Amide I modes of alpha-helical polypeptide in liquid water: Conformation fluctuation, phase correlation, and linear and nonlinear vibrational spectra
Article Abstract:
A theoretical study is performed on chain length and site dependencies of amide I local mode frequencies of alpha-helical polyalanines by carrying out semiemphirical quantum chemistry calculations. A theoretical model that could be used to quantatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2004
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Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra: Helix-coil transition kinetics
Article Abstract:
The temperature-jump molecular dynamics (T-jump MD) simulations and infrared (IR) spectra are used to examine the helix-coil transition kinetics of secondary structures of polyalanine peptide. A novel way is described for determining the melting temperature by the temperature dependence of center frequency and full width at half-maximum of amide 1 band.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water
Article Abstract:
Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in is studied in aqueous solutions and are simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The site-specific isotope-labeling effects on the IR and 2D IR are discussed.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
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