comput Chem

Small molecule aggregators non-specifically inhibit multiple unrelated proteins, rendering them therapeutically useless. They frequently appear as false hits and thus need to be eliminated in high-throughput screening campaigns. Computational methods have been explored for identifying aggregators, which have not been tested in screening large compound libraries. We used 1319 aggregators and 128,325 non-aggregators to develop a support vector machines (SVM) aggregator identification model, which was tested by four methods. The first is five fold cross-validation, which showed comparable aggregator and significantly improved non-aggregator identification rates against earlier studies. The second is the independent test of 17 aggregators discovered independently from the training aggregators, 71% of which were correctly identified. The third is retrospective screening of 13M PUBCHEM and 168K MDDR compounds, which predicted 97.9% and 98.7% of the PUBCHEM and MDDR compounds as non-aggregators. The fourth is retrospective screening of 5527 MDDR compounds similar to the known aggregators, 1.14% of which were predicted as aggregators. SVM showed slightly better overall performance against two other machine learning methods based on five fold cross-validation studies of the same settings. Molecular features of aggregation, extracted by a feature selection method, are consistent with published profiles. SVM showed substantial capability in identifying aggregators from large libraries at low false-hit rates.

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Stability of the hydration layer of tropocollagen: A QM study.

Publication Date: 2010 Mar PMID: 19569200
Authors: Palfi, V. K. - Perczel, A.
Journal: J Comput Chem

Collagen is a triple helical protein, highly hydrated in nature. Bella and Berman (J Mol Biol 1996, 264, 734) have reported the structure of the first hydration layer. Water molecules form bridges of different length around the POG repeats and self assemble into left-handed helical water threads. To explore the stability of these specifically hydrated places, we have designed suitable QM models: each comprises a triple helix formed by 18 residues surrounded by 8 to 12 explicit waters. Two sets of amino acids were used, one standing for the core structural subunit of tropocollagen (POG-model) and one for its natural enzyme recognition sites (AAG-model). We have determined the stability order of the water binding places, the strongest being -8.1 kcal mol(-1), while the weakest -6.1 kcal mol(-1) per hydrogen bond. In X-ray structures, each triplet of tropocollagen is shielded by six to nine water molecules. Beside the mandatory six, the "surplus" three water molecules further strengthen the binding of all the others. However, the displacement of selected water molecules turns out to be energy neutral. These water binding places on the surface of the triple helix can provide explanation on how an almost liquid-like hydration environment exists between the closely packed tropocollagens (Henkelman et al., Magn Reson Med 1994, 32, 592). It seems that these water reservoirs or buffers can provide space for "hole conduction" of water molecules and thus contribute to the elasticity of collagen.

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Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein.

Publication Date: 2010 Mar PMID: 19569185
Authors: Murata, K. - Nagata, N. - Nakanishi, I. - Kitaura, K.
Journal: J Comput Chem

Solvent dipole ordering (SDO), introduced by Higo et al. (Proteins Struct Funct Genet 2000, 40, 193), is an entity that captures an aspect of hydration structure. We have studied SDO in the ligand binding site of two proteins (FK506 binding protein and dihydrofolate reductase) and found that the high SDO regions overlap significantly with the 3D structures of known inhibitors bound to the proteins. Thus, the SDO region might be used to predict the preferred molecular shape of ligands that bind to a protein. Based on this finding, we propose a novel docking procedure using model molecules that mimic the shape of the SDO region. To prove the validity of thisapproach, we performed a redocking experiment for p38 mitogen-activated protein kinase ligands using model molecules for search queries; we succeeded in identifying the binding conformations and binding modes of known inhibitors.

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Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation.

Publication Date: 2010 Mar PMID: 19569184
Authors: Li, H. - Fedorov, D. G. - Nagata, T. - Kitaura, K. - Jensen, J. H. - Gordon, M. S.
Journal: J Comput Chem

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6-31G* level) is used to optimize the solution structure of the 304-atom Trp-cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the alpha-helix, beta-turn and the extended form in solution are elucidated for polyalanine.

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An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions.

Publication Date: 2010 Mar PMID: 19569183
Authors: Anandakrishnan, R. - Onufriev, A. V.
Journal: J Comput Chem

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long-distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof-of-concept implementation of the HCP shows that for large structures it can lead to speed-up factors of up to several orders of magnitude relative to the exact pairwise O(N(2)) all-atom computation used as a reference. For structures with more than 2000-3000 atoms the relative accuracy of the HCP (relative root-mean-square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models.

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A fast method for large-scale De Novo peptide and miniprotein structure prediction.

Publication Date: 2010 Mar PMID: 19569182
Authors: Maupetit, J. - Derreumaux, P. - Tuffery, P.
Journal: J Comput Chem

Although peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large-scale experiments is still missing. We introduce a new approach-PEP-FOLD-to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model-derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse-grained energy score. On a benchmark of 52 peptides with 9-23 amino acids, PEP-FOLD generates lowest-energy conformations within 2.8 and 2.3 A Calpha root-mean-square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27-49 amino acids, PEP-FOLD reaches an accuracy of 3.6 and 4.6 A Calpha root-mean-square deviation for the most-native and lowest-energy conformations, using the nonflexible regions identified by NMR. PEP-FOLD simulations are fast-a few minutes only-opening therefore, the door to in silico large-scale rational design of new bioactive peptides and miniproteins.

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Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason?

Publication Date: 2010 Mar PMID: 19557765
Authors: Schlund, S. - Basilio Janke, E. M. - Weisz, K. - Engels, B.
Journal: J Comput Chem

This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by approximately 10 kJ mol(-1), whereas the very promising SCS-MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double zeta basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split-valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low-temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria.

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