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Force Field Parameters (force + field_parameter)
Selected AbstractsModeling dioxygen binding to the non-heme iron-containing enzymesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2006A. V. Nemukhin Abstract The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non-heme 2-oxoglutarate-dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia-inducible factor asparaginyl hydroxylase (FIH-1). DFT calculations for the 37-atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical,molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end-on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [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] The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Michio Iwaoka Abstract Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like ,-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] Specific force field parameters determination for the hybrid ab initio QM/MM LSCF methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2002Nicolas Ferré Abstract The pure quantum mechanics method, called Local Self-Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post-Hartree,Fock method, based on the restricted or unrestricted Hartree,Fock Slater determinant, and Kohn,Sham-based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 610,624, 2002 [source] Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Tran Trung Tran Abstract When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010,1025, 2001 [source] Investigation of the Adsorption and Self Assembly of Isocyanide Derivatives on Au(111) SurfaceCHINESE JOURNAL OF CHEMISTRY, Issue 9 2007Jun-Hong Zhou Abstract The adsorption and self-assembly of isocyanide derivatives on Au(111) surface were investigated by density functional theory (DFT) and molecular dynamics simulation. The calculation for phenyl isocyanide by DFT was based on cluster and slab models. The self-assembled monolayers of 2-isocyanoazulene and 1,3-diethoxycarbonyl- 2-isocyanoazulene on Au(111) were simulated using Au-C force field parameters developed by us. It was found that the top site was the most preferred position, and the isocyanoazulene and its derivatives could form the ordered face to edge self-assembled monolayer on gold surface indeed, and the molecules stood on the gold surface vertically. [source] | ||||||||||