Background: Structure, dynamics, and free energies of solvated ions and ion-pairing in solution have longbeen an active research topic being investigated by various experimental and theoretical methods. Metal ions,in particular, calcium (Ca2+) and magnesium (Mg2+) are essential for biochemical functions of cells.Motivations: Previous studies and our study have shown that molecular dynamics simulations usingempirical force field resulted in excess ion cluster formation in concentrated electrolyte solutions; theseresults will therefore lead to inaccurate coordination numbers of ions with water molecules. These artifactswill potentially lead to inaccurate coordination of cations with high-density negatively charged biomolecularsystems such as DNA and phospholipids. This problem might be due to the use of inaccurate cation-anionLennard-Jones interacting parameters, generally approximated by Lorentz-Berthelot combining rule.Methodology: We propose to apply the “NBFIX” method proposed by Rous and coworkers to systemicallyoptimize the Ca2+Cl and Mg2+Cl interacting L-J parameters. The experimentally measured M2+H2Ocoordination numbers and osmotic pressure for a wide range of salt concentration are the targets in ouroptimization. Moreover, the Ca2+O(in PO4group) and Mg2+O(in PO4group) interacting L-Jparameters will also be systemically optimized to reproduce the experimentally measured M2+ locationwithin phospholipid bilayers and molecular electrometers.Objectives: (1) Obtain optimized Ca2+Cl and Mg2+Cl interacting L-J parameters for MD simulations ofhigh concentration CaCl2 and MgCl2 electrolyte solutions; (2). Obtain optimized Ca2+O(in PO4group)and Mg2+O(in PO4group) interacting L-J parameters for MD simulations of high-density negativelycharged DNA/RNA and phospholipid bilayers.Broader Impact: This project will serve as an interface for integrating research and fundamental education.The computational methods used and developed in this project will be incorporated into the graduate-levelcourses. The broader impact of this project includes the training of interdisciplinary undergraduates andgraduate students for studying biomolecular simulations. Accurate force field is one of the most importantfactors to drive the fast development of molecular dynamics simulations.
|Effective start/end date||1/08/17 → 31/07/18|
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This project contributes towards the following SDG(s):