Previous Index Next
Page 26
(previous) (Page 000026) (next)

square deviation (rms dev) between calculated and measured obser-'
vables for three force fields: CFF "12—6-1" (i.e. "12—6" for LJ
and "1" for Coulomb), CFF "9—6—1" and MCM328s29, semi—empirical
force field which uses a special function for the hydrogen bond,
and theoretical values for dispersion parameters and partial
charges. The data base comprises 14 carboxylic acids and 12
amides. The 11 observables represented are: Lattice energies
(heats of sublimation), UCU (unit~cell~vector) lengths, UCV angles,
cell volumes, close inter—atomic contact distances (d<4A), and 6
hydrogen—bond ovservables * 2 distances and 4 angles.

A close examination of this table and those which follow in
the bench mark paper‘3 can tell us not only which force field is
better and which.observables are better represented. One can look
for systematic trends of rms deviations, search for their cause or
origin, and indicate the way to replace poorer potentials by better
ones. Thus, for example, it is noted that rms deviations are
smaller in amides than in carboxylic acids in both 12—6—1 and 9—6-1.
The reason could be traced to two facts: Amide crystals contain
twice as much hydrogen bonds than carboxylic acids (there are 2 NH
bonds per amide vs one OH bond per carboxyl), and hydrogen bond
distances are better fit to experiment than alkane contact dis—
tances (most terms in "d<4"). The indication is that the alkane
non—bonded interactions need a reevaluation. Indeed we are trying
out some ideas to improve the Van der Waals potential for alkanes.
Such an improvement may be important for a better representation
of hydrophobic, non polar groups. Hydrophobic regions, typical
of the interior of globular proteins, are most suitable for
potential energy calculations related to protein structure, since
they do not involve solvent (water) interaction with proteins.
Therefore, reducing the errors in the Van der Waals potential to
the level of that of the polar interactions is a desirable goal
from the point of view of potential energy calculations in struc-
tural molecular biology.










l. P. M. Morse, Phys.Rev. 34:57 (1929).

2. K. S. Pitzer, Disc.Faraday Soc. 10:66 (1951).

3. F. London, Z.Physik.Chem.B 11:222 (1930).

4. J. C. Slater and J. G. Kirkwood, Phys.Rev. 37:682 (1931).

5. H. L. Kramer and D. R. Herschbach, J.Chem.Phys. 53:2792 (1970).
6. J. E. Lennard—Jones, Proc.Roy.Soc. London A 106:463 (1924).

7. B. M. Axilrod and E. Teller, J.Chem.Phys. 11:299 (1943).

8. N. R. Kestner and O. Sinanoglu, J.Chem.Ehys. 38:1730 (1963).
9. R. s. Mulliken, J.Chem.Pth. 23:1833 (1955).

'10. A. T. Hagler and A. Lapiccirella, Biopolymers 15:1167 (1976).
.11. S. Lifson, A. T. Hagler and P. Dauber, J.Am.Chem.Soc. 101:5111



Previous Index Next