The objective of this proposal is to develop and apply new integrated multi-level quantum methods to study metal-ion catalyzed phosphate hydrolysis reactions in RNA. The focus of the methods development include (a) the design of new linear-scaling electronic structure methods for biomolecules, b) the development of new hybrid QM/MM potentials to model phosphate hydrolysis reactions in enzymes, and c) the implementation of a new linear-scaling smooth solvation potential for quantum mechanical geometry optimization and frequency calculations. The new methods will be implemented into the CHARMM molecular modeling package and made widely available. The applications will focus on a small monophosphate hydrolysis model system, and on the hammerhead ribozyme self-cleavage reaction. These systems will be studied with classical molecular simulation, hybrid QM/MM methods, and high-level density-functional calculations. Of particular interest is the relationship between structure and activity, and the role of metal ions in catalysis. These systems pose important biological questions and present special theoretical challenges. The goal of the proposed work is to make advances to overcome these challenges.
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