TY - JOUR

T1 - Amide I modes of α-Helical polypeptide in liquid water

T2 - Conformational fluctuation, phase correlation, and linear and nonlinear vibrational spectra

AU - Ham, Sihyun

AU - Hahn, Seungsoo

AU - Lee, Chewook

AU - Kim, Tae Kyung

AU - Kwak, Kyungwon

AU - Cho, Minhaeng

PY - 2004/7/1

Y1 - 2004/7/1

N2 - Chain length and site dependencies of amide I local mode frequencies of α-helical polyalanines are theoretically studied by carrying out semiempirical quantum chemistry calculations. A theoretical model that can be used to quantitatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed. Using this theoretical model and performing molecular dynamics simulation of an α-helical polyalanine in liquid water, we investigate conformational fluctuation and hydrogen-bonding dynamics by monitoring amide I frequency fluctuations. The instantaneous normal-mode analysis method is used to obtain densities of states of the one- and two-exciton bands and to quantitatively investigate the extent of delocalization of the instantaneous amide I normal modes, Also, by introducing a novel concept of the so-called weighted phase-correlation factor, the symmetric natures of the delocalized amide I normal modes are elucidated, and it is also shown that there is no unique way to classify any given amide I normal mode of the α-helical polyalanine in liquid water to be either A-mode-like or E1-mode-like. From the ensemble8veraged dipole strength spectrum and density of one-exciton states, the amide I infrared absorption spectrum is numerically calculated and its asymmetric line shape is theoretically described. Considering both transitions from the ground state to one-exciton states and those from one-exciton states to two-exciton states, we calculate the two-dimensional IR pump-probe spectra and directly compare them with recent experimental results. A brief discussion on the cross-peaks previously observed in the two-dimensional difference spectrum is presented.

AB - Chain length and site dependencies of amide I local mode frequencies of α-helical polyalanines are theoretically studied by carrying out semiempirical quantum chemistry calculations. A theoretical model that can be used to quantitatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed. Using this theoretical model and performing molecular dynamics simulation of an α-helical polyalanine in liquid water, we investigate conformational fluctuation and hydrogen-bonding dynamics by monitoring amide I frequency fluctuations. The instantaneous normal-mode analysis method is used to obtain densities of states of the one- and two-exciton bands and to quantitatively investigate the extent of delocalization of the instantaneous amide I normal modes, Also, by introducing a novel concept of the so-called weighted phase-correlation factor, the symmetric natures of the delocalized amide I normal modes are elucidated, and it is also shown that there is no unique way to classify any given amide I normal mode of the α-helical polyalanine in liquid water to be either A-mode-like or E1-mode-like. From the ensemble8veraged dipole strength spectrum and density of one-exciton states, the amide I infrared absorption spectrum is numerically calculated and its asymmetric line shape is theoretically described. Considering both transitions from the ground state to one-exciton states and those from one-exciton states to two-exciton states, we calculate the two-dimensional IR pump-probe spectra and directly compare them with recent experimental results. A brief discussion on the cross-peaks previously observed in the two-dimensional difference spectrum is presented.

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U2 - 10.1021/jp048678e

DO - 10.1021/jp048678e

M3 - Article

AN - SCOPUS:3142704435

SN - 1520-6106

VL - 108

SP - 9333

EP - 9345

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

IS - 26

ER -