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.

Polypeptides, Chemistry, Physical and theoretical, Physical chemistry

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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.

Alanine, Structure, Chemical properties, Report

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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.

Quantum chemistry, Aqueous solution reactions

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