Wang Jianping, Cai Kaicong, Ma Xiaoyan
Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.
Chemphyschem. 2009 Sep 14;10(13):2242-50. doi: 10.1002/cphc.200900301.
Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L-alpha-glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal-mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two-dimensional infrared (2D IR) spectra, which are simulated using time-domain third-order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.
对四种具有代表性的生物分子进行了量子化学计算、分子动力学模拟以及线性和非线性红外光谱模拟，这四种生物分子分别是：纤维二糖、丙氨酸三肽、L-α-甘油磷酸乙醇胺以及DNA碱基单体鸟嘌呤。评估了这些分子在真空中的非谐跃迁频率和非谐性。进行了瞬时简正模式分析，并研究了在TIP3P水中溶剂化的分子的振动频率分布相关性。预计生物分子的许多局部和区域运动是非谐耦合的，并且它们的振动频率在很大程度上是相关的。这些耦合和相关的振动运动可以通过飞秒宽带二维红外（2D IR）光谱中的成对交叉峰轻松可视化，该光谱是使用时域三阶非线性响应函数模拟的。二维红外交叉峰的独特光谱轮廓网络，包括峰取向以及正负信号模式，显示出与耦合和相关性密切相关。结果表明，由溶剂相互作用以及固有振动相互作用驱动的振动耦合和相关性取决于振动模式，因此取决于化学基团，并构成了生物分子中普遍存在的非谐振动器的结构和动力学基础。
