Simulation protocols for coherent femtosecond vibrational spectra of peptides

被引：120

作者：

Zhuang, W ^{[1
]}

Abramavicius, D ^{[1
]}

Hayashi, T ^{[1
]}

Mukamel, S ^{[1
]}

机构：

[1] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA

来源：

JOURNAL OF PHYSICAL CHEMISTRY B | 2006年 / 110卷 / 07期

关键词：

D O I：

10.1021/jp055813u

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Two algorithms for simulating the response of peptides to sequences of IR pulses are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D2O. A fluctuating vibrational-exciton Hamiltonian for the amide I mode is constructed from molecular dynamics trajectories. Coupling with the environment is described using a density functional theory electrostatic map. The cumulant expansion of Gaussian fluctuation incorporates motional narrowing due to fast frequency fluctuations and is adequate for NMA and for isotopically labeled bands in large peptides. Real-space truncation of the scattering matrix of the nonlinear exciton equations significantly reduces the computational cost, making it particularly attractive for slow fluctuations in large globular proteins.

引用

页码：3362 / 3374

页数：13

共 91 条

[31] Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map [J].