L-alanyl-L-alanine in the zwitterionic state: structures determined in thepresence of explicit water molecules and with continuum models using density functional theory

The structures and relative energies for L-alanyl-L-alanine (LALA) in the p resence of explicit water molecules have been determined by using the densi ty functional theory (DFT) Becke3-Lee-Yang-Parr functional and the 6-31G* b asis set (B3LYP/6-31G*). In aqueous solution the dominant state of LALA is the zwitterionic form, while its neutral form is dominant in vacuo. Attempt s to locate or determine a gas-phase zwitterionic species failed. That is, on the B3LYP/6-31G* potential energy surface, there is no barrier to proton transfer from the positively charged ammonium group to the negatively char ged carboxylate group, or from the ammonium group to the adjacent carbonyl oxygen and from the amide nitrogen to the carboxylate group. To stabilize t he zwitterion, we modelled the system by adding explicit water molecules an d by placing the zwitterion within a sphere surrounded by a medium with a d ielectric constant of 78.5, that is, within the Onsager continuum model, wh ere the recommended cavity radius is obtained from a solute volume calculat ion. The zwitterionic species is only stable in the presence of water at th e B3LYP/6-31G* level. This makes it imperative to include water molecules t o model the zwitterionic species of LALA, peptides and amino acids at the B 3LYP/6-31G* level. Finally, the zwitterionic structure stabilized by explic it water molecules has also been modelled within the Onsager theory. Here t he Onsager model represents the effects due to the bulk water and the expli cit water molecules stand for the effect due to direct H-bonding between th e zwitterion and the solvent, that is, the first solvation shell. We used m olecular dynamics simulations utilizing the CHARMm force field to produce s tructural input for the subsequent quantum-mechanical simulations. The stru ctures determined using various methods to model the LALA zwitterionic form in aqueous solution were compared. We were able to find additional stable structures for LALA by adding water molecules and optimizing it which could not be obtained by using the Onsager theory. This shows that one must be c areful when using continuum models to study peptides and proteins or other methods which do not take into account the explicit interactions between th e solute and the first solvent shell. (C) 1999 Elsevier Science B.V. All ri ghts reserved.