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

Hunter College, New York NY

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Abstract

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.