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

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

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 resid...

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Main Authors: Das, Gunajyoti, Mandal, Shilpi
Format: Online
Language:English
Published: Hindawi Publishing Corporation 2013
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789318/
id pubmed-3789318
recordtype oai_dc
spelling pubmed-37893182013-10-22 Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides Das, Gunajyoti Mandal, Shilpi Research Article 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 Φ and Ω dihedrals, planarity of the peptide planes, and geometry around the C7   α-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. Hindawi Publishing Corporation 2013 2013-09-18 /pmc/articles/PMC3789318/ /pubmed/24151555 http://dx.doi.org/10.1155/2013/939865 Text en Copyright © 2013 G. Das and S. Mandal. https://creativecommons.org/licenses/by/3.0/ 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.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Das, Gunajyoti
Mandal, Shilpi
spellingShingle Das, Gunajyoti
Mandal, Shilpi
Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
author_facet Das, Gunajyoti
Mandal, Shilpi
author_sort Das, Gunajyoti
title Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
title_short Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
title_full Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
title_fullStr Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
title_full_unstemmed Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides
title_sort nearest-neighbor interactions and their influence on the structural aspects of dipeptides
description 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 Φ and Ω dihedrals, planarity of the peptide planes, and geometry around the C7   α-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.
publisher Hindawi Publishing Corporation
publishDate 2013
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789318/
_version_ 1612015950081556480

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