Document Type


Date of Award


Degree Name

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


Chemical Engineering, Chemistry and Environmental Science

First Advisor

Tamara M. Gund

Second Advisor

David S. Kristol

Third Advisor

Arthur Greenberg


Conformational search and molecular mechanics calculations were combined to investigate the structural flexibility of isoquinolone, the anatoxin series, and the ferruginine series. Ring searching allow all rational conformations to be generated.

Isoquinolone shows conformational similarity to isoarecolone but is much less potent which suggests that the proximity of the methyl group beta to the carbonyl groups affects the bioactivity of isoquinolone. The very active agonist-anatoxin, without a similar conformation as isoarecolone, shared a similar electrostatic potential contour in the vicinity between the two atoms connected to the electro-positive nitrogen and hydrogen bonding site. These phenomena were not found in ferruginine which has a similar conformation to anatoxin but less potent. The comparison of the various series implied that the geometric position of the nitrogen is not essential, but that the electrostatic potential around the binding sites is important.

Two FORTRAN programs were implemented and adapted to aid the molec-ular modeling. FDRING made an improvement in the speed of ring perception. CAGEATOM suggests a faster method to represent the electrostatic potential distribution on van der Waals surface.



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.