Biomedical Engineering Reference
In-Depth Information
4.8 Some Commercial Force Fields
With these principles in mind, it is time to examine some of the common force fields found
in professional molecular modelling programs.
4.8.1 Dreiding
This force field (Mayo
et al.
1990) is parameterized for all atom types that any chemist
would expect for the elements H, C, N, O, P, S, F, Cl, Br and I. In terms of the 'standard'
expression we write
2
k
AB
R
AB
−
R
e,AB
2
2
k
ABC
cos θ
ABC
−
cos θ
e,ABC
2
1
1
U
=
+
bonds
bends
U
0
2
k
2
(ψ
ψ
e
)
2
+
(1
−
cos (
n
(χ
−
χ
0
)))
+
−
(4.20)
dihedrals
out-of -plane
C
1
AB
R
1
AB
−
C
AB
R
AB
+
nonbonded
4.8.2 MM1
In his review, Allinger (1976) essentially defined what we now call the MM1 force field. He
treated hydrocarbons only, ignored the Coulomb terms and used an exp-6 Lennard-Jones
potential.
Once all the standard cases have been successfully treated, one naturally looks at the
difficult ones. In the case of hydrocarbons, these difficult cases comprise strained rings
such as cyclobutane. The problem with cyclobutane is that, whilst having all carbon atoms
planar can minimize the angular deformation from tetrahedral, the molecule is actually
puckered by a substantial angle from planarity. In addition, the C-C bond lengths are
unusually large. The obvious solution is to say that a four-membered ring is different from
any other hydrocarbon and that the bond angle does not have a natural tetrahedral value,
Bicyclic and related molecules
Figure 4.6
Bicyclic and related molecules
