Journal of Computational Chemistry

doi: 10.1002/jcc.540170901pmid: N/A

Krissinel', Evgenii B.; Agmon, Noam

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1085::AID-JCC1>3.0.CO;2-Opmid: N/A

We introduce a general and versatile MS Windows application for solving the spherically symmetric diffusion problem, involving up to two coupled spherically symmetric Smoluchowski equations. The application is based on a modular, configurable, user‐friendly graphical interface, in which input parameters are introduced through a graphical representation of the system of partial differential equations and output attributes can be obtained graphically during propagation. The numerical algorithm consists of finite differencing in space and Chebyshev propagation in time; it includes an implementation of virtual gridding, which enhances the accuracy of calculating boundary conditions and steep potentials. The program has b een checked against a wide collection of analytical solutions and applied to an experimentally open problem in excited‐state proton‐transfer to solvent. © 1996 by John Wiley & Sons, Inc.

Siegbahn, Per E. M.

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1099::AID-JCC2>3.0.CO;2-Npmid: N/A

Structures of the H3O+‐OH ion pair surrounded by up to three water molecules have been studied. Since the ion‐pair structure is always above the corresponding neutral water structure, a constrained geometry optimization is needed. The energy difference between the ion‐pair structure and the neutral water structure is studied as a function of the number of surrounding water molecules. The effect of the surrounding water solvent is also studied by placing the model system in a spherical cavity in a dielectric medium. The main results are that the energy difference stabilizes at 10–20 kcal/mol for the larger clusters and that an effect indicating a mechanism for charge separation can be noticed on the geometries of these clusters. Results obtained using gradient‐corrected density‐functional theory are compared to a configuration interaction treatment using a scaling procedure of the correlation energy. © 1996 by John Wiley & Sons, Inc.

Li, Xiang‐Yuan; Tian, An‐Min; He, Fu‐Cheng; Yan, Guo‐Sen

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1108::AID-JCC3>3.0.CO;2-Wpmid: N/A

In the research of electron transfer (ET) reactions, the theoretical calculation of the ET matrix element VBA is of special importance. Some examples in which the two electron‐localized states have a zero overlap were found. Thus, a new procedure for VBA calculation was developed and applied to the investigation of the donor‐acceptor 90° oriented ET reactions. This procedure, which is a supplement necessary to the recently developed approach suitable for a nonorthogonal case, was derived in detail. To check the rationality of the zero value of VBA in the reaction O2O−2 → O−2O2, the angle dependence of SBA and VBA between two electron‐localized states was calculated. © 1996 by John Wiley & Sons, Inc.

Chipot, Christophe; Kollman, Peter A.; Pearlman, David A.

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1112::AID-JCC4>3.0.CO;2-Vpmid: N/A

We investigated the convergence behavior of potential of mean force (PMF) calculations using free energy perturbation (FEP), thermodynamic integration (TI), and “slow growth” (SG) techniques. The critical comparison of these alternative approaches is illustrated by the study of three different systems: two tagged argon atoms in a periodic box of argon, two methane molecules, and two benzene molecules maintained in a “T‐shaped” conformation, both dimers embedded in a periodic box of water. The complete PMF simulations were carried out considering several protocols, in which the number of intermediate “λ” states, together with the amount of sampling per individual state, were varied. In most cases, as much as 1 ns of molecular dynamics (MD) sampling was used to derive each free energy profile. For the different systems examined, we find that FEP and TI unquestionably constitute robust computational methods leading to results of comparable accuracy. We also show that proper convergence of the free energy calculations, and further quantitative interpretation of the PMFs, requires total simulation times much higher than has been hitherto estimated. In some circumstances, the free energy profiles derived from FEP calculations tend to be slightly poorer than those obtained with TI, as a probable consequence of the greater sensitivity of FEP to the window spacing δλ. In the context of TI, and to a lesser extent FEP, simulations, it appears preferable to employ a limited number of “λ” points of the integrand involving extensive sampling, rather than numerous points with fewer samplings. Finally, we note that, at least in the case of nonpolar interactions, PMFs of reasonable quality can be generated using SG, and at a substantially lower cost than with either FEP or TI. © 1996 by John Wiley & Sons, Inc.

Blondel, Arnaud; Karplus, Martin

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1132::AID-JCC5>3.0.CO;2-Tpmid: N/A

A new set of formulae is developed for the derivatives of torsion angle energy terms and is introduced into the program CHARMM. These formulae, which are based on derivatives of the torsion angle itself, avoid the singularities introduced by use of the derivatives of the torsion angle cosine. The potential energy can include any differentiable function of the torsion angle and there is no need for a special treatment for cases where planar conformations are not extrema. The resulting code is simpler than the original version and yields correct derivatives in all practical situations. Because the minimum of the torsion energy can be at any angle, the functionality of the existing energy routines is generalized. © 1996 by John Wiley & Sons, Inc.

Meza, J. C.; Judson, R. S.; Faulkner, T. R.; Treasurywala, A. M.

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1142::AID-JCC6>3.0.CO;2-Spmid: N/A

We present results from the application of two conformational searching methods: genetic algorithms (GA) and direct search methods for finding low energy conformations of organic molecules. GAs are in a class of biologically motivated optimization methods that evolve a population of individuals in which individuals who are more “fit” have a higher probability of surviving into subsequent generations. The parallel direct search method (PDS) is a type of pattern search method that uses an adaptive grid to search for minima. Both methods found energies equal to or lower than the energy of the relaxed crystal structure in all cases, at a relatively small cost in CPU time. We suggest that either method would be a good candidate to find 3‐D conformations in a large scale screening application. © 1996 by John Wiley & Sons, Inc.

Delley, Bernard

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1152::AID-JCC7>3.0.CO;2-Rpmid: N/A

A method for refining high order numerical integration schemes is described. Particular focus is on integration schemes over the unit sphere with octahedral symmetry. The method is powerful enough that new integration schemes can be found from rough intuitive guesses. New schemes up to order 59 are presented. © 1996 by John Wiley & Sons, Inc.

Svensson, Bo R.; Woodward, Clifford E.

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1156::AID-JCC8>3.0.CO;2-Rpmid: N/A

We describe a new method to simulate confined fluids in equilibrium with a bulk. The equilibrium is first located at a low density, where conventional methods relying upon real or virtual particle exchanges are reliable. Thereafter, the chemical potential of the fluid is increased by the same amount in both systems using a variation of a recently developed free energy difference method in an isobaric (isotension) ensemble. The method, illustrated here for a simple fluid in a planar slit, is shown to be reliable up to high densities. As the method does not rely upon particle exchanges it is ideally suited to the simulation of equilibria in complex fluids, e.g., molecular liquids and polymers. © 1996 by John Wiley & Sons, Inc.

Kudo, Takako; Hashimoto, Fujiko; Gordon, Mark S.

doi: 10.1002/(SICI)1096-987X(19960715)17:9<1163::AID-JCC9>3.0.CO;2-Qpmid: N/A

The geometry optimizations for several conformations of tri‐, tetra‐, and pentacyclosiloxane (H2SiO)n (n = 3, 4, and 5) were carried out, and the relative stabilities were compared at the Hartree‐Fock (HF) and second order perturbation theory (MP2) levels of theory using the 6–31G* and 6–311G(d, p) basis sets. At the highest levels of theory, the only minimum for n = 4 (D4) occurs at the highly symmetric D4h structure. In contrast, several, nearly isoenergetic, minima are found on the D5 surface. These have C1, C2, Cs, and D5h symmetries. While the C1 structure has the lowest MP2/6–311G(d, p) energy, this species is predicted to be highly fluxional, and the distribution of isomers is dependent on temperature. © 1996 by John Wiley & Sons, Inc.