Biomedical Engineering Reference
In-Depth Information
23
Dealing with the Solvent
Chemical reactions generally take place in condensed media. I have had very little to say so
far about the presence or absence of a solvent, and many of the applications discussed have
referred to single, isolated molecules at 0 K and in free space. The benchmark molecular
dynamics (MD) andMonte Carlo (MC) applications discussed in earlier chapters dealt with
arrays of particles with particularly simple potentials, and the quantum mechanical models
have made no mention of a solvent.
23.1 Solvent Models
The obvious way to take account of the solvent in a MM calculation is to physically add
solvent molecules and then optimize the molecular geometry, but such calculations tend
to be particularly compute-intensive and the necessary computer power simply was not
available to the pioneers in the field. The same comment obviously holds for quantum
mechanical studies.
In a medium of relative permittivity ε
r
, the mutual potential energy of two point charges
Q
A
and
Q
B
is reduced by a factor of ε
r
. Typical values are shown in Table 23.1.
Relative permittivities are temperature dependent, and they are usually recorded as a
power series in the temperature:
b
T
K
c
T
K
2
ε
r
=
+
+
+···
a
Early workers in the MM field attempted to allow for the presence of a solvent by
modifying any electrostatic contribution to their force field. The problem was that the
chosen factor was at first sight quite arbitrary, and bore little relation to the values in
Table 23.1. For example, a value of 2.5 was often used for liquid water. All kinds of
convincing arguments were used to justify such choices, for example the two atoms A and
