M. Knapp-Mohammadya, K. J. Jalkanena, F. Nardib, R. C. Wadeb and S. Suhaia, *
a Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
b European Molecular Biology Laboratory, Postfach 102209, Meyerhofstr. 1, D-69012 Heidelberg, Germany
Received 28 August 1998. Available online 11 January 1999.
Abstract
The structures and relative energies for L-alanyl-L-alanine (LALA) in the presence of explicit water molecules have been
determined by using the density functional theory (DFT) Becke3LeeYangParr functional and the 6-31G* basis set (B3LYP/6-31G*).
In aqueous solution the dominant state of LALA is the zwitterionic form, while its neutral form is dominant in vacuo. Attempts 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 charged carboxylate group, or from the ammonium group to the adjacent carbonyl oxygen and from the amide nitrogen to the carboxylate group. To stabilize the zwitterion,
we modelled the system by adding explicit water molecules and by placing the zwitterion within a sphere surrounded by a medium with a dielectric constant of 78.5, that is, within
the Onsager continuum model, where the recommended cavity radius is obtained from a solute volume calculation. The zwitterionic species is only stable in the presence of water at
the B3LYP/6-31G* level. This makes it imperative to include water molecules to model the zwitterionic species of LALA, peptides and amino acids at the B3LYP/6-31G*
level. Finally, the zwitterionic structure stabilized by explicit water molecules has also been modelled within the Onsager theory. Here the Onsager model represents the effects due to
the bulk water and the explicit water molecules stand for the effect due to direct H-bonding between the zwitterion and the solvent, that is, the first solvation shell. We used molecular
dynamics simulations utilizing the CHARMm force field to produce structural input for the subsequent quantum-mechanical simulations. The structures 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 careful when using continuum models to study peptides and proteins or other methods which do not take
into account the explicit interactions between the solute and the first solvent shell.
Chemical Physics : 1 January 1999, Volume 240, Issues 1-2, Pages 63-77