Charge calculations in molecular mechanics. III: Amino acids and peptides

Atomic charges obtained with a previously published charge scheme are given for amino acids and peptides. In order to do this, a method of handling charged species with the basic scheme2,3 has been developed. The charges obtained for alkylammonium ions and carboxylate ions with the scheme are presented and compared with CNDO and ab initio values. The calculated experimental dipole moments of the zwitterionic forms of glycine, alanine and β‐alanine are then discussed. Finally, the atomic charges obtained for the naturally occurring amino acids are given, both in the form of the N‐acetyl‐N′‐methyl amino acid amides, used as models for the amino acid residues in enzymes, and as the free zwitterionic amino acids. The charges obtained show a good correlation with n. m. r. chemical shifts of both carbon and hydrogen atoms.

[1]  Peter A. Kollman,et al.  Molecular mechanics simulation of protein-ligand interactions: binding of thyroid hormone analogs to prealbumin , 1982 .

[2]  H. Scheraga,et al.  Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. , 1977, Macromolecules.

[3]  N. L. Allinger,et al.  Conformational analysis—CXIX : Charge distribution in the molecular mechanics method1 , 1977 .

[4]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[5]  H. Eyring,et al.  The Inductive Effect and Chemical Reactivity. I. General Theory of the Inductive Effect and Application to Electric Dipole Moments of Haloalkanes , 1951 .

[6]  H. Scheraga,et al.  Influence of local interactions on protein structure. I. Conformational energy studies of N‐acetyl‐N′‐methylamides of pro‐X and X‐pro dipeptides , 1977, Biopolymers.

[7]  Norman L. Allinger,et al.  Treatment of electrostatic effects within the molecular-mechanics method. 1 , 1983 .

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

[9]  Lee Griffiths,et al.  Approaches to charge calculations in molecular mechanics , 1982 .

[10]  Peter A. Kollman,et al.  A method of describing the charge distribution in simple molecules , 1978 .

[11]  Peter A. Kollman,et al.  Molecular mechanics studies of enzyme-substrate interactions: the interaction of L- and D-N-acetyltryptophanamide with α-chymotrypsin , 1983 .

[12]  K. B. Wiberg.  Infrared intensities. The methyl halides. Effect of substituents on charge distributions , 1979 .

[13]  M. Bowers,et al.  Quantitative proton affinities, ionization potentials, and hydrogen affinities of alkylamines , 1976 .

[14]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[15]  K. B. Wiberg.  Effect of substituents on the electron densities in methane. .sigma. and .pi. Interactions in saturated systems , 1980 .

[16]  K. Kopple,et al.  Solvent-dependent conformational distributions of some dipeptides , 1980 .

[17]  P A Kollman,et al.  Electrostatic potentials of proteins. 1. Carboxypeptidase A. , 1976, Journal of the American Chemical Society.