Document Detail


Influence of vibrational energy flow on isomerization of flexible molecules: incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization.
MedLine Citation:
PMID:  16392479     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The conformational isomerization of a dipeptide, N-acetyl-tryptophan methyl amide (NATMA), is studied computationally by including important dynamical corrections to Rice-Ramsperger-Kassel-Marcus (RRKM) theory for the transition rate between pairs of isomers. The dynamical corrections arise from incomplete or sluggish vibrational energy flow in the dipeptide, a property suggested by the mode-selective chemistry that has been observed by Dian et al. [J. Chem. Phys. 120, 133 (2004)]. We compute the extent and rate of vibrational energy flow in NATMA quantum mechanically using local random matrix theory, which we then use to correct the RRKM theory rates. The latter rates are then introduced into a master equation to study the population dynamics of the dipeptide. Incomplete or slow vibrational energy flow is found to enhance the conformational selectivity of NATMA over RRKM estimates.
Authors:
Johnson K Agbo; David M Leitner; David A Evans; David J Wales
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  123     ISSN:  0021-9606     ISO Abbreviation:  J Chem Phys     Publication Date:  2005 Sep 
Date Detail:
Created Date:  2006-01-05     Completed Date:  2007-07-11     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  124304     Citation Subset:  IM    
Affiliation:
Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA.
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MeSH Terms
Descriptor/Qualifier:
Chemistry, Physical / methods*
Dipeptides / chemistry*
Hydrogen Bonding
Ions
Isomerism
Kinetics
Models, Statistical
Models, Theoretical
Molecular Conformation
Software
Thermodynamics
Tryptophan / analogs & derivatives*,  chemistry
Chemical
Reg. No./Substance:
0/Dipeptides; 0/Ions; 6367-17-5/N-acetyltryptophan methylamide; 73-22-3/Tryptophan

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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