Journal of Computational Chemistry
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Theoretical investigation of the relative stabilities of <i>X</i>SS<i>X</i> and <i>X</i><sub>2</sub>SS isomers (<i>X</i> = F, Cl, H, and CH<sub>3</sub>) Abstract The structures and relative stabilities of a series of disulfide (X SSX ) and thiosulfoxide (X 2 SS) isomers have been studied for X = F, Cl, CH3 , and H, using various levels of conventional ab initio and density functional theory (DFT). The X SSX isomers are more stable than the X 2 SS isomers for all substituents. The energy gap ΔE (X ) between the two isomers increases (i.e., X SSX becomes more stable with respect to X 2 SS), and the S S bond contracts in the series for X = F, Cl, CH3 , H. The results are interpreted by means of natural population analysis (NPA) (e.g., the interaction between the disulfide moiety SX ·). The bonding in the hypervalent X 2 SS species is similar to the bonding in the nonhypervalent X SSX and does not involve a special role for sulfur‐3d orbitals. These orbitals acquire only minimal populations and are not to be conceived as valence orbitals. The DFT and conventional ab initio results, Xα/DZP and MP2/6‐31G** optimized structures and isomerization energies (at the highest levels of both methods), agree well. © 1995 by John Wiley & Sons, Inc.
Journal of Computational Chemistry - Tập 16 Số 4 - Trang 465-477 - 1995
Role and effective treatment of dispersive forces in materials: Polyethylene and graphite crystals as test cases Abstract A semiempirical addition of dispersive forces to conventional density functionals (DFT‐D) has been implemented into a pseudopotential plane‐wave code. Test calculations on the benzene dimer reproduced the results obtained by using localized basis set, provided that the latter are corrected for the basis set superposition error. By applying the DFT‐D/plane‐wave approach a substantial agreement with experiments is found for the structure and energetics of polyethylene and graphite, two typical solids that are badly described by standard local and semilocal density functionals. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Journal of Computational Chemistry - Tập 30 Số 6 - Trang 934-939 - 2009
Density functional theory for efficient <i>ab initio</i> molecular dynamics simulations in solution Abstract We present a density functional for first‐principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 662–666, 2002
Journal of Computational Chemistry - Tập 23 Số 6 - Trang 662-666 - 2002
An all atom force field for simulations of proteins and nucleic acids Abstract We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc. , 106 , 765 (1984). The parameters of our function are based on calculations on ethane, propane, n −butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.
Journal of Computational Chemistry - Tập 7 Số 2 - Trang 230-252 - 1986
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs Abstract Different microscopic and semimicroscopic approaches for calculations of electrostatic energies in macromolecules are examined. This includes the Protein Dipoles Langevin Dipoles (PDLD) method, the semimicroscopic PDLD (PDLD/S) method, and a free energy perturbation (FEP) method. The incorporation of these approaches in the POLARIS and ENZYMIX modules of the MOLARIS package is described in detail. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions, as well as the effects of the ionic strength and external pH. Determination of the hydrophobic energy involves an approach that considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. Ionic strength effects are studied by modeling the ionic environment around the given system using a grid of residual charges and evaluating the relevant interaction using Coulomb's law with the dielectric constant of water. The performance of the FEP calculations is significantly enhanced by using special boundary conditions and evaluating the long‐range electrostatic contributions using the Local Reaction Field (LRF) model. A diverse set of electrostatic effects are examined, including the solvation energies of charges in proteins and solutions, energetics of ion pairs in proteins and solutions, interaction between surface charges in proteins, and effect of ionic strength on such interactions, as well as electrostatic contributions to binding and catalysis in solvated proteins. Encouraging results are obtained by the microscopic and semimicroscopic approaches and the problems associated with some macroscopic models are illustrated. The PDLD and PDLD/S methods appear to be much faster than the FEP approach and still give reasonable results. In particular, the speed and simplicity of the PDLD/S method make it an effective strategy for calculations of electrostatic free energies in interactive docking studies. Nevertheless, comparing the results of the three approaches can provide a useful estimate of the accuracy of the calculated energies. © 1993 John Wiley & Sons, Inc.
Journal of Computational Chemistry - Tập 14 Số 2 - Trang 161-185 - 1993
Using pseudo amino acid composition to predict protein structural class: Approached by incorporating 400 dipeptide components Abstract The proteins structure can be mainly classified into four classes: all‐α, all‐ β, α/β, and α + β protein according to their chain fold topologies. For the purpose of predicting the protein structural class, a new predicting algorithm, in which the increment of diversity combines with Quadratic Discriminant analysis, is presented to study and predict protein structural class. On the basis of the concept of the pseudo amino acid composition (Chou, Proteins: Struct Funct Genet 2001, 43, 246; Erratum: Proteins Struct Funct Genet 2001, 44, 60), 400 dipeptide components and 20 amino acid composition are, respectively, selected as parameters of diversity source. Total of 204 nonhomologous proteins constructed by Chou (Chou, Biochem Biophys Res Commun 1999, 264, 216) are used for training and testing the predictive model. The predicted results by using the pseudo amino acids approach as proposed in this paper can remarkably improve the success rates, and hence the current method may play a complementary role to other existing methods for predicting protein structural classification. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Journal of Computational Chemistry - Tập 28 Số 9 - Trang 1463-1466 - 2007
New spherical‐cutoff methods for long‐range forces in macromolecular simulation Abstract New atom‐ and group‐based spherical‐cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom‐based method, force switching, leaves short‐range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group‐based cutoffs is presented: Switched group‐shifting shifts the group–group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom‐based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen‐bonding system consisting of two N ‐methyl acetamide molecules and by full MD simulation. Thirty‐five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom‐based shifting are each able to approximate no‐cutoff results when a cutoff at or beyond 12 Å is used. However, atom‐based potential‐energy switching and truncation unacceptably contaminate group–group electrostatic interactions. Group‐based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K/ps in the simulations of hydrated MbCO). The distance‐dependent dielectric (ϵ ∝︁ r ) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom‐based spherical cutoffs, whereas switched group‐shifting is the preferred group‐based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 Å or beyond is much more important than the differences among the three best cutoff methods. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
Journal of Computational Chemistry - Tập 15 Số 7 - Trang 667-683 - 1994
CHARMM-GUI<i>Membrane Builder</i>toward realistic biological membrane simulations
Journal of Computational Chemistry - Tập 35 Số 27 - Trang 1997-2004 - 2014
Additive empirical force field for hexopyranose monosaccharides Abstract We present an all‐atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all‐atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the α‐ and β‐anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas‐phase and condensed‐phase properties of small‐molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides, and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute–water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc‐pVTZ//MP2/6‐31G(d) level of theory. Although not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well‐reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Journal of Computational Chemistry - Tập 29 Số 15 - Trang 2543-2564 - 2008
Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis Abstract We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to bond formation by spatial integration of the deformation density over the atomic Voronoi cell. We compare our method to the well‐known Mulliken, Hirshfeld, Bader, and Weinhold [Natural Population Analysis (NPA)] charges for a variety of biological, organic, and inorganic molecules. The Mulliken charges are (again) shown to be useless due to heavy basis set dependency, and the Bader charges (and often also the NPA charges) are not realistic, yielding too extreme values that suggest much ionic character even in the case of covalent bonds. The Hirshfeld and VDD charges, which prove to be numerically very similar, are to be recommended because they yield chemically meaningful charges. We stress the need to use spatial integration over an atomic domain to get rid of basis set dependency, and the need to integrate the deformation density in order to obtain a realistic picture of the charge rearrangement upon bonding. An asset of the VDD charges is the transparency of the approach owing to the simple geometric partitioning of space. The deformation density based charges prove to conform to chemical experience. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 189–210, 2004
Journal of Computational Chemistry - Tập 25 Số 2 - Trang 189-210 - 2004
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