Molecular dynamics (MD) simulation is a computational chemistry technique used to observe how a molecular system behaves as time passes. MD is based on solving Newton’s equations of motion. This requires the use of force fields to describe the potential energy function of each different molecule type in molecular system. In order to develop a force field, charges, bonds, angles, and dihedrals must be parameterized to fit quantum mechanics (QM) data. By basing the force field on QM data, MD simulations have higher accuracy while still using the low computational cost of molecular mechanics. This project focuses on developing well-fit force fields for β-lactam class antibiotics for future MD simulations. Full antibiotics are too large of a molecule to parameterize from scratch, so instead we broke them down into fragments. Smaller molecule fragments allow less terms to be optimized which greatly simplifies force field development. By the transferable nature of parameters in CHARMM force fields, the fragment parameters can be transferred to connecting molecules. Due to this, we can build up larger organic molecule force fields piece by piece.In this work, we developed CHARMM force fields for cephalothin, cefotaxime, ceftazidime, and aztreonam.
"Force Field Development of β-lactam Class Antibiotics,"
SMU Journal of Undergraduate Research: Vol. 5:
1, Article 2.
Available at: https://scholar.smu.edu/jour/vol5/iss1/2
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