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Title: Non-linear vibrational modes in biomolecules : a periodic orbits description
Authors: Farantos, Stavros C. 
Kampanarakis, Alexandros 
Varotsis, Constantinos 
Daskalakis, Vangelis 
Farantos, Stavros C. 
Kampanarakis, Alexandros 
Keywords: Cytochrome oxidase;Biomolecules;Molecules;Spectroscopy
Category: Physical Sciences
Field: Natural Sciences
Issue Date: 2012
Publisher: Elsevier
Source: Chemical physics, 2012, Volume 399, Pages 258-263
Abstract: The vibrational harmonic normal modes of a molecule, which are valid at energies close to an equilibrium point (a minimum, maximum or saddle of the potential energy surface), are extended by periodic orbits to high energies where anharmonicity and coupling of the degrees of freedom are significant. In this way the assignment of the spectra, and thus the extraction of dynamics in highly excited molecules, can be obtained. New vibrational modes emanating from bifurcations of periodic orbits and long living localized trajectories signal the birth and localization of new quantum states. In this article we review and further study non-linear vibrational modes for model biomolecules such as alanine dipeptide and the active site in the oxoferryl oxidation state of the enzyme cytochrome c oxidase. We locate periodic orbits which exhibit high anhamonicity and lead to center-saddle bifurcations. These modes are associated to an isomerization process in alanine dipeptide and to frequency shifts in the oxoferryl observed by modifying the Coulomb field around the Imidazole-Fe IV = O species
ISSN: 03010104
DOI: 10.1016/j.chemphys.2011.07.031
Rights: © 2011 Elsevier B.V. All rights reserved
Type: Article
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