Booth Id:
CHEM042
Category:
Energy: Sustainable Materials and Design
Year:
2016
Finalist Names:
Hajlasz, Natalia
Abstract:
Metal cations and especially Mg2+ play a very important role in many biological processes such as RNA folding and catalysis. In order for Mg2+ to interact with RNA, a water molecule must first dissociate from its water hydration shell: this process is very slow and a rare event due to the shell’s rigidity. The accurate simulation of Mg2+-water dissociation is necessary for future simulations of processes that involve Mg2+ interaction, but the length of the process makes it unfeasible to simulate using regular brute force methods. The overall purpose of this study is to find a working methodology to effectively simulate Mg2+-water dissociation. Previous simulations of the Mg2+-water system using umbrella sampling and TST approximations have been unable to obtain accurate results for the dissociation rate constant of the system. Instead, this study utilizes the weighted ensemble (WE) path sampling approach along with a two-dimensional progress coordinate that tracks the distance and orientation of the dissociating water molecule. These methods were tested on the faster but similar Ca2+-water system with the TIP3P water model and AMBER99SB-ILDN all-atom force field parameters. The results proved successful for the methodology since dissociation events were captured and the simulation results reached convergence. The achieved stability concludes that the methods used (the progress coordinate with weighted ensemble) result in sampling efficiency that will allow for the simulation of Mg2+-water. In addition, the accurate estimate of the rate constant of dissociation provides evidence to consider the water model and force field used in this simulation as reasonably accurate in describing ion-water interactions and as utile for the simulation of Mg2+-water dissociation.