THEORETICAL STUDY OF H BOND ENERGIES IN FINITE BONDING CHAINS OF AMIDES

酰胺有限键链氢键能的理论研究

• 批准号: 6450699
• 负责人: Joseph J Dannenberg
• 金额: $ 5.95万
• 依托单位: HUNTER COLLEGE
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-04-01 至 2002-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6450699
• 关键词: chemical models; computer simulation; energy source; formamide; hydrogen bond; intermolecular interaction; molecular dynamics; molecular orbital; protein folding

The major purpose of this project is to provide data on cooperative hydrogen bonding that can be used to improve theoretical approaches to protein folding. High level (post Hartree-Fock) calculations on a potential surface that includes the counterpoise correction for basis set superposition error will be performed. We shall consider finite aggregates of small amides (formamide) in various conformations, particularly those that are important in proteins (i.e. alpha-helices and beta-sheets). The data will be organized as a function of the number of amides in the H-binding chain and the six intermolecular parameters that define the interaction of each pair of adjacent formamides (one distance, two angles, and three dihedrals). Empirical functions will be fitted to the data with the goal of rapidly, and accurately, estimating the H-bonding interactions for different environments. Care will be taken to eliminate whichever parameters have little effect upon the H-bonding energies. The resulting empirical functions can be used to study the dynamics of protein folding.

该项目的主要目的是提供合作氢键的数据，可用于改进蛋白质折叠的理论方法。将在潜在表面上进行高水平（后Hartree-Fock）计算，包括基组叠加误差的平衡校正。我们将考虑各种构象的小酰胺（甲酰胺）的有限聚集体，特别是那些在蛋白质中很重要的（即α-螺旋和β-折叠）。数据将被组织为H-结合链中酰胺数量的函数和定义每对相邻甲酰胺相互作用的六个分子间参数（一个距离，两个角度和三个二面角）。经验函数将被拟合到数据中，目标是快速，准确地估计不同环境下的氢键相互作用。将注意消除对H键合能影响很小的任何参数。由此产生的经验函数可以用来研究蛋白质折叠的动力学。