Derivation of parameters for conformational calculations on carbohydrate systems, including bacterial cell wall peptidoglycan

Abstract

The use of software designed for the prediction of minimum-energy conformations of peptides and proteins has been extended to include a number of glycoconjugates. For this purpose it was necessary to derive empirical interatomic parameters for sugars consistent with the existing amino-acid parameter set. The principle source is high-grade ab initio quantum-mechanical calculations. Parameters describing the anomeric effect were derived from the ab initio surface of dimethoxymethane. Parameters describing the pyranose ring were optimised against the energy profiles of 2-ethyltetrahydropyran and further refined against the profiles of 2-methoxytetrahydropyran to take account of the anomeric and exo-anomeric effects. Optimisation against the ab initio surface of methoxymethanol was used to study the anomeric hydroxyl. The use of arbitrary rotation potentials to model the anomeric and exo-anomeric effects was avoided by extension of an orbital force field method through specific parametrisation of lone-pair molecular orbitals. Assumptions and limitations inherent in the derivation and use of potentials are discussed.