Multi-level Quantum Methods for Phosphate Hydrolysis

本论文的目标是发展和应用新的多能级量子方法来研究金属离子催化的RNA磷酸盐水解反应。方法开发的重点包括：（a）设计新的线性标度的电子结构方法的生物分子，B）新的混合QM/MM潜力的发展，模拟磷酸盐水解反应的酶，和c）实施一个新的线性标度的光滑溶剂化潜力的量子力学几何优化和频率计算。这些新方法将在CHARMM分子建模软件包中实现，并广泛使用。应用将集中在一个小的单磷酸水解模型系统，并在锤头状核酶自切割反应。这些系统将研究与经典的分子模拟，混合QM/MM方法，和高层次的密度泛函计算。特别感兴趣的是结构和活性之间的关系，以及金属离子在催化中的作用。这些系统提出了重要的生物学问题，并提出了特殊的理论挑战。拟议工作的目标是取得进展，克服这些挑战。

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.