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Kinetics and Dynamics pp 331–353Cite as

QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis

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Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 12))

Abstract

Combined quantum mechanical/molecular mechanical (QM/MM) models have been established as efficient approaches to simulate chemical reactions in complex molecular systems including enzymes. The QM/MM Hamiltonian is defined based on partitioning a molecular system into a reactive center and its surrounding, namely, the QM and MM regions. How to properly treat the QM/MM interface, which involves both covalent and non-covalent interactions, has been one of the central focuses in QM/MM method development. Techniques for energy minimization and conformational sampling based on QM/MM Hamiltonians have also been continuously developed, with the goal to determine reaction paths and potential/free energy surfaces of complex molecular systems efficiently and reliably. Accompanying method development, there have been an increasing number of studies applying QM/MM to various enzyme systems and providing new insights into their mechanisms.

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Acknowledgements

The support from Chinese Natural Science Foundation with grant number 30970560 is gratefully acknowledged.

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Authors and Affiliations

  1. School of Life Sciences, University of Science and Technology of China and Hefei National Laboratory of physical Sciences at the Micro Scales, Hefei, Anhui, 230026, China

    Haiyan Liu

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  1. Haiyan Liu
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Correspondence to Haiyan Liu .

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Editors and Affiliations

  1. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Piotr Paneth

  2. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Agnieszka Dybala-Defratyka

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Liu, H. (2010). QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis. In: Paneth, P., Dybala-Defratyka, A. (eds) Kinetics and Dynamics. Challenges and Advances in Computational Chemistry and Physics, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3034-4_12

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