摘要:

AbstractA comparison is made of the performance of the MINDO/3, MNDO, AM1, and PM3 methods in calculating the nature of the dimer reconstruction observed on the silicon (100) crystal surface. Based on this case study we conclude that MINDO/3 gives the most realistic results, with PM3 calculations being quite similar but both MNDO and AM1 missing some key features of this system and giving rather unrealistic charge distributions. Hence use of PM3 is recommended for Si containing molecules where a lack of parameters or other restrictions prevent the use of MINDO/3.

ISSN:0192-8651    

DOI:10.1002/jcc.540120402

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractThe effect of mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious man

ISSN:0192-8651    

DOI:10.1002/jcc.540120403

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractThe conformations of simple alkyl substituted 1,2‐diphenylethanes and the diastereoisomers of 3‐amino‐1,2,3‐triphenyl‐1‐propyl chloride were studied by the MM2 force field with the addition of electrostatic corrections to the aromatic force field as proposed recently by Allinger and Lii (dipole‐dipole interactions) and independently by Pettersson and Liljefors (charge‐charge interactions). Computations were also carried out with a modified version of the MM2 program utilizing the MM3 van der Waals potential function and parameters for C (type 2,sp2hybridized) and H (type 5). The inclusion of dipole moments for the Csp2Csp3and Csp2H bonds significantly improves the results. A lower value for theV1parameter for the torsional unit CarCalCalCarhad to be used instead of the MM2 value of 2.1 kcal/mol. Computations were carried out also with the hybrid MM‐EHMO procedure. The latter method appears to work correctly also with 1,2

ISSN:0192-8651    

DOI:10.1002/jcc.540120404

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractAn efficient algorithm is presented for the numerical solution of the Poisson–Boltzmann equation by the finite difference method of successive over‐relaxation. Improvements include the rapid estimation of the optimum relaxation parameter, reduction in number of operations per iteration, and vector‐oriented array mapping. The algorithm has been incorporated into the electrostatic program DelPhi, reducing the required computing time by between one and two orders of magnitude. As a result the estimation of electrostatic effects such as solvent screening, ion distributions, and solvation energies of small solutes and biological macromolecules in solution, can be performed rapidly, and with minimal computing facil

ISSN:0192-8651    

DOI:10.1002/jcc.540120405

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractAb initioSCF‐MO Hartree–Fock calculations were performed using the STO‐3G, 6‐31G, and 6‐31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine‐atom clusters, [C(OH)4]qt, with charge numberqt= 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the CO bond lengths are appreciably longer than typical CO bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed‐proton model by 6.80 eV with the 6‐31G* basis set. The free‐H model compared favorably with the x‐ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α‐quartz. In the fixed‐H models, the twofold local symmetry was found to be retained whenqtis 0 but not whenqtis + 1. For the latter ion, the unrestricted H‐F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6‐31G) compared to the diamagnetic neutral one. Conclusions reached with the nine‐atom clusters were confirmed by a series of calculations

ISSN:0192-8651    

DOI:10.1002/jcc.540120406

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractThe finite difference method for solving the Poisson–Boltzmann equation is used to calculate the reaction field acting on a macromolecular solute due to the surrounding water and ions. Comparisons with analytical test cases indicate that the solvation forces can be calculated rapidly and accurately with this method. These forces act to move charged solute atoms towards the solvent where they are better solvated, and to screen interactions between charges. A way of combining such calculations with conventional molecular dynamics force fields is proposed which requires little modification of existing molecular dynamics programs. Simulations on the alanine dipeptide show that solvent forces affect the conformational dynamics by reducing the preference for internal H‐bonding forms, increasing theR‐alpha helix preference and reducing transition barriers. These solvent effects are similar to previous explicit solvent simulations, but require little more computation than vacuum simulations. The method should scale up with little increase in computational cost to larger molecules such as proteins and nucleic

ISSN:0192-8651    

DOI:10.1002/jcc.540120407

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractCurrent methods for assigning atomic multipoles focus on reproduction of the molecular electrostatic potential. Another aspect of electrostatic interaction, which is usually overlooked, is the forces that an external electric field exerts on the nuclei of a molecule. In a self‐consistent theory, both the electrostatic potential and force should be accounted for. However, in general it is not easy to meet this requirement for the force. For planar molecules, though, a formal solution is available in terms of atomic multipoles that are extracted from the molecular multipolar tensors. These Force‐Related (FR) atomic multipoles are discussed in detail for some typical diatomics and planar polyatomics, and are shown to provide a solid uniform framework for treating both aspects of the electrostatics. In contrast, the commonly used potential‐derived charges (i.e., the atomic charges obtained by fitting the electrostatic potential) can yield large deviations with respect to electrostatic forces on the nuclei, even when the electrostatic potential is very well repro

ISSN:0192-8651    

DOI:10.1002/jcc.540120408

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractThis article summarizes the detailed equations for the time‐dependent Hartree–Fock treatment of nonlinear properties for perturbations made up of a static electric field and an oscillating field. Explicit expressions for all nonlinear processes up to third order are obtained in terms of the density matrices at the same order. For processes at second and third order in perturbation, expressions in terms of lower order quantities are also obtained by applying the (2n+ 1) theorem of perturbation theory. The corresponding computer implementation in the HONDO program is descri

ISSN:0192-8651    

DOI:10.1002/jcc.540120409

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

摘要:

AbstractThe Gō–Scheraga algorithm to produce rigid‐geometry chain closures for polypeptide chains (N. Gō and H.A. Scheraga,Macromolecules,3, 178, 1970) has been updated to allow each residue in the chain to adopt different bond lengths or bond angles. A treatment of five‐residue local chain deformations is presented in detail. For chain sections shorter than five residues in length, it is shown that satisfactory closures may be obtained by direct fitting, indicating that the rigid‐geometry approximation is adequate to model even short sections of chains having perturbed local geometry. The new implementation of the algorithm has been applied to several problems in protein structure determination and molecular modeling. The first of these is the problem of finding standard‐geometry closures for short regions of chains having irregular geometry. It is shown that standard‐geometry closures which superimpose well upon the coordinates of the irregular structures may be obtained routinely for chain sections that are five amino acid residues or more in length. Another application of the algorithm is to generate a large number of closures for a short segment of a protein chain, as a method to search the conformational space of this segment. The latter application should prove useful in studies in which the conformation of some region of a given protein has not been determined experimentally. Such applications include the modeling of proteins which have a sequence homology to a crystallized protein, and modeling regions of crystallized proteins which are not well‐defined in electr

ISSN:0192-8651    

DOI:10.1002/jcc.540120410

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY

ISSN:0192-8651    

DOI:10.1002/jcc.540120401

出版商:John Wiley&Sons, Inc.    

年代:1991

数据来源: WILEY