Journal of Computational Chemistry

Bu, Yuxiang; Sun, Haitao; Niu, Hongbo

doi: 10.1002/(SICI)1096-987X(19990730)20:10<989::AID-JCC1>3.0.CO;2-Epmid: N/A

The electron transfer reactivity of the O2+O 2− system in low‐spin coupling is studied at the second‐order unrestricted Møller–Plesset (full)/6‐311+G* basis set level by using different transition state structures. The properties and stabilities of the encounter complexes are compared for the five selected coupling structures: two T type, collinear, parallel, and crossing. The activation barriers and the coupling matrix elements are also calculated. The results indicate that the structures of the encounter complexes directly affect the electron transfer mechanism and rate. These encounter complexes are structurally unstable, the contact distances between the acceptor O2 and the donor O 2− are generally large, the interaction is weak, and the structures are floppy. The electronic transmission factor for the reacting system, O2+O 2−, is less than unity; thus, the electron transfer reaction is nonadiabatic in nature. Analysis of the dependence of relevant kinetic parameters on various influencing factors has shown that the effect of the solvent medium on the coupling matrix element is small but that on the electron transfer rate is very large. Among the five selected transition state structures, the electron transfer is more likely to take place via T1‐type and P‐type structures. In the low‐spin coupling the favorable electronic states for two reacting species are 1∑ g+(O2) and X2Πg(O 2−) instead of X3∑ g−(O2) and X2πg(O 2−), which are favorable for the high‐spin (quartet state) coupling mechanism. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 989–998, 1999

Cullen, John

doi: 10.1002/(SICI)1096-987X(19990730)20:10<999::AID-JCC2>3.0.CO;2-Apmid: N/A

Presently the most reliable approach for the study of reaction pathways where chemical bonds are broken and formed is to carry out CASSCF calculations followed by corresponding multireference perturbation or CI treatments. The latter step generally relaxes the “antibonding character” of the CASSCF results. In this study we demonstrate that similar results can be well approximated by using a less optimized MCSCF method and not performing the multireference perturbation or CI step at all. This is accomplished by performing a complete CI calculation within the active orbital space of the generalized valence bond perfect pairing (GVB‐PP) model. The local bond/antibond character of the orbital space of the GVB‐PP method also allows development of a fast, but robust, Bethe–Goldstone algorithm, which reconstructs the CI energy to an accuracy of a few tenths of a millihartree for most types of bond breaking cases found in chemical reactions. This algorithm executes at a speed proportional to N p4 where Np is the number of localized electron pairs in the active space. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 999–1008, 1999

Faller, Roland; Schmitz, Heiko; Biermann, Oliver; Müller‐Plathe, Florian

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1009::AID-JCC3>3.0.CO;2-Cpmid: N/A

In this study we demonstrate an automatic method of force field development for molecular simulations. Parameter tuning is taken as an optimization problem in many dimensions. The parameters are automatically adapted to reproduce known experimental data such as the density and the heat of vaporization. Our method is more systematic than guessing parameters and, at the same time, saves human labor in parameterization. It was applied successfully to several molecular liquids. As a test, force fields for 2‐methylpentane, tetrahydrofurane, cyclohexene, and cyclohexane were developed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1009–1017, 1999

Reddy, M. Rami; Erion, Mark D.

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1018::AID-JCC4>3.0.CO;2-Bpmid: N/A

Molecular dynamics (MD) simulations in conjunction with the thermodynamic cycle perturbation approach has been used to calculate relative solvation free energies for acetone to acetaldehyde, acetone to pyruvic acid, acetone to 1,1,1‐trifluoroacetone, acetone to 1,1,1‐trichloroacetone, acetone to 2,3‐butanedione, acetone to cyclopropanone, and formaldehyde hydrate to formaldehyde. To evaluate the dependence of relative solvation free energy convergence on MD simulation length and starting configuration two studies were performed. In the first study, each simulation started from the same well‐equilibrated configuration and the length was varied from 153 to 1530 ps. In the second study, the relative solvation free energy differences were calculated starting from three different configurations and using 510 ps of MD simulation for each mutation. These results clearly indicate that, even for molecules with limited conformational flexibility, a simulation length of 510 ps or greater is required to obtain satisfactory convergence and, for the mutations of large structural changes between reactant and product, such as cyclopropanone to acetone, require much longer simulation lengths to achieve satisfactory convergence. These results also show that performing one long simulation is better than averaging results from three shortest simulations of the same length using different starting conformations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1018–1027, 1999

Cummins, Peter L.; Gready, Jill E.

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1028::AID-JCC5>3.0.CO;2-7pmid: N/A

The aqueous solvation free energies of ionized molecules were computed using a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1, MNDO, and PM3 semiempirical molecular orbital methods for the solute molecule and the TIP3P molecular mechanics model for liquid water. The present work is an extension of our model for neutral solutes where we assumed that the total free energy is the sum of components derived from the electrostatic/polarization terms in the Hamiltonian plus an empirical “nonpolar” term. The electrostatic/polarization contributions to the solvation free energies were computed using molecular dynamics (MD) simulation and thermodynamic integration techniques, while the nonpolar contributions were taken from the literature. The contribution to the electrostatic/polarization component of the free energy due to nonbonded interactions outside the cutoff radii used in the MD simulations was approximated by a Born solvation term. The experimental free energies were reproduced satisfactorily using variational parameters from the vdW terms as in the original model, in addition to a parameter from the one‐electron integral terms. The new one‐electron parameter was required to account for the short‐range effects of overlapping atomic charge densities. The radial distribution functions obtained from the MD simulations showed the expected H‐bonded structures between the ionized solute molecule and solvent molecules. We also obtained satisfactory results by neglecting both the empirical nonpolar term and the electronic polarization of the solute, i.e., by implementing a nonpolarization model. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1028–1038, 1999

Aplincourt, P.; Ruiz–López, M. F.; Assfeld, X.; Bohr, F.

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1039::AID-JCC6>3.0.CO;2-0pmid: N/A

We have investigated the structure of HO2 and a series of alkyl peroxyl radicals ROO using a variety of quantum mechanical methods. We first compute the geometries, vibrational frequencies, electronic charge distributions, and spin densities for the series of radicals considered in the gas phase. Significant differences with respect to previous calculations have been pointed out in a few cases. In particular, we show the fundamental importance of electronic correlation when computing net atomic charges and spin densities, which have generally been estimated in the litterature by means of Hartree–Fock SCF electronic densities. Solvation effects on the geometry and electronic structure have been estimated by carrying out self‐consistent reaction field computations in a polarizable continuum environment with relative dielectric permittivity equal to that of liquid water. Large electronic polarization is predicted in such conditions. This may be important in order to understand reactive properties of the radicals in different media. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1039–1048, 1999

Apostol, Izydor; Szpankowski, Wojciech

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1049::AID-JCC7>3.0.CO;2-Xpmid: N/A

A modified Sammon algorithm was developed to display a relationship between proteins based on their amino acid composition. In the first stage of the method, a 19‐dimensional compositional space of representative proteins was mapped into a two‐dimensional space (2D) using the original Sammon projection creating a contour map. In the second stage, this contour map was used as a reference for new proteins projected into 2D. Data analysis showed that proteins belonging to the same structural classes formed characteristic and distinct clusters, which could be potentially useful in the prediction of protein structural classes. However, we observed significant overlapping of the clusters, which may explain the limited success of previous protein folding prediction based solely on amino acid composition. Regardless, the modified Sammon projections can generate a unique index for each individually projected protein related to its amino acid composition, which may be a useful tool in the exploratory classification of proteins. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1049–1059, 1999

Acioli, Paulo Hora; Magela e Silva, Geraldo

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1060::AID-JCC8>3.0.CO;2-Ipmid: N/A

The control of charge transport on a polymer chain by impurity molecules working as switches is studied. Charge propagation is estimated using a backpropagation neural network approach. The supervised learning is accomplished using theoretical results in which the chain is modeled by a tight‐binding Hamiltonian extended to include the effects of an external electric field. The charge transport through the sites that work like a switch is analyzed by the numerical integration of the equations of motion. For a donor–acceptor pair of impurities, we found that the chain offers a wide range of devices, from simple switches to perfect molecular rectifiers. The influence of the parameters of the molecules on the charge transport, the role of the length of separation between the sites where the impurity molecules bond, as well as the changes they must undergo to characterize each kind of molecular switch are determined. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1060–1066, 1999

Lee, Sang‐Ho; Palmo, Kim; Krimm, Samuel

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1067::AID-JCC9>3.0.CO;2-Vpmid: N/A

With currently used definitions of out‐of‐plane angle and bond angle internal coordinates, Cartesian derivatives have singularities, at ±π/2 in the former case and π in the latter. If either of these occur during molecular mechanics or dynamics simulations, the forces are not well defined. To avoid such difficulties, we provide new out‐of‐plane and bond angle coordinates and associated potential energy functions that inherently avoid these singularities. The application of these coordinates is illustrated by ab initio calculations on ammonia, water, and carbon dioxide. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1067–1084, 1999

Torre, A.; Lain, L.; Bochicchio, R.; Ponec, R.

doi: 10.1002/(SICI)1096-987X(19990730)20:10<1085::AID-JCC10>3.0.CO;2-Xpmid: N/A

The population analysis of higher order densities previously described by us and other investigators, has been applied to the description of 1,5—X2B3H3(X=N, CH, P, SiH, BH−) members of the closo‐borane family. The calculated results, obtained at the SCF level, suggest the presence of three‐center nonclassical bonds in the majority of systems studied. The good agreement between our results and those obtained from more sophisticated methods make this procedure a suitable and simple tool for detecting and localizing three‐center bonds. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1085–1090, 1999