Molecular dynamics simulation study of N-methylacetamide in water. II. Two-dimensional infrared pump–probe spectra
- 22 July 2003
- journal article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 119 (4) , 2256-2263
- https://doi.org/10.1063/1.1580808
Abstract
A theoretical description of two-dimensional (2D) IR pump–probe spectroscopy of a three-level system is presented by taking into account the system–bath interaction. By using the correlation function of the fluctuating amide I mode frequency of -methylacetamide in which was obtained by carrying out both ab initio calculations and MD simulations, the time-resolved 2D pump–probe spectra as a function of pump–probe pulse delay time are calculated and compared with experiment. We found that the vibrational dephasing becomes homogeneous on the 2 ps time scale, which is a bit faster than the experimental result. It is theoretically shown that the degree of slant of 2D contours is linearly proportional to the correlation function of the fluctuating amide I mode frequency. Consequently, it is suggested that the 2D IR pump–probe spectroscopy can provide a direct information on the vibrational frequency fluctuation dynamics and on the magnitude of static inhomogeneity.
Keywords
This publication has 36 references indexed in Scilit:
- Correlation between electronic and molecular structure distortions and vibrational properties. II. Amide I modes of NMA–nD2O complexesThe Journal of Chemical Physics, 2003
- Vibrational Dynamics, Mode Coupling, and Structural Constraints for Acetylproline-NH2The Journal of Physical Chemistry B, 2002
- Determining Vibrational Solvation-Correlation Functions from Three-Pulse Infrared Photon EchoesThe Journal of Physical Chemistry B, 2002
- Dihedral Angles of Tripeptides in Solution Directly Determined by Polarized Raman and FTIR SpectroscopyBiophysical Journal, 2002
- Ultrafast vibrational spectroscopy in condensed phasesPhysChemComm, 2002
- Dynamics of the Primary Processes of Protein Folding: Helix NucleationThe Journal of Physical Chemistry B, 2001
- Signatures of β-Peptide Unfolding in Two-Dimensional Vibrational Echo Spectroscopy: A Simulation StudyJournal of the American Chemical Society, 2001
- Stimulated Photon Echoes from Amide I VibrationsThe Journal of Physical Chemistry A, 1999
- Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solutionBiophysical Journal, 1995
- Amide-I excitations in molecular-mechanics models ofαhelix structuresPhysical Review A, 1989