摘要:

AbstractA numerical algorithm for locating both minima and transition states designed for use in theab initioprogram package GAUSSIAN 82 is presented. It is based on the RFO method of Simons and coworkers and is effectively the numerical version of an analytical algorithm (OPT = EF) previously published in this journal. The algorithm is designed to make maximum use of external second derivative information obtained from prior optimizations at lower levels of theory. It can be used with any wave function for which an energy can be calculated and is about two to three times faster than the default DFP algorithm (OPT = FP) supplied with GAUSSIAN 82.

ISSN:0192-8651    

DOI:10.1002/jcc.540080502

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractA computer program has been developed that calculates, using the weighted least‐squares technique, the overall formation constants,Bi, of mononuclear complexes, the standard deviations ofBi,SDVi, and an estimate of goodness of fit, Goodness‐of‐Fit Parameter (GOFP), given a set of average ligand numbers,VNj, the corresponding free ligand concentrations,VAj, and an error parameterP. The formation function used is ∑(VNj–i) · (Bi) · (VAj)i= 0 whereiranges from O tonwith a maximum of 10 andjranges from O tolwith a maximum of 40. TheBiand (Bi–SDVi) must be positive and GOFP must be either unity or as close to unity as possible. An option is available that allows the computation ofP, if it is not provided, so that GOFP is equal or very close to unity. The method has been applied to the formation of the complexes Cadmium‐Imidazole, Cobalt(II)‐Bis(2‐Quinaldylphenyl Ketone), Copper‐Ammonia, Silver‐4‐Aminobutan‐1‐ol Nitrate, and Copper(II)‐Bis(2‐Quinaldylphenyl Ketone). The results are quite satisfactory and reliable as compared with other computational techniques. Input data and results for the f

ISSN:0192-8651    

DOI:10.1002/jcc.540080503

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractThe molecular mechanics (MMP2) program and procedures for the treatment of conjugated hydrocarbons, and some of the results which they can achieve are described. The program is an updated version of the similar MMP1 program, but contains some differences. It is based on an SCF π system calculation, rather than on the VESCF method used earlier. All parameters are compatible with those in the MM2 program. Hence it is possible to calculate heats of formation, resonance energies, and structures for conjugated hydrocarbons in a way that is consistent with the calculations on non‐conjugated molecules. The overall results as far as structure and energy are somewhat better than they were with the MMP1 progr

ISSN:0192-8651    

DOI:10.1002/jcc.540080504

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractA theoretical study of stacking patterns of various hydrogen‐bonded base pair complexes has been undertaken. Modified Rayleigh‐Schrodinger perturbation theory for intermediate range interactions, has been employed to evaluate the stacking interactions using multicentered‐multipole expansion method. Net atomic charge and corresponding dipole components located at each of the atomic centers have been computed by CNDO/2 method. An analysis of the intermolecular forces involved in the stable formation of the various base pair complexes, has been presented and the results have been discussed in the light of experimental as well as other theoretical observations. The possibility of relative preference of the left‐handed configuration for alternating sequences has been quantitatively e

ISSN:0192-8651    

DOI:10.1002/jcc.540080505

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractWe describe a set of simple VAX assembly language, Fortran‐callable subroutines for performing vectorscalar‐multiply‐and‐add operations which can increase processing speed by more than 10%. The routines are simple enough that they may be translated readily for use on other m

ISSN:0192-8651    

DOI:10.1002/jcc.540080506

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractAn improved algorithm is presented for rapid calculation of the hessian matrix for the conformational energy of a protein as a function of only dihedral angles. The speed of the calculation, which is about one order faster than by the previous method, is achieved by two considerations. First, the algorithm is designed to take advantage of the supercomputer pipeline architecture. Second, long‐range, nonbonded interactions are cut off and long‐range electrostatic interactions are approximated by dipole‐dipole interactions in order to reduce the number of pairwise interactions that have to be computed. The results of benchmark tests of the program are given as applied for four globular proteins of different

ISSN:0192-8651    

DOI:10.1002/jcc.540080507

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractLarge randomly sparse matrix vector products are important in a number of applications in computational chemistry, such as matrix diagonalization and the solution of simultaneous equations. Vectorization of this process is considered for the CRAY XMP, CRAY 2, and CYBER 205, using a matrix of dimension of 20 000 with from 1% to 6% nonzeros. Efficient SCATTER/GATHER capabilities add coding flexibility and yield significant improvements in performance. For the CYBER 205, it is shown that minor changes in the IO can reduce the CPU time by a factor of 50. Similar changes in the CRAY codes make a far smaller improvement.

ISSN:0192-8651    

DOI:10.1002/jcc.540080508

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractA 27‐picosecond (ps) molecular dynamics calculation has been carried out for the 1:2 enzyme‐ligand complex between porcine pancreatic elastase (PPE) and acetyl‐alanine‐proline‐alanine (APA). A data analysis has been carried out using a total of 450 structures. During the simulation, the root‐mean‐square fluctuations (RMSF) increased compared with the x‐ray data. Some differences of the hydrogen bond arrangement in the MD average structures are found especially for SER 195, suggesting the fluctuations of the ligand molecules. The radius of gyration decreased a little during the simulation. Although intermolecular hydrogen bonds between two substrates (APA1 and APA2) has not been found by a 1.65‐Å high‐resolution x‐ray diffraction study, the MD calculation showed the intermolecular hydrogen bond between them to be 3.2 Å. The extended active site of PPE is so wide compared with the size of a tripeptide that such a hydrogen‐bound hexapeptide can be more specific than tripeptides, which is consistent with the kinetic

ISSN:0192-8651    

DOI:10.1002/jcc.540080509

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractThe method of Lagrangian multipliers is used to constrain torsion angles during molecular mechanics refinement for the purpose of plotting strain energy against a reaction coordinate. A complete two‐dimensional analysis of the conformational interconversion from δ‐ to λ‐[Co(ethane‐1,2‐diamine) (NH3)4]3+reveals a mechanism in which the transition state geometry has an envelope conformation and an inversion barrier of 15.7kJmol−1. Substitution at the carbon atoms, variation of the metal‐nitrogen distance, and replacement of the amine ligands with bidentate amines only slightly alters the inversion barrier. Substitution at the nitrogen atoms of the bidentate ligand increases the inversion barrier significantly to 24.6 kJ mol−1for (N,N,N′,N′‐tetramethylethane

ISSN:0192-8651    

DOI:10.1002/jcc.540080510

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY

摘要:

AbstractA theoretical study of homocyclic sulfur species S6, S7, and S8was carried out using a molecular valence method involving stepwise approximations for orthogonality and core‐valence interactions. The valence shell orbitals are described at the minimal basis level. The geometries of the molecules are predicted well as compared with other theoretical studies and the experimental values. The slight overestimation of the SS bond length is typical to the nonpolarized basis sets. The energies of the valence orbitals are well in accord with the conventional all‐electronab initioresults. The trend in the stabilities of the three molecules is discussed. The present method provides an attractive possibility to study homocyclic and heterocyclic systems involving heavier chalcogens with no increase of the computing t

ISSN:0192-8651    

DOI:10.1002/jcc.540080511

出版商:John Wiley&Sons, Inc.    

年代:1987

数据来源: WILEY