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Comput Chem (comput + chem)
Selected AbstractsA 3D graphical representation of DNA sequence based on numerical coding methodINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2010Zhi Cao Abstract Recently, we introduced a sort of numerical coding method of DNA sequences (Chen et al., MATCH Commun Math Comput Chem, 2008, 60, 291). On the basis of the result of our coding method, we present a 3D graphical representation of DNA sequences. The 3D graphical representation also avoids loss of information accompanying alternative 2D and 3D representation in which the curve standing for DNA overlaps and intersects itself. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Coriolis coupling and nonadiabaticity in chemical reaction dynamicsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Emilia L. Wu Abstract The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D2, F+H2/D2/HD, D++H2, O+H2, and He+H2+, have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D++H2, Ne+H, and He+H2+ in both adiabatic and nonadiabatic context. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Structural, electronic, bonding, magnetic, and optical properties of bimetallic [RunAum]0/+ (n + m , 3) clustersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Dimitrios N. Garbounis Abstract The structural, electronic, bonding, magnetic, and optical properties of bimetallic [RunAum]0/+ (n + m , 3; n, m = 0,3) clusters were computed in the framework of the density functional theory (DFT) and time-dependent DFT (TD-DFT) using the full-range PBE0 non local hybrid GGA functional combined with the Def2-QZVPP basis sets. Several low-lying states have been investigated and the stability of the ground state spinomers was estimated with respect to all possible fragmentation schemes. Molecular orbital and population analysis schemes along with computed electronic parameters illustrated the details of the bonding mechanisms in the [RunAum]0/+ clusters. The TD-DFT computed UV-visible absorption spectra of the bimetallic clusters have been fully analyzed and compared to those of pure gold and ruthenium clusters. Assignments of all principal electronic transitions are given and interpreted in terms of contribution from specific molecular orbital excitations. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [source] A generalized higher order kernel energy approximation methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Stewart N. Weiss Abstract We present a general mathematical model that can be used to improve almost all fragment-based methods for ab initio calculation of total molecular energy. Fragment-based methods of computing total molecular energy mathematically decompose a molecule into smaller fragments, quantum-mechanically compute the energies of single and multiple fragments, and then combine the computed fragment energies in some particular way to compute the total molecular energy. Because the kernel energy method (KEM) is a fragment-based method that has been used with much success on many biological molecules, our model is presented in the context of the KEM in particular. In this generalized model, the total energy is not based on sums of all possible double-, triple-, and quadruple-kernel interactions, but on the interactions of precisely those combinations of kernels that are connected in the mathematical graph that represents the fragmented molecule. This makes it possible to estimate total molecular energy with high accuracy and no superfluous computation and greatly extends the utility of the KEM and other fragment-based methods. We demonstrate the practicality and effectiveness of our model by presenting how it has been used on the yeast initiator tRNA molecule, ytRN (1YFG in the Protein Data Bank), with kernel computations using the Hartree-Fock equations with a limited basis of Gaussian STO-3G type. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Identifying and reducing error in cluster-expansion approximations of protein energiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Seungsoo Hahn Abstract Protein design involves searching a vast space for sequences that are compatible with a defined structure. This can pose significant computational challenges. Cluster expansion is a technique that can accelerate the evaluation of protein energies by generating a simple functional relationship between sequence and energy. The method consists of several steps. First, for a given protein structure, a training set of sequences with known energies is generated. Next, this training set is used to expand energy as a function of clusters consisting of single residues, residue pairs, and higher order terms, if required. The accuracy of the sequence-based expansion is monitored and improved using cross-validation testing and iterative inclusion of additional clusters. As a trade-off for evaluation speed, the cluster-expansion approximation causes prediction errors, which can be reduced by including more training sequences, including higher order terms in the expansion, and/or reducing the sequence space described by thecluster expansion. This article analyzes the sources of error and introduces a method whereby accuracy can be improved by judiciously reducing the described sequence space. The method is applied to describe the sequence,stability relationship for several protein structures: coiled-coil dimers and trimers, a PDZ domain, and T4 lysozyme as examples with computationally derived energies, and SH3 domains in amphiphysin-1 and endophilin-1 as examples where the expanded pseudo-energies are obtained from experiments. Our open-source software package Cluster Expansion Version 1.0 allows users to expand their own energy function of interest and thereby apply cluster expansion to custom problems in protein design. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] TmoleX,A graphical user interface for TURBOMOLEJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Claudia Steffen Abstract We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Connectivity and binding-site recognition: Applications relevant to drug designJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2010Christopher J. R. Illingworth Abstract Here, we describe a family of methods based on residue,residue connectivity for characterizing binding sites and apply variants of the method to various types of protein,ligand complexes including proteases, allosteric-binding sites, correctly and incorrectly docked poses, and inhibitors of protein,protein interactions. Residues within ligand-binding sites have about 25% more contact neighbors than surface residues in general; high-connectivity residues are found in contact with the ligand in 84% of all complexes studied. In addition, a k-means algorithm was developed that may be useful for identifying potential binding sites with no obvious geometric or connectivity features. The analysis was primarily carried out on 61 protein,ligand structures from the MEROPS protease database, 250 protein,ligand structures from the PDBSelect (25%), and 30 protein,protein complexes. Analysis of four proteases with crystal structures for multiple bound ligands has shown that residues with high connectivity tend to have less variable side-chain conformation. The relevance to drug design is discussed in terms of identifying allosteric-binding sites, distinguishing between alternative docked poses and designing protein interface inhibitors. Taken together, this data indicate that residue,residue connectivity is highly relevant to medicinal chemistry. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Closed loop folding units from structural alignments: Experimental foldons revisitedJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2010Sree V. Chintapalli Abstract Nonoverlapping closed loops of around 25,35 amino acids formed via nonlocal interactions at the loop ends have been proposed as an important unit of protein structure. This hypothesis is significant as such short loops can fold quickly and so would not be bound by the Leventhal paradox, giving insight into the possible nature of the funnel in protein folding. Previously, these closed loops have been identified either by sequence analysis (conservation and autocorrelation) or studies of the geometry of individual proteins. Given the potential significance of the closed loop hypothesis, we have explored a new strategy for determining closed loops from the insertions identified by the structural alignment of proteins sharing the same overall fold. We determined the locations of the closed loops in 37 pairs of proteins and obtained excellent agreement with previously published closed loops. The relevance of NMR structures to closed loop determination is briefly discussed. For cytochrome c, cytochrome b562 and triosephophate isomerase, independent folding units have been determined on the basis of hydrogen exchange experiments and misincorporation proton-alkyl exchange experiments. The correspondence between these experimentally derived foldons and the theoretically derived closed loops indicates that the closed loop hypothesis may provide a useful framework for analyzing such experimental data. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sitesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2010Tzong-Yi Lee Abstract Protein acetylation, which is catalyzed by acetyltransferases, is a type of post-translational modification and crucial to numerous essential biological processes, including transcriptional regulation, apoptosis, and cytokine signaling. As the experimental identification of protein acetylation sites is time consuming and laboratory intensive, several computational approaches have been developed for identifying the candidates of experimental validation. In this work, solvent accessibility and the physicochemical properties of proteins are utilized to identify acetylated alanine, glycine, lysine, methionine, serine, and threonine. A two-stage support vector machine was applied to learn the computational models with combinations of amino acid sequences, and the accessible surface area and physicochemical properties of proteins. The predictive accuracy thus achieved is 5% to 14% higher than that of models trained using only amino acid sequences. Additionally, the substrate specificity of the acetylated site was investigated in detail with reference to the subcellular colocalization of acetyltransferases and acetylated proteins. The proposed method, N-Ace, is evaluated using independent test sets in various acetylated residues and predictive accuracies of 90% were achieved, indicating that the performance of N-Ace is comparable with that of other acetylation prediction methods. N-Ace not only provides a user-friendly input/output interface but also is a creative method for predicting protein acetylation sites. This novel analytical resource is now freely available at http://N-Ace.mbc.NCTU.edu.tw/. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Redox-induced configuration conversion for thioacetamide dimer can function as a molecular switchJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2010Haiying Liu Abstract The electronic switching properties of thioacetamide dimer (TAD) were investigated using the nonequilibrium Green's function method combined with density functional theory for design of a novel molecular switch. The H-bonded TAD can be converted upon hole-trapping to a three-electron (3e)-bonded configuration with a S,S linkage which could provide a more favorable channel for charge transfer than the before. The redox-induced configuration conversion between the H-bonded and the 3e-bonded TADs could govern the charge migration through the molecular junction with a considerable difference in conduction currents. The calculated I,V characteristic curves of two configurations exhibit a switching behavior with an On-Off ratio in a range of about 4.3,7.6 within the applied voltages. Clearly, this hypothetical scheme provides a potential way to explore the novel conformation-dependent molecular switch. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [source] SKATE: A docking program that decouples systematic sampling from scoringJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2010Jianwen A. Feng Abstract SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in-house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross-docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin-dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Time-dependent quantum study of H(2S) + FO(2,) , OH(2,) + F(2P) reaction on the 13A, and 13A, statesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2010Fahrettin Gogtas Abstract The dynamics of the H(2S) + FO(2,) , OH(2,) + F(2P) reaction on the adiabatic potential energy surface of the 13A, and 13A, states is investigated. The initial state selected reaction probabilities for total angular momentum J = 0 have been calculated by using the quantum mechanical real wave packet method. The integral cross sections and initial state selected reaction rate constants have been obtained from the corresponding J = 0 reaction probabilities by means of the simple J -Shifting technique. The initial state-selected reaction probabilities and reaction cross section do not manifest any sharp oscillations and the initial state selected reaction rate constants are sensitive to the temperature. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [source] Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL systemJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2010Oscar Bertran Abstract The PUPIL system is a combination of software and protocols for the systematic linkage and interoperation of molecular dynamics and quantum mechanics codes to perform QM/MD (sometimes called QM/MM) calculations. The Gaussian03 and Amber packages were added to the PUPIL suite recently. However, efficient parallel QM codes are critical because calculation of the QM forces is the overwhelming majority of the computational load. Here we report details of incorporation of the deMon2k density functional suite as a new parallel QM code. An additional motivation is to add a highly optimized, purely DFT code. We illustrate with a demonstration study of the influence of perchlorate as a dopant ion of the poly(3,4-ethylenedioxythiophene) conducting polymer in explicit acetonitrile solvent using Amber and deMon2k. We discuss unanticipated requirements for use of a scheme for semi-empirical correction of Kohn-Sham eigenvalues to give physically meaningful one-electron gap energies. We provide comparison of both geometric parameters and electronic properties for nondoped and doped systems. We also present results comparing deMon2k and Gaussian03 calculation of forces for a short sequence of steps. We discuss briefly some difficult problems of quantum zone SCF convergence for the anionically doped system. The difficulties seem to be caused by well-know deficiencies in simple approximate exchange-correlation functionals. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Theoretical studies on the structure and protonation of Cu(II) complexes of a series of tripodal aliphatic tetraamines: Good correlations with the experimental dataJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2010Sadegh Salehzadeh Abstract DFT(B3LYP) studies on first protonation step of a series of Cu(II) complexes of some tripodal tetraamines with general formula N[(CH2)nNH2][(CH2)mNH2][(CH2)pNH2] (n = m = p = 2, tren; n = 3, m = p = 2, pee; n = m = 3, p = 2, ppe; n = m = 3, tpt; n = 2, m = 3, p = 4, epb; and n = m = 3, p = 4; ppb) are reported. First, the gas-phase proton macroaffinity of all latter complexes was calculated with considering following simple reaction: [Cu(L)]2+(g) + H+(g) , [Cu(HL)]3+(g). The results showed that there is a good correlation between the calculated proton macroaffinities of all complexes with their stability constants in solution. Then, we tried to determine the possible reliable structures for microspecies involved in protonation process of above complexes. The results showed that, similar to the solid state, the [Cu(L)(H2O)]2+ and [Cu(HL)(H2O)2]3+ are most stable species for latter complexes and their protonated form, respectively, at gas phase. We found that there are acceptable correlations between the formation constants of above complexes with both the , and , of following reaction: [Cu(L)(H2O)]2+(g) + H+(g) + H2O(g) , [Cu(HL)(H2O)2]3+(g). The , of the latter reaction can be defined as a theoretically solvent,proton macroaffinity of reactant complexes because they have gained one proton and one molecule of the solvent. The unknown formation constant of [Cu(epb)]2+ complex was also predicted from the observed correlations. In addition, the first proton affinity of all complexes was studied in solution using DPCM and CPCM methods. It was shown that there is an acceptable correlation between the solvent,proton affinities of [Cu(L)(H2O)]2+ complexes with formation constants of [Cu(HL)(H2O)2]3+ complexes in solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Parallel Fock matrix construction with distributed shared memory model for the FMO-MO methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2010Hiroaki Umeda Abstract A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-31G level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Molecular docking studies of selected tricyclic and quinone derivatives on trypanothione reductase of Leishmania infantumJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2010Santhosh Kannan Venkatesan Abstract Visceral leishmaniasis, most lethal form of Leishmaniasis, is caused by Leishmania infantum in the Old world. Current therapeutics for the disease is associated with a risk of high toxicity and development of drug resistant strains. Thiol-redox metabolism involving trypanothione and trypanothione reductase, key for survival of Leishmania, is a validated target for rational drug design. Recently published structure of trypanothione reductase (TryR) from L. infantum, in oxidized and reduced form along with Sb(III), provides vital clues on active site of the enzyme. In continuation with our attempts to identify potent inhibitors of TryR, we have modeled binding modes of selected tricyclic compounds and quinone derivatives, using AutoDock4. Here, we report a unique binding mode for quinone derivatives and 9-aminoacridine derivatives, at the FAD binding domain. A conserved hydrogen bonding pattern was observed in all these compounds with residues Thr335, Lys60, His461. With the fact that these residues aid in the orientation of FAD towards the active site forming the core of the FAD binding domain, designing selective and potent compounds that could replace FAD in vivo during the synthesis of Trypanothione reductase can be deployed as an effective strategy in designing new drugs towards Leishmaniasis. We also report the binding of Phenothiazine and 9-aminoacridine derivatives at the Z site of the protein. The biological significance and possible mode of inhibition by quinone derivatives, which binds to FAD binding domain, along with other compounds are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Theoretical investigation of an energetic fullerene derivativeJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Bisheng Tan Abstract A self-consistent estimation method for the thermochemical properties of N -methyl-3-(2,,4,,6,-trinitrobenzene)-fulleropyrrolidine (MTNBFP) is presented. This method is based on enthalpy of formation (,fH) and enthalpy of combustion obtained from BLYP/DNP calculations of the total energies and frequencies for MTNBFP. The enthalpy of formation was calculated by an optimized set of isodesmic reactions given the available experimental ,fH of relative compounds. MTNBFP has a high enthalpy of formation, 2782.2 kJ/mol. Detonation velocity and detonation pressure were also presented in terms of Kamlet and Jacobs equations. Drop hammer impact sensitivity tests and blasting point per 5 s tests indicate MTNBFP may be a potential candidate primary explosive. To understand the test results well, we proposed a series of chemical reaction mechanisms and interpreted the relationship between impact sensitivity and electronic structures from the viewpoint of nitro group charge, electrostatic potential, and vibrational modes. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Xian-Hui Wu Abstract The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two-layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn-bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate-determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn-bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate-determining step is the proton transfer from Zn-OH to 6-NH2 of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Theoretical study of the microhydration of mononuclear and dinuclear uranium(VI) species derived from solvolysis of uranyl nitrate in waterJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Milan On Abstract The structures and energetics of mononuclear and dinuclear uranium species formed upon speciation of uranyl(VI) nitrate, UO2(NO3)2, in water are investigated by quantum chemistry using density functional theory and the wavefunction-based methods (MP2, CCSD, CCSD(T)). We provide a discussion of the basic coordination patterns of the various mono- and dinuclear uranyl compounds [(UO2)m(X,Y)2m,1(H2O)n]+ (m = 1, 2; n = 0,4) found in a recent mass spectrometric study (Tsierkezos et al., Inorg Chem 2009, 48, 6287). The energetics of the complexation of the uranyl dication to the counterions OH, and NO3, as well as the degradation of the dinuclear species were studied by reference to a test set of 16 representative molecules with the MP2 method and the B3LYP, M06, M06-HF, and M06-2X DFT functionals. All DFT functionals provide structures and energetics close to MP2 results, with M06 family being slightly superior to the standard B3LYP functional. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010 [source] ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Benjamin Waldher Abstract The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] 27 ps DFT molecular dynamics simulation of ,-maltose: A reduced basis set study,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Udo Schnupf Abstract DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as ,-maltose. In a recent publication (Momany et al., J. Mol. Struct. THEOCHEM, submitted) forces for dynamics were generated from B3LYP/6-31+G* electronic structure calculations. The implicit solvent method COSMO was applied to simulate the solution environment. Here we present a modification of the DFT method that keeps the critical aspects of the larger basis set (B3LYP/6-31+G*) while allowing the less-essential atom interactions to be calculated using a smaller basis set, thus allowing for faster completion without sacrificing the interactions dictating the hydrogen bonding networks in ,-maltose. In previous studies, the gg,-gg-c solvated form quickly converged to the "r" form during a 5 ps dynamics run. This important conformational transition is tested by carrying out a long 27 ps simulation. The trend for the "r" conformer to be most stable during dynamics when fully solvated, is confirmed, resulting in ,20/80% c/r population. Further, the study shows that considerable molecular end effects are important, the reducing end being fairly stable, the O6H pointing at the O5, while the nonreducing end moves freely to take on different conformations. Some "kink" and transition state forms are populated during the simulation. The average H1,···H4 distance of 2.28 Å confirms that the syn form is the primary glycosidic conformation, while the average C1,O1,C4 bond angle was 118.8°, in excellent agreement with experimental values. The length of this simulation allowed the evaluation of vibrational frequencies by Fourier transform of the velocity correlation function, taken from different time segments along the simulation path. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Li-Dong Gong Abstract Based on the molecular face (MF) theory, the molecular face surface area (MFSA) and molecular face volume (MFV) are defined. For a variety of organic molecules and several inorganic molecules, the MFSA and MFV have been studied and calculated in terms of an algorithm of our own via the Matlab package. The MFV shows a very good linear relationship with the experimentally measured critical molar volume. It is also found that the MFSA and MFV have significant linear correlations with those of the commonly used hard-sphere model and the electron density isosurface. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Maarten G. Wolf Abstract To efficiently insert a protein into an equilibrated and fully hydrated membrane with minimal membrane perturbation we present a computational tool, called g_membed, which is part of the Gromacs suite of programs. The input consists of an equilibrated membrane system, either flat or curved, and a protein structure in the right position and orientation with respect to the lipid bilayer. g_membed first decreases the width of the protein in the xy -plane and removes all molecules (generally lipids and waters) that overlap with the narrowed protein. Then the protein is grown back to its full size in a short molecular dynamics simulation (typically 1000 steps), thereby pushing the lipids away to optimally accommodate the protein in the membrane. After embedding the protein in the membrane, both the lipid properties and the hydration layer are still close to equilibrium. Thus, only a short equilibration run (less then 1 ns in the cases tested) is required to re-equilibrate the membrane. Its simplicity makes g_membed very practical for use in scripting and high-throughput molecular dynamics simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Investigation of excited-state properties of fluorene,thiophene oligomers by the SAC-CI theoretical approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Potjaman Poolmee Abstract Excited states of fluorene-ethylenedioxythiophene (FEDOT) and fluorene- S,S -dioxide-thiophene (FTSO2) monomers and dimers were studied by the symmetry-adapted cluster (SAC)-configuration interaction (CI) method. The absorption and emission peaks observed in the experimental spectra were theoretically assigned. The first three excited states of the optimized conformers, and the conformers of several torsional angles, were computed by SAC-CI/D95(d). Accurate absorption spectra were simulated by taking the thermal average for the conformers of torsional angles from 0° to 90°. The conformers of torsional angles 0°, 15°, and 30° mainly contributed to the absorption spectra. The full width at half-maximum of the FEDOT absorption band is 0.60 eV (4839 cm,1), which agrees very well with the experimental value of 0.61 eV (4900 cm,1). The maximum absorption wavelength is located at 303 nm, which is close to those of the experimental band (327 nm). The calculated absorption spectrum of FTSO2 showed two bands in the range of 225,450 nm. This agrees very well with the available experimental spectrum of a polymer of FTSO2, where two bands are detected. The excited-state geometries were investigated by CIS/6-31G(d). These showed a quinoid-type structure which exhibited a shortening of the inter-ring distance (0.06 Å for FEDOT and 0.04 Å for FTSO2). The calculated emission energy of FEDOT is 3.43 eV, which agrees very well with the available experimental data (3.46 eV). The fwhmE is about 0.49 eV (3952 cm,1), while the experimental fwhm is 0.43 eV (3500 cm,1). For FTSO2, two bands were also found in the emission spectrum. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] A self-adaptive genetic algorithm-artificial neural network algorithm with leave-one-out cross validation for descriptor selection in QSAR studyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Jingheng Wu Abstract Based on the quantitative structure-activity relationships (QSARs) models developed by artificial neural networks (ANNs), genetic algorithm (GA) was used in the variable-selection approach with molecule descriptors and helped to improve the back-propagation training algorithm as well. The cross validation techniques of leave-one-out investigated the validity of the generated ANN model and preferable variable combinations derived in the GAs. A self-adaptive GA-ANN model was successfully established by using a new estimate function for avoiding over-fitting phenomenon in ANN training. Compared with the variables selected in two recent QSAR studies that were based on stepwise multiple linear regression (MLR) models, the variables selected in self-adaptive GA-ANN model are superior in constructing ANN model, as they revealed a higher cross validation (CV) coefficient (Q2) and a lower root mean square deviation both in the established model and biological activity prediction. The introduced methods for validation, including leave-multiple-out, Y-randomization, and external validation, proved the superiority of the established GA-ANN models over MLR models in both stability and predictive power. Self-adaptive GA-ANN showed us a prospect of improving QSAR model. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of proteinJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Huameng Li Abstract 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. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Reaction mechanism of methanol decomposition on Pt-based model catalysts: A theoretical studyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Cui-Yu Niu Abstract The decomposition mechanisms of methanol on five different Pt surfaces, the flat surface of Pt(111), Pt-defect, Pt-step, Pt(110)(1 × 1), and Pt(110)(2 × 1), have been studied with the DFT-GGA method using the repeated slab model. The adsorption energies under the most stable configuration of the possible species and the activation energy barriers of the possible elementary reactions involved are obtained in this work. Through systematic calculations for the reaction mechanism of methanol decomposition on these surfaces, we found that such a reaction shows the same reaction mechanism on these Pt-based model catalysts, that is, the final products are all H (Hads) and CO (COads) via OH bond breaking in methanol and CH bond scission in methoxy. These results are in general agreement with the previous experimental observations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010. [source] Half metallic properties of LaSrVMoO6JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Weiyu Song Abstract The recent synthesized LaSrVMoO6 was speculated to be compensated half metal, i.e., half metal with zero magnetic moment. Based on the experimental structure, our first principles study indicates that it is ferrimagnetic and half metallic with the magnetic moment 2.0 ,B when the electron correlation of Mo 4d electrons is larger than 2.72 eV. This indicates the strong electron correlation effect of Mo 4d electrons. Nonetheless, the obtained large magnetic moment (2.0 ,B) contradicts with the experimental observed nearly zero magnetic moment. Although the large antisite defects of the experimental sample might be the reason to reduce the saturated magnetic moment, further physical insights need to be investigated. The spin-orbit coupling effect has minor effect on the studied properties. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Practical modeling of molecular systems with symmetriesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Sergei Grudinin Abstract A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree-based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree-based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Force field-dependant structural divergence revealed during long time simulations of Calbindin d9kJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Elad Project Abstract The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S2 order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] | ||||||||||