Mennucci Benedetta, Martínez José M
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy.
J Phys Chem B. 2005 May 19;109(19):9818-29. doi: 10.1021/jp050034z.
This paper represents the first part of a study of solvation in peptides using quantum-mechanical and classical approaches. In this study, the peptide is modeled as its simplest analogue, namely, N-methyl-acetamide, and the effects of the solvent (here water, and in the second part of the study, water and acetone) are introduced at three different levels, e.g., through a continuum description, using solute-solvent clusters, and using the same clusters embedded in an external continuum. In turn, the solute-solvent clusters have been obtained in two alternative ways, either by using QM optimization procedures or extracting a proper set of structures from MD simulations. In this part of the study, geometries, IR, and UV spectra are calculated in terms of the different solvation models, and the results are analyzed and compared to get insights about different aspects of solvation involving dynamic and static effects on one hand and bulk or specific interactions on the other hand.
本文是一项使用量子力学和经典方法研究肽溶剂化的研究的第一部分。在本研究中，肽被建模为其最简单的类似物，即N-甲基乙酰胺，并且在三个不同层次上引入了溶剂的影响（此处为水，在研究的第二部分中为水和丙酮），例如，通过连续介质描述、使用溶质-溶剂簇以及使用嵌入外部连续介质中的相同簇。反过来，溶质-溶剂簇通过两种替代方法获得，要么使用量子力学优化程序，要么从分子动力学模拟中提取一组合适的结构。在研究的这一部分中，根据不同的溶剂化模型计算几何结构、红外光谱和紫外光谱，并对结果进行分析和比较，以深入了解溶剂化的不同方面，一方面涉及动态和静态效应，另一方面涉及整体或特定相互作用。
