摘要:

AbstractStudies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (ROOH) and dialkyl peroxides (R1OOR2). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wil

ISSN:0192-8651    

DOI:10.1002/jcc.540140702

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractWe present a storage‐efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight‐binding models of ordered and disordered 2‐D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10−4is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley&S

ISSN:0192-8651    

DOI:10.1002/jcc.540140703

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractIt is suggested to improve the MNDO model by the explicit inclusion of valence‐shell orthogonalization corrections, penetration integrals, and effective core potentials (ECPs) in the one‐center part of the core Hamiltonian matrix. Guided by analytic formulas and numericalab initioresults, the orthogonalization corrections are expressed in terms of the resonance integrals that are represented by a new empirical parametric function. All two‐center Coulomb interactions and ECP integrals are evaluated analytically in a Gaussian basis followed by a uniform Klopman–Ohno scaling. One particular implementation of the proposed NDDO SCF approach is described and parameterized for the elements H, C, N, O, and F. In a statistical evaluation of ground‐state properties, this implementation shows slight but consistent improvements over MNDO, AM1, and PM3. Significant improvements are found for excited states, transition states, and strong hydrogen bonds. Possible further enhancements of the current implementation are discussed. © 1993 John Wiley

ISSN:0192-8651    

DOI:10.1002/jcc.540140704

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThree different optimization algorithms are applied to solving the problem of finding the best side‐chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540140705

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractA systematic study of the suitability of PM3‐derived molecular electrostatic potentials (MEPs) is presented. Forty‐six MEP minima, 81 electrostatic charges, and 17 electrostatic dipoles were determined at the PM3 level and compared with those obtained from theab initio6‐31G* wave function, as well as from the semiempirical MNDO and AM1 wave functions. The statistical results of the comparison analysis between semiempirical andab initio6‐31G* MEPs show that PM3 is in general reliable for the study of the MEP minima but a mediocre method as a source of electrostatic charges. © 1993 John Wiley&S

ISSN:0192-8651    

DOI:10.1002/jcc.540140706

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe two‐step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley&Sons, I

ISSN:0192-8651    

DOI:10.1002/jcc.540140707

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe use of a cluster of workstations as an alternative supercomputer resource is demonstrated using theab initiodirect SCF and RPA code DISCO. DISCO was implemented using several different mechanisms to achieve the requisite parallelization. The various parallel software mechanisms are characterized based upon several different criteria, including portability, ease of use, and relative efficiency. The application of direct SCF and RPA techniques to study the static polarizability of paranitroaniline is described. © 1993 John Wiley&Sons, Inc

ISSN:0192-8651    

DOI:10.1002/jcc.540140708

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe conformational behavior of cellobiose (D‐glc‐ß(1→4)‐D‐glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulationsin vacuoat 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic ϕ, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed betweengt,gg, andtgconformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long‐lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the4C1conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John

ISSN:0192-8651    

DOI:10.1002/jcc.540140709

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractThe conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observedin vacuodue to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley&Sons, Inc

ISSN:0192-8651    

DOI:10.1002/jcc.540140710

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY

摘要:

AbstractAtomic monopole “point charges” are routinely determined through a least squares fit to molecular electrostatic potentials [potential‐derived (PD) charges]. Previously, it has been shown that these charges vary with variation in molecular conformation. Also, it has been observed that these swings in charges are highly correlated between neighboring atoms. Here, we examine the least squares variance–covariance data matrices for a set of data in the literature and find further indications of high colinearity within the data. These colinearities effectively reduce the dimensionality of the data to a value well below the number of atoms in the molecules. This suggests that the data is not of sufficient dimensionality to support calculation of the charges for all of the atoms in a statistically significant way. We experiment with fixing the charges of atoms whose PD charges reflect large errors in the fit. The resulting estimates of fit of the remaining charges are little degraded from the estimates of fit when the charges of all of the atoms are fit. In addition, the charges that are fit take what would be considered more reasonable and “chemically intuitive” values, often of smaller magnitude. Although most of the free charges continue to vary with molecular conformation, their range is no larger than when all charges were fit and, in some cases, the ranges of the charges for the fit atoms is actually reduced over those that are found when all of the atoms take part in the fitting procedure. The errors of fit are lower and the unconstrained charges appear more reasonable when more chemically “reasonable” charges are used for the fixed values. This suggests that in many cases charges are transferable between molecules. Further, it shows a way to justifiably reduce the large fluctuations in PD charges that occur with variations in conformation. © 1993 John

ISSN:0192-8651    

DOI:10.1002/jcc.540140711

出版商:John Wiley&Sons, Inc.    

年代:1993

数据来源: WILEY