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Biochemistry Research International
Volume 2013 (2013), Article ID 939865, 12 pages
http://dx.doi.org/10.1155/2013/939865
Research Article

Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides

Department of Chemistry, North Eastern Hill University, Shillong 793022, India

Received 9 July 2013; Accepted 15 August 2013

Academic Editor: Emil Pai

Copyright © 2013 Gunajyoti Das and Shilpi Mandal. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

In this theoretical study, the role of the side chain moiety of C-terminal residue in influencing the structural and molecular properties of dipeptides is analyzed by considering a series of seven dipeptides. The C-terminal positions of the dipeptides are varied with seven different amino acid residues, namely. Val, Leu, Asp, Ser, Gln, His, and Pyl while their N-terminal positions are kept constant with Sec residues. Full geometry optimization and vibrational frequency calculations are carried out at B3LYP/6-311++G(d,p) level in gas and aqueous phase. The stereo-electronic effects of the side chain moieties of C-terminal residues are found to influence the values of and dihedrals, planarity of the peptide planes, and geometry around the C7   -carbon atoms of the dipeptides. The gas phase intramolecular H-bond combinations of the dipeptides are similar to those in aqueous phase. The theoretical vibrational spectra of the dipeptides reflect the nature of intramolecular H-bonds existing in the dipeptide structures. Solvation effects of aqueous environment are evident on the geometrical parameters related to the amide planes, dipole moments, HOMOLUMO energy gaps as well as thermodynamic stability of the dipeptides.