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.     

A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges

We report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods.     

A new scale of atomic electronegativities

A new formula for the calculation of atomic electronegativities from the atomic size and nuclear effective charge is proposed. The formula has the same dimensionality as the one used for the thermochemical scale. The calculated ionic and van der Waals atomic electronegativities are used for the interpretation of the bond nature in binary and coordination compounds (in particular, the bond ionicity is calculated in molecules and crystals of the AB type).Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 1, pp. 32–37, January, 1993.     

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations

We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations-water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies-within 0.43 kcal/mol (except for the special case of the CH(3)SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas.     

Electronegativity and Bader's bond critical point

The electronegativities () of some 36 atoms/groups (including some 6 ionic ones) X are calculated from the atomic charges in the corresponding methyl species CH₃X that were obtained by applying Bader's theory of atoms in molecules. The numerical values of the for the various groups studied are reasonable and correlate linearly with the two existing experimental scales for group electronegativity, Inamoto's i scale and the ¹J_CC (ortho-ipso) coupling constants in the monosubstituted benzenes, to satisfactory extents. The relations between the values and some “critical properties” of the various CH₃X molecules considered are also studied. It is suggested that in a molecule PX, r_P/R where r_P is the distance of Bader's critical point on the bond PX of length R from the atom P or the binding atom of the group P can be a very good measure of the electronegativity of the atom/group X. © 1992 by John Wiley & Sons, Inc.     

Multicenter point charge model for high-quality molecular electrostatic potentials from AM1 calculations

The natural atomic orbital/point charge (NAO-PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater-type hybrids and the results used to set up polynomials and look-up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6-31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC-ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package. © 1993 John Wiley & Sons, Inc.     

The electrostatic potential at atomic sites as a reactivity index in the hydrogen bond formation

The paper reviews results from computational studies by molecular orbital and density functional theories on several series of hydrogen bonded complexes. These studies aim at quantifying the reactivity of molecules for the complexation process. Excellent linear relationships are found between the electrostatic potential values at the sites of the electron donor and electron accepting atoms and the energy of hydrogen bond formation (ΔE). The series studied are: (a) complexes of R–CHO and R–CN molecules with hydrogen fluoride; (b) complexes of mono-substituted acetylene derivatives with ammonia; (c) (HCN)_n hydrogen bonded cluster for n=2–7. All 22 studied complexes of carbonyl and nitrile compounds with hydrogen fluoride fall in the same dependence between the energy of hydrogen bond formation and the electrostatic potential at the atomic site of the carbonyl oxygen and nitrile nitrogen atoms, with linear regression correlation coefficient r=0.979. In the case of complexes of mono-substituted acetylene and diacetylene derivatives with NH₃, the correlation coefficient for the dependence between the electrostatic potential at the acidic hydrogen atom and ΔE equals 0.996. For the series of hydrogen bonded (HCN)_n clusters, the correlation coefficient for the relationship between the electrostatic potential at the end nitrogen atom and ΔE is r=0.9996. Similarly, the analogous relationship with the electrostatic potential at the end hydrogen atom has a regression coefficient equal to 0.9994. The dependencies found are theoretically substantiated by applying the Morokuma energy decomposition scheme. The results show that the molecular electrostatic potential at atomic sites can be successfully used to predict the ability of molecules to form hydrogen bonds.     

The correlation of proton affinities with atomic charges and electronegativities for the group 14 to 17 hydrides

Proton affinities for hydrides of formula $\mathrm{AH}^{-}_{n-1}$ containing the elements A from the second to the fifth period of the periodic table and groups 14 to 17 are predicted at the Hartree–Fock, MP2 and B3LYP levels of theory employing both core potential basis sets and the 3‐21G basis set. The core potential methods perform well when compared with all electron calculations using the 3‐21++G** basis set. The proton affinities of the hydrides containing elements from groups 15 and 16 of the periodic table are more accurate than those with elements from groups 14 and 17. A cancellation of errors appears to occur more completely if the protonated and nonprotonated molecules contain both bond and lone pairs before and after the protonation reaction. Proton affinities correlate nearly linearly with the atomic charges on the hydrogen atoms when these charges are determined by the generalized atomic polar tensor (GAPT) method. This tendency can be associated, in principle, with the group electronegativities as introduced by Iczkowski and Margrave. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1119–1131, 2000     

Molecular similarity based on atomic electrostatic potential

We propose a new similarity measure operating in the space spanned by the potential values, evaluated at atoms constituting the benzene ring and the COOH group in para-substituted benzoic acids and at benzene ring atoms in monosubstituted benzenes. The similarity measures are equivalent to the Euclidean distance between points in that space. Only the distances between the potentials at corresponding atoms in different molecules are included. The distances for benzene rings were very similar, regardless of whether they were calculated in para-substituted acids or in monosubstituted benzenes. As reference reactions, dissociation of benzoic acids and nitration of monosubstituted benzenes have been used. The effects of reduction of dimensionality of the potential space on the comparison of similarity measures with the free energies of the reference reactions have been investigated. It became obvious that the potentials at individual atoms in molecules of the acids and monosubstituted benzenes are mutually correlated to a high degree.     

Correlations between F NMR chemical shifts and bond dissociation energies, enthalpies of formation and group electronegativities

Correlations between ¹⁹F NMR chemical shifts (Φ) in fluorohalohydrocarbons and enthalpies of formation, bond dissociation energies, group contribution to enthalpies of formation and enthalpies of formation of free radicals are presented. A good correlation between these properties has been found with the square root of Φ. A relationship between fluorine chemical shifts and group electronegativities is also discussed.     

The electrostatical molecular potential — A tool for the prediction of electrostatic molecular interaction properties

Starting from the molecular potential we get, by using elementary electrostatics, information about energetically favoured regions for interaction with ions and dipoles around H₂O and H₂CO. The molecule-dipole interaction is represented by the electric field patterns.     

Polarization-corrected molecular electrostatic potential for the cation binding problem

The molecular electrostatic potential (MESP) and polarization-corrected MESP (PMESP) minima for some small molecules are calculated on the surface generated by rolling cations (Li⁺ and Na⁺) on their van der Waals surfaces. The cation binding energies of these molecules are obtained with HF/6-31G^** level ab initio calculations. A noteworthy outcome of the present study is that the plot of these binding energies and the corresponding PMESP surface minimum values turns out to be remarkably linear with a slope close to unity. The PMESP is thus found to work as a powerful tool for unearthing the patterns of cation binding sites and energetics for molecular systems.     

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.     

基团电负性研究 VI. 基团电负性与烷基衍生物的标准生成热

本文试用前文建立的基团电负性, 通过研究ΔΔFH°(RX/CH3X)与基团电负性xG的定量关系, 从而建立一个简单方法用以计算几乎所有烷基衍生物RX(X=F, OH, Cl, NH2,Br, SH, I, OH3)的标准生成热。     

Multipole expansions of the electrostatic molecular potential

Multipole expansions of the electrostatic molecular potential up to the hexadecapole terms are examined for H₂O, NH₃ and C₂H₄NH. A reasonable approximation to get unexpensive first order representations of the electrostatic potential for regions outside the van der Waals volume is found.     

胰岛素单体、双体分子静电势的计算

计算了三方二锌胰岛素晶胞不对称单位中两个胰岛素分子单体及其双体的分子静电势。结果表明:胰岛素两个单体分子的构象不同,其分子表面静电势也不相同,由于它们的构象是类似的,所以其电势分布也是接近的,单体胰岛素分子的表面静电势呈偶极型分布,双体的表面静电势基本保持单体的特征。文中还比较了两个单体分子及其集聚后的静电势变化。