A simple method for calculating atomic charges in charged molecular systems of biochemical interest

A previously developed method for calculating atomic charge in neutral molecules is modified so as to account for charged molecular species. The method is based on the orbital electronegativity (EN) concept and utilizes an EN equalization principal. Since only one linear equation is required per bond in the molecule, the scheme is extremely simple to use and thus is readily applicable to larger molecules of interest to biochemistry. Atom charge results are compared to ab initio calculations as well as experimental data from NMR and X‐ray diffraction studies. It is shown that the method compares very well even with higher level theoretical methods for a variety of charged molecules including alanine and protonated adenine. It is also shown that NMR chemical shift data for charged amino acids are correlated quite well with atomic charges from the present method. In addition charges obtained from X‐ray diffraction data for both ionic alanine and 2′‐deoxycytidine‐5′‐monophosphate are also reproduced very well.

[1]  Raymond J. Abraham,et al.  Charge calculations in molecular mechanics. III: Amino acids and peptides , 1985 .

[2]  W. L. Jolly,et al.  Estimation of atomic charges by an electronegativity equalization procedure calibrated with core binding energies , 1973 .

[3]  Frank A. Momany,et al.  Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid , 1978 .

[4]  Wilfried J. Mortier,et al.  Electronegativity-equalization method for the calculation of atomic charges in molecules , 1986 .

[5]  P. Politzer,et al.  Properties of atoms in molecules. V. Easy procedure for estimating atomic charges from calculated core-electron energies , 1973 .

[6]  C. Gatti,et al.  A Low-Temperature (23 K) Study of L-alanine: Topological Properties of Experimental and Theoretical Charge Distributions , 1988 .

[7]  David L. Grier,et al.  Electron density analysis of substituted carbonyl groups , 1982 .

[8]  J. Mullay.  A method for calculating atomic charges in large molecules , 1988 .

[9]  P A Kollman,et al.  Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions. , 1979, Journal of medicinal chemistry.

[10]  R. S. Mulliken.  Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[11]  R. Bader,et al.  Molecular fragments or chemical bonds , 1975 .

[12]  Ji-Min Yan,et al.  Point-Charge Models for Molecules Derived from Least-Squares Fitting of the Electric Potential , 1988 .

[13]  John Mullay,et al.  Atomic and group electronegativities , 1984 .

[14]  J. Mullay.  A simple method for calculating reliable atomic charges in large molecules , 1988 .

[15]  Philip Coppens,et al.  Experimental charge densities in chemistry: what is next? , 1989 .

[16]  C. Townes,et al.  The Ionic Character of Diatomic Molecules , 1955 .

[17]  Peter Politzer,et al.  Properties of atoms in molecules. I. Proposed definition of the charge on an atom in a molecule , 1970 .

[18]  S. Fliszar,et al.  Charge distributions and chemical effects: Part XV. SCF—Xα—SW studies of alkanes , 1980 .

[19]  Robert F. Hout,et al.  Representation of electron densities. 1. Sphere fits to total electron density surfaces , 1984 .

[20]  B. Pullman,et al.  ELECTRONIC STRUCTURE OF THE ALPHA-AMINO ACIDS OF PROTEINS. I. CHARGE DISTRIBUTIONS AND PROTON CHEMICAL SHIFTS. , 1963, Biochimica et biophysica acta.

[21]  P. Kollman,et al.  An approach to computing electrostatic charges for molecules , 1984 .

[22]  S H Kim,et al.  Determinations of atomic partial charges for nucleic acid constituents from x‐ray diffraction data. I. 2′‐Deoxycytidine‐5′‐monophosphate , 1985, Biopolymers.

[23]  Jerzy Cioslowski,et al.  A new population analysis based on atomic polar tensors , 1989 .

[24]  W. Horsley,et al.  Carbon-13 magnetic resonance studies of amino acids and peptides. , 1968, Journal of the American Chemical Society.