Abstract by Madison Porter
Chemistry and Biochemistry
Collision-Sampling and Peptide-Catalysis
Current methods for calculating reaction coordinates take a lot of computing power for large reaction/solvent systems such as peptide catalysts . The Michaelis group has proposed a solution to this problem by creating a program that can calculate the reaction coordinates of peptide-catalyst systems and predict the reactivity of future peptide-catalyst systems — all using molecular dynamics which uses significantly less computational power. Our group has invented a collision-sampling method based on our bifunctional Macmillan-thiourea catalyst system to determine the reaction coordinates of a Diels-Alder reaction. We have to compare this sampling method to other methods and lab results to prove its validity and reliability. Crystal structures and a calculated CYANA structure from NMR data show that our collision -sampling method predicts an accurate structure for the bifunctional peptide in its low-energy conformation.