Université d'Evry Val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environment, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
J Phys Chem B. 2011 May 12;115(18):5526-35. doi: 10.1021/jp111140f. Epub 2011 Feb 23.
Density functional theory based molecular dynamics simulations are used to study the structure, infrared (IR) spectroscopy, circular dichroism (CD) spectroscopy, and coupling between the amide I vibrations of a bridged cyclic diamide in the gas phase and in aqueous solution. IR spectra computed via the dipole moment time correlation function show a large red-shift of 30 cm(-1) in the amide I vibration in solution compared to the gas phase, and are in good agreement with experiment. Conformationally averaged CD spectra computed using the CIS(D) method are highly sensitive to the structures used, and structures sampled in the aqueous phase simulation are required to obtain qualitatively correct CD spectra. Analysis of the coupling between the amide I modes shows that in the aqueous phase there is an increased localization of the vibrations on the individual peptide groups and a reduction in the mode coupling parameter compared to the gas phase. Overall, the results illustrate the significance of incorporating molecular dynamics in the simulation of IR and CD spectra.
基于密度泛函理论的分子动力学模拟用于研究桥连环状二酰胺在气相和水溶液中的结构、红外（IR）光谱、圆二色（CD）光谱以及酰胺 I 振动之间的耦合。通过偶极矩时间相关函数计算得到的 IR 光谱显示，与气相相比，溶液中酰胺 I 振动的红移大 30cm(-1)，与实验结果非常吻合。使用 CIS(D)方法计算的构象平均 CD 光谱对所使用的结构非常敏感，并且需要在水相模拟中采样结构以获得定性正确的 CD 光谱。对酰胺 I 模式之间的耦合进行分析表明，在水溶液中，与气相相比，振动在单个肽基团上的定位增加，并且模式耦合参数降低。总的来说，这些结果说明了在 IR 和 CD 光谱模拟中纳入分子动力学的重要性。
