摘要:

AbstractPEFF is a new computer program designed to assist in the development of empirical force fields used in molecular mechanics calculations. Its main features are: constrained and unconstrained energy minimization available with four different techniques, rigid group refinement, crystal lattice summations, calculation of normal modes, thermodynamic functions and crystallographic temperature factors, vibrational corrections of calculated crystal structures, and a multidimensional driver to scan the energy hypersurface. Used in force field optimization mode, the program employs a least‐squares method to fit the force field parameters to a set of experimental dat

ISSN:0192-8651    

DOI:10.1002/jcc.540130302

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractUsing the natural bond orbital method, one may associate the valence bond configuration and Lewis structure concepts to wave functions consisting of molecular orbitals and thus gain intuitive insight into the molecular potential energy curves. Natural bond orbital analysis of the restricted open shell Hartree–Fock and unrestricted Hartree–Fock wave functions for the BeH ground state provides an intuitive model to help understand the nature of the bonding in this open shell species. The contrasting behavior of the bonding orbitals for different spins can be attributed to differences in the Pauli repulsive interactions with the lonepair orbitals. Such behavior occurs in BeH(2Σ) but does not in CO+(2Π) because the Pauli repulsion depends on the orbital ov

ISSN:0192-8651    

DOI:10.1002/jcc.540130303

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe performance of a Runge‐Kutta method of fourth order in dynamic simulations within Davydov's so‐called |D2〉 state ansatz is studied by comparison with analytical solutions available for two special cases. Further, the Runge–Kutta method is compared with the one‐step procedure used by Su and Schrieffer. A detailed analysis of the structure and energetics of Davydov solitons is given. The differences in the dynamics between open chain ends and periodic boundary conditions are also discussed. The properties of the soliton detector plot introduced by Lomdahl and Kerr are studied. Finally, three widely used initial states for Davydov soliton dynamics are

ISSN:0192-8651    

DOI:10.1002/jcc.540130304

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractMNDO‐PM3 calculations, carried out on an experimentally determined structure of an intermediate in the cycloaddition of an electrophilic azide and a nucleophilic 1,3‐dipolarophile, show that the semiempirical MO scheme models this structure closely. Transition structures for formation of the intermediate and ring closure of the latter are descri

ISSN:0192-8651    

DOI:10.1002/jcc.540130305

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractHartree–Fock self‐consistent field calculations on the 3‐21G(*) level of approximation have been performed to phosphorylcholine and its derivatives in a geometry close to an X‐ray structure of an antibody/antigen complex. Wave functions have been analyzed using different methods for derivation of atomic charges used as Coulomb charges in empirical force fields for molecular dynamics simulations. Among the three applied methods—Mulliken population analysis, natural population analysis, and electrostatical fit—the natural population analysis seems to give best results for thes

ISSN:0192-8651    

DOI:10.1002/jcc.540130306

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractA rigid‐geometry approach to protein conformational searches has been used to calculate stable structures for localized regions of the molecules bovine pancreatic ribonuclease A and human lysozyme. The search method is essentially an application of the local deformation algorithm of Gō and Scheraga [Macromolecules,3, 178–187 (1970)]. A series of local chain deformations is produced in the polypeptide chain. The deformations are screened to eliminate structures having serious atomic overlaps or energetically unreasonable backbone dihedral angles. The remaining structures are refined by energy minimization and the rms deviations of the energy‐minimized structures, relative to the native structures, are calculated. The correlation between low rms deviation and low energy is reasonably good, indicating that this method should be useful in generating a small number of candidate structures for further energy refinement. Further applications to proteins with an unknown structure, such as homology‐based modeling applications, should now be amenable to this type of p

ISSN:0192-8651    

DOI:10.1002/jcc.540130307

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractLinearized embedding is a variant on the usual distance geometry methods for finding atomic Cartesian coordinates given constraints on interatomic distances. Instead of dealing primarily with the matrix of interatomic distances, linearized embedding concentrates on properties of the metric matrix, the matrix of inner products between pairs of vectors defining local coordinate systems within the molecule. Here, the approach is used to explore the full conformation space allowed to small cyclic alkanes, given the constraint of exact bond lenghts and bond angles. Useful general tools developed along the way are expressions for rotation matrices in any number of dimensions and a generalization of spherical coordinates to any number of dimensions. Analytical results give some novel views of the conformation spaces of cyclopropane, cyclobutane, cyclopentane, and eyclohexane. A combination of numerical and analytical approaches gives the most comprehensive description to date of the cycloheptane conformation space with fixed bond lengths and angles. In this representation, the pseudorotation paths of cyclohexane and cycloheptane are closed curved lines on the surfaces of spheres.

ISSN:0192-8651    

DOI:10.1002/jcc.540130308

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractThe solvation free energies of thymine and adenine were calculated using free energy methods to examine the effect of applying Lennard–Jones 6‐12 and 10‐12 perturbations to the hydrogen‐bonding groups. The calculations were performed using a new free energy algorithm developed for the AMBER 4.0 program package that allows an interaction described by a Lennard–Jones 6‐12 potential to be changed into one described by a hydrogen bond 10‐12 potential. The algorithm applied allows this change to occur smoothly without the generation of more extrema on the potential surface. Results using this algorithm have been compared with those determined using the standard AMBER 3.0 Revision A program package, which provides for 6‐12 to 6‐12 parameter perturbations only. We have also developed a procedure to perform pyrimidine to purine nucleoside mutations to calculate the relative free energies of solvation directly. The theoretical results are compared to experimental energies derived from solvation and vaporization data taken from the literature. The free energies calculated using the new algorithm show good agreement with the derived experimental values. This is also true for the calculations that employ the 6‐12 function only, but with 6‐12 parameters modified to reflect the correct hydrogen‐bonding interactions. However, perturbation of the “standard” 6‐12 parameters without changing the functional form proves to be less effective in determining solvation free energies correctly, and demonstrates the importance of accurate hydrogen bond descriptio

ISSN:0192-8651    

DOI:10.1002/jcc.540130309

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractFor the calculation of atomic charges in molecules, a new fast procedure based on extended Mulliken population analysis is presented. The reliability of the new population analysis is tested within the AM1 approximation and the results are compared in detail with those obtained by different methods reported in the literature.

ISSN:0192-8651    

DOI:10.1002/jcc.540130310

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY

摘要:

AbstractMolecular docking explores the binding modes of two interacting molecules. The technique is increasingly popular for studying protein‐ligand interactions and for drug design. A fundamental problem problem with molecular docking is that orientation space is very large and grows combinatorially with the number of degrees of freedom of the interacting molecules. Here, we describe and evaluate algorithms that improve the efficiency and accuracy of a shape‐based docking method. We use molecular organization and sampling techniques to remove the exponential time dependence on molecular size in docking calculations. The new techniques allow us to study systems that were prohibitively large for the original method. The new algorithms are tested in 10 different protein‐ligand systems, including 7 systems where the ligand is itself a protein. In all cases, the new algorithms successfully reproduce the experimentally determined configurations of the ligand in the pr

ISSN:0192-8651    

DOI:10.1002/jcc.540130311

出版商:John Wiley&Sons, Inc.    

年代:1992

数据来源: WILEY