Journal of Computational Chemistry

doi: 10.1002/jcc.540140701pmid: N/A

Chen, Kuohsiang; Allinger, Norman L.

doi: 10.1002/jcc.540140702pmid: N/A

Studies 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 Wiley & Sons, Inc.

Koslowski, T.; Von Niessen, W.

doi: 10.1002/jcc.540140703pmid: N/A

We 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 10−4 is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley & Sons, Inc.

Kolb, Matthias; Thiel, Walter

doi: 10.1002/jcc.540140704pmid: N/A

It 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 numerical ab initio results, 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 & Sons, Inc.

Tufféry, P.; Etchebest, C.; Hazout, S.; Lavery, R.

doi: 10.1002/jcc.540140705pmid: N/A

Three 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, Inc.

Alemán, Carlos; Luque, F.J.; Orozco, M.

doi: 10.1002/jcc.540140706pmid: N/A

A 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 the ab initio 6‐31G* wave function, as well as from the semiempirical MNDO and AM1 wave functions. The statistical results of the comparison analysis between semiempirical and ab initio 6‐31G* 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 & Sons, Inc.

Pratt, Lawrence M.; Chu, C.C.

doi: 10.1002/jcc.540140707pmid: N/A

The 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, Inc.

Feyereisen, Martin W.; Kendall, Rick A.; Nichols, Jeff; Dame, David; Golab, Joseph T.

doi: 10.1002/jcc.540140708pmid: N/A

The use of a cluster of workstations as an alternative supercomputer resource is demonstrated using the ab initio direct 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.

Hardy, B.J.; Sarko, A.

doi: 10.1002/jcc.540140709pmid: N/A

The 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 simulations in vacuo at 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 between gt,gg, and tg conformations 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 the 4C1 conformation, 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 Wiley & Sons, Inc.

Hardy, B.J.; Sarko, A.

doi: 10.1002/jcc.540140710pmid: N/A

The 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 observed in vacuo due 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.