Journal of Computational Chemistry

Jorge, F. E.; De Castro, E. V. R.; Da Silva, A. B. F.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1565::AID-JCC1>3.0.CO;2-Ppmid: N/A

The generator coordinate Hartree–Fock method is applied to generate a universal Gaussian basis set for the heavy atoms from Ce (Z=58) through Lr (Z=103). The Hartree–Fock energies obtained with our universal Gaussian basis set are compared with the new numerical Hartree–Fock results of Koga et al., when available, and with geometrical Gaussian basis sets results available in the literature. The universal Gaussian basis set presented here is generated taking into account the shell constraint (the sharing of exponential functions between all s, p, d, and f atomic orbitals), and can be used as starting basis set in ab initio relativistic Hartree–Fock–Roothaan calculations. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1565–1569, 1997

Cortis, Christian M.; Friesner, Richard A.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1570::AID-JCC2>3.0.CO;2-Opmid: N/A

We present an automatic three‐dimensional mesh generation system for the solution of the Poisson–Boltzmann equation using a finite element discretization. The different algorithms presented allow the construction of a tetrahedral mesh using a predetermined spatial distribution of vertices adapted to the geometry of the dielectric continuum solvent model. A constrained mesh generation strategy, based on Bowyer's algorithm, is used to construct the tetrahedral elements incrementally and embed the Richards surface of the molecule into the mesh as a set of triangular faces. A direct mesh construction algorithm is then used to refine the existing mesh in the neighborhood of the dielectric interface. This will allow an accurate calculation of the induced polarization charge to be carried out while maintaining a sparse grid structure in the rest of the computational space. The inclusion of an ionic boundary at some finite distance from the dielectric interface can be automatically achieved as the grid point distribution outside the solute molecule is constructed using a set of surfaces topologically equivalent to this boundary. The meshes obtained by applying the algorithm to real molecular geometries are described. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1570–1590, 1997

Cortis, Christian M.; Friesner, Richard A.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1591::AID-JCC3>3.0.CO;2-Mpmid: N/A

The automatic three‐dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson–Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary element calculations using our triangulated molecular surface. The overall scaling of the method is found to be approximately linear in the number of atoms in the system. The finite element mesh structure can be exploited to compute the gradient of the polarization energy in 10–20% of the time required to solve the equation itself. The resulting timings for the larger systems considered indicate that energies and gradients can be obtained in about half the time required for a finite difference solution to the equation. The development of a multilevel version of the algorithm as well as future applications to structure optimization using molecular mechanics force fields are also discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1591–1608, 1997

Nguyen, D. T.; Scheiner, A. C.; Andzelm, J. W.; Sirois, S.; Salahub, D. R.; Hagler, A. T.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1609::AID-JCC4>3.0.CO;2-Vpmid: N/A

The potential energy surface of un‐ionized glycine has been explored with density functional theory. The performance of several nonlocal functionals has been evaluated and the results are presented in the context of available experimental information and post‐Hartree–Fock quantum chemical results. The zero‐point and thermal vibrational energies along with vibrational entropies play a very important role in determining the relative stability of glycine conformers; the realization of this has led to some revision and reinterpretation of the experimental results. Uncertainties in the vibrational contributions to the energy differences of several tenths of a kilocalorie/mole remain. The uncertainty in the vibrational free energy is even larger, about 1 kcal/mol. In the final analysis, we suggest that the best estimate of the electronic energy difference between the two lowest glycine conformers should be revised downward from 1.4 to 1.0 kcal/mol. Thirteen stationary points on the potential energy surface have been localized. For the majority of these, there is close agreement among various nonlocal density functionals and the post‐Hartree–Fock methods. However, the second conformer (IIn), which has a strong hydrogen bond between the hydroxyl hydrogen and the nitrogen of the amine group, presents a distinct challenge. The relative energy of this conformer is extremely sensitive to the basis set, the level of correlation, or the functional used. The widely used BP86, PP86, and BP91 nonlocal functionals overestimate the strength of the hydrogen bond and predict that this conformer is the lowest energy structure. This contradicts both experiment and high‐level post‐Hartree–Fock studies. The adiabatic connection method (ACM) and the BLYP functional yield the correct order. The ACM method, in particular, gives energies which are in reasonable agreement with MP2, although these are somewhat low as compared with experiment. Based on this study, ACM should perform well for this type of bioorganic application, with typical errors of a few tenths of a kilocalorie/mole and only rarely exceeding 0.5 kcal/mol. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1609–1631, 1997

Dixon, Richard W.; Kollman, Peter A.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1632::AID-JCC5>3.0.CO;2-Spmid: N/A

A computational approach to the inclusion of off‐center charges in both additive and nonadditive molecular mechanics calculations is presented. The additional sites in the molecular skeleton are placed in the approximate locations of the chemically intuitive electron lone pair, and are treated as formal particles throughout the calculation. The increase in the number of charge sites results in overall improvement in the energy associated with the angular dependence of hydrogen bonds and improved statistical accuracy of the electrostatic potential derived charges. The addition of lone pairs also results in improved accuracy in relative solvation free energy calculation for the pyridine to benzene and methanol to methane mutations. Because the number of atoms that require lone pairs is small, the extra accuracy can be achieved with little computational overhead. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1632–1646, 1997

Martínez‐Núñez, Emilio; Vázquez, Saulo A.; Mosquera, Ricardo A.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1647::AID-JCC6>3.0.CO;2-Rpmid: N/A

A conformational analysis of two model compounds of vitamin D was carried out by means of theoretical computations, Ab initio calculations were carried out using the standard 6‐31G* basis set at the Hartree–Fock (HF) level of theory. In addition, the Møller–Plesset (MP2) correlation treatment was applied on the simplest model. Semiempirical calculations were also performed using the AM1 Hamiltonian. The results predict stable A‐ring twist forms with energies in the order of 4–6 kcal/mol relative to the global minimum, significantly higher than those reported from molecular mechanics calculations. In addition, a folded conformation was found by the HF optimizations; however, its stability is predicted to be very poor. Comparison of the theoretical results with experimental data is discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1647–1655, 1997

Fukunishi, Yoshifumi; Suzuki, Makoto

doi: 10.1002/(SICI)1096-987X(199710)18:13<1656::AID-JCC7>3.0.CO;2-Qpmid: N/A

We propose an empirical method for evaluating the potential of mean force (pmf) of solute molecules in water by modifying the solvent‐accessible surface (SAS) method described by Eisenberg et al. We re‐evaluated the SAS energy for each united atom composing the solute. We took into account the energy required to generate a void between adjacent solute molecules and the Coulombic interactions between atom‐centered point charges of solute molecules containing C, O, P, K+, Na+, and Cl− atoms in water. The modified SAS method well reproduced the various pmfs given by MD calculations or the integral equation method. The large activation energy of K+–18‐crown‐6 complexation can be explained mostly by the void energy. The computational time required for the modified SAS method is approximately three to four orders of magnitude less than that by MD calculations. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1656–1663, 1997

McDowell, Sean A. C.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1664::AID-JCC8>3.0.CO;2-Ppmid: N/A

The change in the electric field at a nucleus in a molecule due to bond stretch is related to the force constant of the stretched bond. The validity of this relationship using approximate wave functions at the SCF and MP2 levels of theory is tested for the diatomic molecules H2, HF, CO, and N2. The effect of basis set variation on H2 is also investigated. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1664–1667, 1997

Liwo, Adam; Dyl, Dariusz; Jeziorek, Danuta; Nowacka, Małgorzata; Ossowski, Tadeusz; Woźnicki, Wiesław

doi: 10.1002/(SICI)1096-987X(199710)18:13<1668::AID-JCC9>3.0.CO;2-Ppmid: N/A

The reaction path of singlet (1Δg) oxygen addition to ethenol (vinyl alcohol)—a model of the reactions of singlet oxygen with aromatic and unsaturated compounds bearing the hydroxy groups—has been studied by means of MCSCF calculations, using various active spaces and basis sets. The effects of dynamic correlation (at the PT2 level) and basis set superposition error (BSSE) on relative energies were also investigated. It was found that including polarization functions is necessary to obtain geometries of the oxygen moiety consistent with the available experimental data. Two possible reaction products were considered: 1‐hydroxy‐1,2‐dioxethane (peroxide) and 2‐hydroperoxyethanal‐1 (hydroperoxide); their energies are 24.1 and 36.6 kcal/mol (44.1 and 78.2 kcal/mol with the PT2 contribution and BSSE correction) below the dissociation limit, respectively (all energies reported here refer to the 6‐31G** basis set and an active space composed of eight orbitals and ten electrons). A common stage of both reactions is the formation of a peralcoxyl intermediate with one of the oxygen atoms attached to the unsubstituted carbon atom; the energies of the respective transition state and that of the intermediate are 30.2 and 18.7 kcal/mol (15.9 and 10.3 kcal/mol with the PT2 contribution and BSSE correction) above the dissociation limit, respectively. The energy of this transition state is the dominant energy barrier to the reaction. The intermediate can then undergo conversion to the dioxethane product, to the perepoxide intermediate, or via a proton transfer, directly to the hydroperoxide, the last route being the most probable one. The perepoxide intermediate, after a proton transfer, also readily gives the hydroperoxide. It was also found that the unimolecular conversion from dioxethane to hydroperoxide via a proton transfer from the hydroxy group accompanied with ring cleavage requires an activation energy of at least 56 kcal/mol, making this reaction path highly improbable. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1668–1681, 1997

Marynick, Dennis S.

doi: 10.1002/(SICI)1096-987X(199710)18:13<1682::AID-JCC10>3.0.CO;2-Kpmid: N/A

In part I of this series, the PESP (parameterized electrostatic potential) method was described and applied to the calculation of electrostatic‐potential‐derived charges for a wide variety of organic and inorganic systems. Based on PRDDO/M wave functions and parameterized against ab initio MP2/6‐31G** calculations, PESP is an order of magnitude faster than ab initio STO‐3G calculations, while achieving a level of accuracy that rivals that of far more sophisticated ab initio methods. In this study, the application of the PESP method to the high potential regions of molecules containing H, C, N, O, F, P, S, Cl, and Br is described. For a collection of 48 molecules and 55 distinct lone pair minima, PESP yields the location and depth of lone pair minima to an average accuracy (relative to MP2/6‐31G**) of 0.03 Å and 2.5 kcal/mol, respectively. Similarly, the location and well depths of minima in the π regions of organic molecules are calculated to an accuracy of 0.08 Å and 1.5 kcal/mol. PESP electrostatic potential maps are, in some cases, virtually indistinguishable from those obtained at the MP2/6‐31G** level. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1682–1693, 1997