Computer simulation of free energies to predict cis/trans equilibria of prolyl peptides and solvation free energies of phenylalanyl peptides
MetadataShow full item record
In Part I, the free energy perturbation (FEP) method, using AMBER, was utilized to calculate the Gibbs free energy difference between cis and trans conformers of Ace-Tyr-Pro- NMe and Ace-Asn-Pro-NMe, from which the ratio of cis to trans conformers was obtained. Our simulation generated much lower %cis for both peptides as compared with experimental values and possible problems in our computational schemes are presented. However, our results were encouraging in that they predicted preference of trans conformers for both peptides and higher %cis for Ace-Tyr-Pro-NMe, compared to Ace-Asn-Pro-NMe, which agrees with experimental results.
Part II applied semi empirical (AMS0L) and microscopic simulation (POLARIS) methods to obtain the solvation free energies of a series of phenylalanyl peptides with various degrees of methylation on their backbone nitrogens. It was clearly predicted that as a peptide length increased, so solvation free energy decreased, indicating less favorable permeability through the cell membrane system, in agreement with data in the literature. AMSOL also showed that solvation free energy change upon methylation was variable depending on the position of the substituted backbone nitrogen, which disagrees with the literature. However, non-systematic solvation free energy change of small amines upon methylation was successfully predicted by AMSOL, in good accord with experimental data.
- Masters Theses 
Showing items related by title, author, creator and subject.
Academic Qualification in Onshore and Offshore Wind Energy within the Framework of the European Academy of Wind Energy and the European Wind Energy Master Program - Examples and Experiences in Germany and Europe Kaern, Moses (Virginia Tech, 2015-06-10)The development of research and education in wind energy in Europe varies greatly between the member states. Building on these national achievements the European Academy of Wind Energy (EAWE) is integrating and connecting ...
Walker, Martha A.; Grisso, Robert D. (Robert Dwight), 1956-; Ignosh, John (Virginia Cooperative Extension, 2009-12-01)This publication explains the federal and state financial incentives to utilitize new energy technologies and how Virginia homeowners can take advantage of these programs.
Contaminant removal from impervious pavements and its relationship with raindrop impact energy, cumulative kinetic energy of rainfall events, and rainwater pH Angelotti, Robert W. (Virginia Polytechnic Institute and State University, 1985)