Antony, J. and Schmidt, B. and Schütte, Ch. (2005) Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes. J. Chem. Phys., 122 (1). 014309.

PDF
Available under License Creative Commons Attribution Noncommercial. 1MB 
Official URL: http://dx.doi.org/10.1063/1.1829057
Abstract
Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH3CONHCH2CONHCH3). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (B3LYP/631+G(d)) level. The ordering of the energetically most stable isomers (C7 and C5) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C7 and C5 minimum energy structures occur on a subpicosecond timescale (700 ... 800 fs). Vibrationally nonadiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two statetwo mode model, the resulting wave packet dynamics is found to be strongly nonadiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a timescale of 200 ... 500 fs with population transfer of more than 50 % between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of timedependent vibrational spectroscopy.
Item Type:  Article 

Subjects:  Mathematical and Computer Sciences > Mathematics 
Divisions:  Department of Mathematics and Computer Science > Institute of Mathematics Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group 
ID Code:  57 
Deposited By:  Admin Administrator 
Deposited On:  03 Jan 2009 20:20 
Last Modified:  03 Mar 2017 14:39 
Repository Staff Only: item control page