Chapter 15. Vibrational Energy Relaxation (Ver) of a CD Stretching Mode in Cytochrome c

  1. M. Toda2,
  2. T. Komatsuzaki3,
  3. T. Konishi4,
  4. R. S. Berry5 and
  5. S. A. Rice6
  1. Hiroshi Fujisaki,
  2. Lintao Bu and
  3. John E. Straub

Published Online: 27 JAN 2005

DOI: 10.1002/0471712531.ch15

Geometric Structures of Phase Space in Multidimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems, Volume 130

Geometric Structures of Phase Space in Multidimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems, Volume 130

How to Cite

Fujisaki, H., Bu, L. and Straub, J. E. (2005) Vibrational Energy Relaxation (Ver) of a CD Stretching Mode in Cytochrome c, in Geometric Structures of Phase Space in Multidimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems, Volume 130 (eds M. Toda, T. Komatsuzaki, T. Konishi, R. S. Berry and S. A. Rice), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/0471712531.ch15

Editor Information

  1. 2

    Physics Department, Nara Women's University, Nara, 630-8506, Japan

  2. 3

    Nonlinear Science Laboratory, Department of Earth and Planetary Sciences, Faculty of Science, Kobe University, Nada, Kobe, 657-8501, Japan

  3. 4

    Department of Physics, Nagoya University, Nagoya, 464-8602, Japan

  4. 5

    Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA

  5. 6

    Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 USA

Author Information

  1. Department of Chemistry, Boston University, Boston, Massachusetts, 02215, USA

Publication History

  1. Published Online: 27 JAN 2005
  2. Published Print: 21 JAN 2005

Book Series:

  1. Advances in Chemical Physics

Book Series Editors:

  1. Stuart A. Rice

Series Editor Information

  1. Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 USA

ISBN Information

Print ISBN: 9780471711582

Online ISBN: 9780471712534

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Keywords:

  • Vibrational energy relaxation (VER);
  • Fermi's golden rule;
  • force–force correlation function;
  • Landau-Teller-Zwanzig formula;
  • Maradudin–Fein formula;
  • quantum correction factor;
  • anharmonicity;
  • cytochrome c

Summary

We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic coupling elements. We find that, for the “lifetime” width parameter γ=3∼30 cm− 1, the VER time is 0.2∼0.3ps, which agrees rather well with the previous classical calculation using the quantum correction factor method, and is consistent with spectroscopic experiments by Romesberg's group. We decompose the VER rate into separate contributions from two modes, and find that the most significant contribution, which depends on the “lifetime” width parameter, comes from those modes most resonant with the CD vibrational mode.