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化学进展 2012, Vol. 24 Issue (06): 1065-1081 前一篇   后一篇

• 量子化学专辑 •

蛋白质二维红外相干光谱的理论研究

宋建, 庄巍*   

  1. 中国科学院大连化学物理研究所 分子反应动力学国家重点实验室 大连 116023
  • 收稿日期:2011-12-01 修回日期:2012-03-01 出版日期:2012-06-24 发布日期:2012-05-11
  • 通讯作者: 庄巍 E-mail:wzhuang@dicp.ac.cn
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Coherent Two Dimensional Infrared Spectroscopy of Proteins: Concepts and Simulations

Song Jian, Zhuang Wei   

  1. State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, LiaoNing, China
  • Received:2011-12-01 Revised:2012-03-01 Online:2012-06-24 Published:2012-05-11
多肽对红外激光脉冲的非线性响应中包含了丰富的结构动力学信息。本文以肽链的酰胺振动跃迁为例,提出了模拟二维红外相干光谱的理论方案。文中首先介绍了激子模型下非线性响应的微扰图像,并基于激子模型、经典分子动力学模拟和密度泛函静电势,构建酰胺振动模式有效波动哈密顿量。采用随机刘维尔方程(SLE)、数值演化(NP)、高斯波动的累积展开等方法计算非线性响应光谱。文章最后对多肽及多肽复合物等体系的二维红外信号进行模拟和讨论。
关键词： 多肽, 非线性响应, 酰胺振动模式, 二维红外光谱
The nonlinear optical response of peptide molecules to femtosecond infrared pulse sequences contains rich information on their structure, fluctuations and motions. we reviewed in this article the basic concepts as well as the simulation protocol for 2DIR signals associated with the amide backbone vibrational transitions of proteins. Starting with a general introduction of the perturbative picture of nonlinear optical response of excitonic systems, an introduction is given for constructing an effective fluctuating vibrational Hamiltonian based on classical MD simulation and a DFT electrostatic map. Several techniques for simulating the nonlinear response using the fluctuating Hamiltonian are then surveyed, these include the stochastic Liouville equations (SLE),numerical propagation (NP) and cumulant expansion of Gaussian fluctuation (CGF). Applications are presented to two dimensional infrared signal of peptides and peptide complexes.
Key words: peptides, nonlinear response, amide vibration, 2DIR

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