Journal of Computational Chemistry

doi: 10.1002/jcc.540120901pmid: N/A

Teixeira‐Dias, J. J. C.; Fausto, R.; de Carvalho, L. A. E. Batista

doi: 10.1002/jcc.540120902pmid: N/A

The CαC internal rotation in 2‐methylpropionic, 2‐methylthiopropionic (thiol and thion forms) and 2‐methyldithiopropionic acids was studied by the ab initio SCF‐MO method using 3‐21G and 3‐21G + d(0.65S) basis sets. Energies and structures of several conformations of these molecules, determined by gradient geometry refinement, are reported and used to assess the effects of oxygen‐by‐sulphur substitution on molecular properties. The nature and relative importance of intramolecular interactions involving both the α‐methyl substituents and the C(X)Y (X, Y O or S) fragment are also discussed.

Horn, Hans; Weiß, Horst; Háser, Marco; Ehrig, Michael; Ahlrichs, Reinhart

doi: 10.1002/jcc.540120903pmid: N/A

The definition and implementation of a rigorous two‐electron integral bound based on Schwarz' inequality both for gradient and hessian calculations is presented. Tests demonstrate the advantages of this easily implemented and effective bound.

von Freyberg, Berthold; Braun, Werner

doi: 10.1002/jcc.540120904pmid: N/A

The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met‐enkephalin. In total, 1881 conformations below −10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root‐mean‐square‐deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below −10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.

Silla, Estanislao; Tuñón, Iñaki; Pascual‐Ahuir, Juan Luis

doi: 10.1002/jcc.540120905pmid: N/A

The algorithm used by the program GEPOL for a finer description of molecular surface (for a fast calculation of molecular area and volume and for an efficient selection of sampling points) is presented in detail. Different types of surfaces such as van der Waals and Richard's molecular surfaces can be computed. As we described in the first article (J.L. Pascual‐Ahuir and E. Silla, J. Comp. Chem., 11, 1047(1990)), GEPOL begins by building a set of spherical surfaces which fill the space which is not solvent accessible. In this second article, a triangular tessellation approach to select the parts of these spherical surfaces which form the molecular surface is described. By using a data coded generic pentakisdodecahedron, each spherical surface is divided in triangular tesserae. A simple method is used to eliminate all triangles found at the intersection volume of the spheres. The center coordinates and the surface of the remaining triangles are used in order to calculate the molecular area and volume and as starting point of the graphic representation of scalar and vector properties. We study the behavior of the method, presenting several examples of application. Special attention is given to the accuracy, spatial invariance and computer efficiency measured by CPU time. Some models of aligned spheres whose area and volume can be found exactly allow us to do a comparative study with a well‐known method, analyzing their behavior in line with their respective graining parameters. A fragment of protein is used as an example of the application of the method for characterizing biomolecular surfaces. Aqueous solubility of organic compounds is studied as an example of the experimental property that depends on the molecular area obtaining a good correlation between the logarithm of the solubility and the area calculated using GEPOL.

Lehd, Michael; Jensen, Frank

doi: 10.1002/jcc.540120906pmid: N/A

The virial theorem for molecules is shown to have two different forms, one employing the energy gradient the other involving the Hellmann–Feynman force. While the former VT can be fulfilled by a uniform scaling of the basis set, the latter cannot be satisfied in certain basis sets, and can give unrealistic results in others. The scaling procedure is applied to molecules at nonstationary points on the potential energy surface and it is found that energy components can change substantially, especially at short bondlengths, while the change in total energy is small. The effects on molecular properties are also small.

Kato, Hiroshi; Tanaka, Eishi

doi: 10.1002/jcc.540120907pmid: N/A

The stabilities Ben and Bn clusters (4 ≤ n ≤ 8) based on the vibrational analysis were investigated by ab initio MO calculations. The computations were performed by using a 3‐21G basis set at the R(U)HF level and at the R(U)MP4 level with the HF optimized structures. Spin‐multiplicities were also considered up to quintet states (n ≤ 7). Of the 120 species that were treated, half of them were considered stable and some of these stable species were obtained by the deformations of transition state and unstable species, following the imaginary normal modes. The transformation barrier between the transition state species and corresponding stable ones was presented. It was found that there were two types of stable clusters: (1) a low symmetry species with lower frequencies and lower geometrical change barriers and (2) a high symmetry one with higher frequencies. The former type was considered as a structural “soft” species and the latter as a “hard” species.

Goodman, Jonathan M.; Still, W. Clark

doi: 10.1002/jcc.540120908pmid: N/A

A new method for searching internal coordinate conformational space systematically via a continuous‐process procedure is described. Unlike previous systematic search methods, the new scheme generates torsionally remote conformers early in the search. It is also unbounded in that the extent of the search need not be specified at the outset. The search begins at low resolution (120° in torsion angle space) and then goes to higher and higher resolution as all points in space at a given resolution have been searched. The search may run without end or be terminated when new conformers cease to be found or when all space at some maximum allowable resolution has been explored. Conformational searches on several medium‐ and large‐ring molecules using the new method are described and the results are compared with those from certain previously described search methods. It is found that the new method is significantly more efficient than previous procedures at finding all low energy conformers of organic molecules.

Brown, T. J. N.; Mallion, R. B.; Pollak, P.; de Castro, Branca R. M.; Gomes, J. A. N. F.

doi: 10.1002/jcc.540120909pmid: N/A

The theorem of Gutman et al. (1983) is applied to calculate the number of spanning trees in the carbon‐carbon connectivity‐network of the recently diagnosed C60‐cluster buckminsterfullerene. This “complexity” turns out to be approximately 3.75 × 1020 and it is found necessary to invoke the device of modulo arithmetic and the “Chinese Remainder Theorem” in order to evaluate it precisely on a small computer. The exact spanningtree count for buckminsterfullerene is 375 291 866 372 898 816 000, or, 225 × 34 × 53 × 115 × 193. A “ringcurrent” calculation by the method of McWeeny may be based on any desired one of this vast number of spanning trees.

Bartolotti, Libero J.; Pedersen, Lee G.; Charifson, Paul S.

doi: 10.1002/jcc.540120910pmid: N/A

Employing the hydrodynamic formulation of time‐dependent Kohn–Sham theory, long range dispersion constants are calculated for some metal ions. We show that these quantities, when used in molecular mechanics calculations or molecular dynamics simulations, lead to excellent results.