Molecular Dynamics Simulations of Curcuminato-(η⁶-p-cymene)ruthenium(II) Docking in the Minor Groove of DNA: Evaluating Equilibrium Stability via 2D RMSD Analysis

Presenter(s)

Jarrod Ring

Abstract or Description

Abstract

Molecular dynamics simulations were conducted to study the interaction between Curcuminato-(η⁶-p-cymene)ruthenium(II) and DNA, focusing on minor groove binding at the N7 position of guanine. The system equilibrated at approximately 170 picoseconds, with the lowest potential energy configuration of -36.271 kcal/mol observed at 251 K at 464 picoseconds. The simulated Ru-N7 distance was 8.55 Å, contrasting with the literature-reported value of 2.824 Å, highlighting the influence of dynamic conditions on the interaction. The root-mean-square deviation (RMSD) matrix stabilized at approximately 1.45 Å at equilibrium, reflecting the conformational stability of the system. Temporal profiles of temperature, potential energy, and total energy further characterized the equilibration and stability processes. These findings advance the understanding of the physical properties of ruthenium-curcumin complexes in biomolecular systems and their potential capacity to act as therapeutic agents.

Mentor

Hannah Leverentz-Culp