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. Author manuscript; available in PMC: 2015 Jul 6.
Published in final edited form as: J Chem Phys. 2004 Jul 15;121(3):1516–1524. doi: 10.1063/1.1752887

FIG. 2.

FIG. 2

A schematic representation of several models with different description of the Glutamate environment: (a) Model I: six water molecules constituting a first solvation shell of the 1C carboxylate; (b) the same for the 5C carboxylate; (c) Model II is a spherical cavity model with the dielectric constant of water and six water molecules around the 1C carboxylate. An analogous model has been prepared for the system with water molecules surrounding the 5C carboxylate (not shown); (d) Model III: the ligand is treated quantum mechanically and the environment is represented as a sphere of partial charges taken from the MD simulation. The sphere radius is 12 Å. (e) Model IV is the same as Model III but the six water molecules which are the closest to the 1C carboxylate has been represented quantum mechanically. Similar model has been prepared with the six water molecules surrounding the 5C carboxylate (not shown).