A method for assessing quantum molecular similarity has been developed
based on the momentum-space representation. The principles of the met
hod are summarized and the results of two applications are presented.
The approach emphasizes the variation of the outer valence electron de
nsity much more than the bonding topology, it avoids several problems
associated with more conventional approaches based on the position-spa
ce representation, and it can now be applied to extended series of lar
ge molecules. The first of the applications involves different sulfony
lurea inhibitors of the enzyme acyl-CoA: cholesterol acyltransferase (
ACAT). The second is concerned with the relative toxicity of a number
of anti-HIV phospholipids. Further experimental work is suggested in b
oth cases.