J. Frau 1 J. Donoso 1 Calculations on the Low F. Mun ˜ oz 1 Energy Conformers of F. Garcı ´a Blanco 2 1 Departament de Quı´mica, N-Acetyl-D-Alanyl-D-Alanine Facultat de Cie ` ncies, Universitat Illes Balears, E-07071 Palma de Mallorca, Islas Baleares, Spain 2 Departamento de Quı´mica Fı ´sica, Facultad de Farmacia, Instituto Pluridisciplinar, Universidad Complutense de Madrid, E-28040, Madrid, Spain Received 18 March 1997; accepted 25 August 1997 Abstract: In this article a conformational analysis of the D-alanyl-D-alanine dipeptide, both charged and neutral, has been carried out. The preferred conformations were determined by means of ab initio and semiempirical quantum, together with empirical force field calculations. The AMBER* force field and the 6-31 / G** and 6-31G** ab initio levels give rise to a coincident minimum energy structure, which, on the other hand, differs from that determined by AM1, 3-21 / G, and 3-21G. The solvent effect on the different charged and neutral conforma- tions have been considered through the AMSOL semiempirical method. A quantification regard- ing the structural similarities between the different dipeptide conformations and the ampicillin has been performed. The results show that the best overlay is attained by the minimum structure energy obtained by using the 6-31 / G** methodology, which presents a planar amidic nitrogen.  1998 John Wiley & Sons, Inc. Biopoly 45: 119–133, 1998 Keywords: conformations of D-alanyl-D-alanine; b-lactam; structural overlay; AMBER force field; AM1; ab initio INTRODUCTION doglycans in the cell wall. Peptidoglycan is made up of b ( 1 – 4 ) linked repeating units of N-acetylglu- Both carboxy and transpeptidases are enzymes re- cosamine (NAG) and N-acetyl muramic acid ( NAM ) . The NAM units are linked to short peptide sponsible for catalyzing the cross-linking of pepti- Correspondence to: Juan Frau Munar, Departament de Quı ´m- ica, Universitat Illes Balears, Crta. Valldemossa, km 7.5, Palma de Mallorca 07071, Islas Baleares, Spain Contract grant sponsor: Spanish Government, DGICYT Contract grant number: PB96-0596 Biopolymers, Vol. 45, 119–133 (1998)  1998 John Wiley & Sons, Inc. CCC 0006-3525/98 / 020119-15 119 / 8K3B$$5540 12-11-97 10:02:01 bpal W: Biopolymers