Document Type


Date of Award


Degree Name

Master of Science in Chemical Engineering - (M.S.)


Chemical Engineering, Chemistry and Environmental Science

First Advisor

Carol A. Venanzi

Second Advisor

Arthur Greenberg

Third Advisor

Gordon Lewandowski


Molecular mechanics calculations were used to investigate beta-cyclodextrin and capped beta-cyclodextrin as models for the active site of alpha-chymotrypsin. The Amber molecular mechanics force field was used to investigate the effect that addition of the caps has on the conformation of the beta-cyclodextrin macrocycle.

The RMS module of Amber was used to calculate differences in position between the atoms of the minimized mimics and those of the X-ray crystal structure. The deviation in position of the atoms of the minimized capped beta-cyclodextrin macrocycle was found to be larger than that of the minimized beta-cyclodextrin, indicating that the caps do affect the conformation of the macrocycle. Molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms indicated that the addition of the caps to the beta-cyclodextrin macrocycle alters the pattern of the map in each plane. However, the general qualitative features of the beta-cyclodextrin and capped beta-cyclodextrin maps are similar.