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The dynamics of conformational isomerization in flexible biomolecules. II. Simulating isomerizations in a supersonic free jet with master equation dynamics
Infrared-induced conformational isomerization of N-acetyl-tryptophan methyl amide is studied theoretically using a microcanonical Rice–Ramsperger–Kassel–Marcus description of the rates ...

The dynamics of conformational isomerization in flexible biomolecules. I. Hole-filling spectroscopy of N-acetyl tryptophan methyl amide and N-acetyl tryptophan amide

J. Chem. Phys. 120, 133 (2004); doi:10.1063/1.1626540

Issue Date: 1 January 2004

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Brian C. Dian, Asier Longarte, Paul R. Winter, and Timothy S. Zwier
Department of Chemistry, 560 Oval Drive, Purdue University, West Lafayette, Indiana 47907-2084
The conformational isomerization dynamics of N-acetyl tryptophan methyl amide (NATMA) and N-acetyl tryptophan amide (NATA) have been studied using the methods of IR-UV hole-filling spectroscopy (HFS) and IR-induced population transfer spectroscopy (IR-PTS), which were developed for this purpose. Single conformations of these molecules were selectively excited in well-defined NH stretch fundamentals. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were recooled into their zero-point levels, partially refilling the hole created in the ground state population of one of the conformers, and creating gains in population in other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion. In HFS, the IR wavelength is fixed and the UV laser tuned in order to determine where the population went following selective infrared excitation. In IR-PTS, the UV is fixed to monitor the population of a given conformation, and the IR is tuned to record the IR-induced changes in the population of the monitored conformer. Besides demonstrating the capability of the experiment to change the downstream conformational population distribution, the IR-PTS scans were used to extract two quantitative results: (i) The fractional populations of the conformers in the absence of the infrared, and (ii) the isomerization quantum yields for each of the six unique amide NH stretch fundamentals (three conformers each with two amide groups). The method for obtaining quantum yields is described in detail. In both NATMA and NATA, the quantum yields show modest conformational specificity, but only a hint of vibrational mode specificity. The prospects for the hole-filling technique for providing insight into energy flow in large molecules are discussed, leaving a more detailed theoretical modeling to the adjoining paper [Evans et al. J. Chem. Phys. 120, 148 (2004)]. ©2004 American Institute of Physics.
History: Received 6 August 2003; accepted 26 September 2003
Permalink: http://link.aip.org/link/?JCPSA6/120/133/1
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EDITORIALLY RELATED

  1. The dynamics of conformational isomerization in flexible biomolecules. II. Simulating isomerizations in a supersonic free jet with master equation dynamics
    David A. Evans et al.
    J. Chem. Phys. 120, 148 (2004)

KEYWORDS and PACS

Keywords
PACS
  • 82.30.Qt
    Isomerization and rearrangement in chemical reactions
  • 87.15.He
    Biomolecular dynamics and conformational changes
  • 33.20.Ea
    Infrared molecular spectra
  • 33.20.Lg
    Ultraviolet molecular spectra
  • 33.50.Dq
    Molecular fluorescence and phosphorescence spectra
  • 87.15.Mi
    Spectra, photodissociation, and photoionization of biomolecules; bioluminescence
  • YEAR: 2004

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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