Analysis of empirical energy function on hydrogen-bonding patterns

Abstract

An empirical energy function is a combination of mathematical equations and their parameterizations to calculate the free energy of a chemical compound. Calculating energy values from some given chemical structure, especially on a protein structure, is a key process to analyze the structural strength of the given compound. Research on the influence of geometric aspects on the energy calculation, however, has not been done intensively considering the importance of geometrical characteristics, such as bond length, when analyzing proteins where its structure plays important role in determination of its biological function. Analysis on the characteristics of geometric features imposed by empirical energy functions are presented and discussed with results from energy calculations by 3 different widely used parameterizations. The result shows visible connection between the calculated energy values and geometric bonding patterns, despite few limitations reported during the analysis.