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Open Access Highly Accessed Open Badges Research article

Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects

Donard S Dwyer

Author Affiliations

LSU Health Sciences Center, School of Medicine, Shreveport, LA 71130 USA

BMC Chemical Biology 2005, 5:2  doi:10.1186/1472-6769-5-2

Published: 3 August 2005



Electronic properties of amino acid side chains such as inductive and field effects have not been characterized in any detail. Quantum mechanics (QM) calculations and fundamental equations that account for substituent effects may provide insight into these important properties. PM3 analysis of electron distribution and polarizability was used to derive quantitative scales that describe steric factors, inductive effects, resonance effects, and field effects of amino acid side chains.


These studies revealed that: (1) different semiempirical QM methods yield similar results for the electronic effects of side chain groups, (2) polarizability, which reflects molecular deformability, represents steric factors in electronic terms, and (3) inductive effects contribute to the propensity of an amino acid for α-helices.


The data provide initial characterization of the substituent effects of amino acid side chains and suggest that these properties affect electron density along the peptide backbone.