On the fragmentation of biomolecules: Fragmentation of alanine dipeptide along the polypeptide chain

Journal Article · Fri Sep 15 04:00:00 EDT 2006 · Journal of Experimental and Theoretical Physics

DOI:https://doi.org/10.1134/S1063776106090160· OSTI ID:21067633

Yakubovich, A V; Solov'yov, A V ^[1]; Greiner, W ^[2]

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1. Russian Academy of Sciences, Ioffe Physicotechnical Institute (Russian Federation)
2. Johann Wolfgang Goethe University, Frankfurt Institute for Advanced Studied (Germany)

The interaction potential between amino acids in alanine dipeptide has been studied for the first time taking into account exact molecular geometry. Ab initio calculation has been performed in the framework of density functional theory taking into account all electrons in the system. The fragmentation of dipeptide along the polypeptide chain, as well as the interaction between alanines, has been considered. The energy of the system has been analyzed as a function of the distance between fragments for all possible dipeptide fragmentation channels. Analysis of the energy barriers makes it possible to estimate the characteristic fragmentation times and to determine the degree of applicability of classical electrodynamics for describing the system energy.

• OSTI ID: 21067633
• Journal Information: Journal of Experimental and Theoretical Physics, Journal Name: Journal of Experimental and Theoretical Physics Journal Issue: 3 Vol. 103; ISSN JTPHES; ISSN 1063-7761
• Country of Publication: United States
• Language: English

Related Subjects

71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
ALANINES
DENSITY FUNCTIONAL METHOD
ELECTRODYNAMICS
ELECTRONS
FRAGMENTATION
POLYPEPTIDES