The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials

The natural atomic orbital/point (NAO-PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO-PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO-PC are found to be in better agreement with those given by RHF/6-31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO-PC model is often slightly worse then the method implemented in MOPAC-ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6-31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.     

Ab initio molecular electrostatic potentials

The ab initio isopotential map of guanine is given and compared to that of adenine. It shows that in contrast to the situation in adenine, the most basic site of guanine is N₇ with a secondary potential minimum at O₆. These results as well as those concerning the secondary out-of-plane attractive regions over the NH₂ group and C₈ H bonds of the two molecules are discussed in connection with the available experimental knowledge concerning the bonding of alkylating carcinogens and mutagens.     

Topography of approximate molecular electrostatic potentials

A new method is described for the approximation of the molecular electrostatic potential (MESP). This method is used for the study of the topography of small molecules. The critical points of the approximate and the exact MESP are compared. It is found that most of the critical points of the exact MESP are retained, but in regions where the exact MESP changes slowly near critical points the number of critical points of the approximate MESP can be reduced.     

Approximate molecular electrostatic potentials from semiempirical wavefunctions

Approximate molecular electrostatic potentials (MESPs) are calculated with the asymptotic density model (ADM) on the basis of semiempirical wavefunctions generated by the SINDO1 method. The approximate MESP is adjusted to obtain good agreement with the exact MESP from 6–31G^* ab initio calculations for small molecules. This form of the MESP is used for the study of the reactivity of small and medium size silicon clusters with 5 to 45 atoms. Special attention is given to the reactivity of various Si₄₅ structures proposed in the literature. © 1997 by John Wiley & Sons, Inc.     

Influence of polarization functions on molecular electrostatic potentials

We study the effects of d-polarization functions, centered on the heavy atoms, on the SCF molecular electrostatic potentials calculated for some molecules. The positions and energies of the minima found are very sensitive to the inclusion of polarization functions in the basis set used. The variations depend on the heavy atom involved and on the possible anisotropy of its charge distribution. These variations are particularly important for second-row atoms.     

On the molecular electrostatic potentials obtained from CNDO wave functions

The various approximations proposed for computing molecular potentials with CNDO wave functions are tested on the case of guanine and shown to be unable to reproduce correctly the essential fine features of theab initio potential.     

Quantitative comparison of molecular electrostatic potentials for structure-activity studies

An approach for representing, efficiently calculating and comparing discrete three-dimensional molecular electrostatic potentials using a quantitative similarity index (MEP-SI) based on a Carbo-type formalism is presented. A radial-type (MACRA) grid representation is described that provides more efficient storage of MEP information than a cubic grid of similar range, appropriate emphasis, and a convenient means for restricting the comparison of MEP functions to a local molecule region. The MACRA based MEP-SI formalism was used to evaluate the suitability of a variety of approximate methods for efficiently calculating the MEP for use in MEP-SI comparison of dissimilar molecules. The Mulliken charge method was found inadequate, while the method of potential-derived charges (PDCs), with additional charges for lone electron pairs included on sulfur, provided an efficient and sufficiently accurate representation of the MEP for this purpose. Convergence of the MEP-SI with respect to MACRA grid extent and mesh size was demonstrated; the effect of MEP error and different grid point emphasis in the MACRA versus the cubic grid results was investigated, and MEP-SI results were compared for different forms of the SI equation. The methodology proposed in this study provides an efficient and practical means for comparing MEP functions for two molecules and gives discriminating results for a sample series of molecular analogues consistent with expectations.     

The molecular electrostatic potentials of the complementary base pairs of DNA

The perturbations in the molecular electrostatic potentials of the bases of the nucleic acids, brought about by hydrogen-bonding into complementary pairs are evaluated by a superposition procedure.     

On the similarity between molecular electron densities, electrostatic potentials and bare nuclear potentials

The similarities among the molecular contours of three scalar fields, viz. electron density (ED), electrostatic potential (ESP) and bare nuclear potential (BNP) have been investigated. The topological resemblance between ESP and ED contour diagrams (as prompted by the Thomas-Fermi model) is more pronounced than that for BNP and ED contour diagrams (as predicted by the local density functional model of Parr, Gadre and Bartolotti) with three-membered ring systems as test cases. An analysis of critical points of these distributions has also been included. Thus it may be conjectured that ED maps may prove useful in predicting reactive sites in molecules.     

Use of the overlap multipole expansion for approximating molecular electrostatic potentials

The molecular electrostatic potentials computed by the overlap-multipole-expansion procedure (OMTP ) are compared to exact electrostatic potentials computed with the same Gaussian basis set, for different molecular species. It is shown that at distances of the molecule larger than 2.2 Å, the OMTP values compared to those of the exact ones are within an error of 0.5 kcal/mol. This error decreases with increasing distance. For distances below this limit the OMTP potentials may be used as a first indication of the trends of the molecule, provided the values to compare are not too close.     

Graph theoretical similarity approach to compare molecular electrostatic potentials

In this work we introduce a graph theoretical method to compare MEPs, which is independent of molecular alignment. It is based on the edit distance of weighted rooted trees, which encode the geometrical and topological information of Negative Molecular Isopotential Surfaces. A meaningful chemical classification of a set of 46 molecules with different functional groups was achieved. Structure--activity relationships for the corticosteroid binding affinity (CBG) of 31 steroids by means of hierarchical clustering resulted in a clear partitioning in high, intermediate, and low activity groups, whereas the results from quantitative structure--activity relationships, obtained from a partial least-squares analysis, showed comparable or better cross-validated correlation coefficients than the ones reported for previous methods based solely in the MEP.     

Analytical calculation of atomic and molecular electrostatic potentials from the Poisson equation

An analytic formulation is given for the total potential in atomic and molecular systems, based on the electrostatic approach from the Hellmann-Feynman theorem. The potential function is obtained from the analytic solution of the Poisson equation using charge densities expressed as a superposition of gaussian functions. The method is independent of the specific LCAO approximation used for the calculation of the charge distribution function. The calculation of the potential and its derivatives to a rapid algorithm form, which can be used for the evaluation of various electronic properties and the treatment of experimental situation, even for large molecular systems.     

On the molecular electrostatic potentials obtained with CNDO and INDO wave functions

Molecular electrostatic potentials computed with CNDO/2 and INDO wave functions are shown to present systematic differences with respect to ab initio potentials in the case of out-of-plane potentials and in-plane vicinal hetero atoms in planar hetero molecules.     

Theoretical studies on the molecular electron densities and electrostatic potentials in azacubanes

Energetics and the charge distributions in azacubanes (C₈NH_8–) have been obtained using the ab initio Hartree–Fock, second-order Mø øller–Plesset perturbation theory and hybrid density functional methods. For diazacubane to hexaazacubane the lowest-energy conformers have nitrogen atoms occupying the face opposite corners of a cube. The topography of the molecular electrostatic potential and the electron density of azacubane conformers have been investigated. The electrostatic potential studies have shown that successive substitution of nitrogen instead of CH groups of cubane engenders smaller and more localized electron-rich regions around the nitrogens of a cube. Further the bond ellipticity and the electron density at the bond critical point of the X–N bonds (X=C or N) in a cubanoid increase from azacubane to octaazacubane. The heats of formation of azacubanes calculated by the isodesmic reaction approach using different levels of theory correlate well with the electron density at the bond critical point of X–N (X=C or N) bonds in a cubanoid.     

Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane

The molecular structures of cycloalkanes (from cyclopropane to cyclodecane) and tetrahedrane were optimized at the Hartree–Fock/6–31G** level and their molecular electric potentials (MEPs) were calculated using a geodesic grid. The MEPs were fitted using net atomic charges and several site charge models. The net atomic charge model gave very poor fits to the MEPs in every case. A model with additional methylene bisector charge sites, similar to one successfully used previously for linear alkanes, greatly improved the fits to the MEPs of these cycloalkanes. The MEPs of the highly strained molecules cyclopropane and tetrahedrane were further studied using ring center and displaced bond charge sites. The fitting of the MEP of cyclopropane was consistent with a banana bond model with asymmetrically displaced electron density in the C C bonds. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 579–585, 1999     

The use of molecular electrostatic potentials in the study of the protonation of toluene

The protonation of toluene has been studied using electrostatic potential plots. A basic assumption is that at the start of the reaction the aromatic hydrogen atom moves out of the plane of the ring forming a tetrahedral carbon. When the charges on the ortho, meta or para centres are considered alone ortho attack is predicted, whereas consideration of the potential due to the sum of the nuclear and electronic charges permits the interpretation of the preferred para-protonation of toluene.     

Correlating the molecular electrostatic potentials of some organic peroxides with their antimalarial activities

The molecular electrostatic potentials (MEPs) of artemisinin (also known as qinghaosu), yingzhaosu A, and some synthetic analogues have been calculated and studied as a means of distinguishing between high and low antimalarial activity. To facilitate comparison, the dimensionality of the MEP was reduced by Kohonen Neural Network transforms. The reduction revealed that peroxides exhibiting high antimalarial activity are characterized by a continuous strip of negative electric potential surrounding the molecule, whereas peroxides of lesser activity show a broken strip.