Abstract:

Enzymes are highly efficient catalysts and essential to life, prompting significant research into how they function. Understanding various structural or electronic properties of enzymes and how they contribute to enzymatic function will help researchers take advantage of catalytic motifs and design bioinspired molecular catalysts. There are several methods of computationally studying enzymatic reactions which focus on different interactions, ranging from Molecular Dynamics simulations to Quantum Mechanical (QM) cluster models of enzymes. In the QM cluster approach, the active site of the enzyme is extracted from the surrounding protein and constraints are put on anchor atoms, where residues are no longer bound by surrounding protein, during geometry optimization to mimic structural constraints. Most QM cluster models fix the crystallographic positions of anchor atoms, sometimes leading to unphysical results and ignoring entropic effects. This seminar will focus on the advancements made by Dasgupta and Herbert to make QM cluster enzyme models more realistic, constraining atoms with a harmonic confining potential rather than fixing atomic positions.1 I will present the theory behind these harmonic constraints, as well as go over a test case from the paper.

1) Saswata Dasgupta and John M. Herbert, J. Phys. Chem. B, 2020, 124 (7), 1137–1147.