PM3 and AM1 Study on �-N-acetyl-muramic Acid and 3 Murein Related Derivatives

Abstract

The energetically favoured conformations of β-N-acetyl-Muramic acid, its C6-O-acetylated form, the methylamide and the methyl-glycoside have been investigated using the semiempirical PM3 and AM1 methods. All these compounds are either components or fragmentary structures of the murein network. The atomic coordinates of the starting set of the β-N-acetyl-Muramic acid molecule have been obtained by a PM3 minimization of one saccharide molecule cut out from the murein single strand model proposed by Barnickel at al. [1]. The sidegroups of the derivatives have been introduced by a molecular editor. These conformations served as starting points in conformational space for a grid search by scanning all sidechain torsional angles for non-hydrogen atoms with exception of the N-acetyl group which was held in cisoid position (i.e. N2-H bond is parallel to C1-H and C3-H bond) and only minimized. The PM3 method with an additional amide correction potential and the AM1 method were used. The torsional angle distributions of the lactyl sidechain (free acid and methylamide), the C6-O-acetylated sidechain and the C1-methoxy sidechain have been investigated, showing distinct energetically favoured torsional angle regions. The results are compared to earlier studies on β-N-acetyl-Muramic acid by J.S. Yadav et al. [2,3] who were using the MNDO and PCILO methods and by P.N.S. Yadav et al. [4] who were using the empirical MM2 force-field.