CHAPTER 7: Computational Studies of Molybdenum and Tungsten Enzymes
Published:30 Sep 2016
U. Ryde, G. Dong, J. Li, M. Feldt, and R. A. Mata, in Molybdenum and Tungsten Enzymes: Spectroscopic and Theoretical Investigations, ed. R. Hille, C. Schulzke, M. L. Kirk, M. L. Kirk, R. Hille, and C. Schulzke, The Royal Society of Chemistry, 2016, pp. 275-321.
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We review computational studies of three important mono-nuclear molybdenum oxo-transfer enzymes, dimethylsulfoxide reductase, sulfite oxidase and xanthine oxidase. We show that calculated energies for these reactions are very sensitive to details in the calculations, in particular to the density-functional method employed and the size of the basis set, but the treatment of dispersion and solvation effects is also crucial, as well as the definition of the reference state. We point out problems with standard quantum-mechanical (QM) cluster calculations, regarding the selection of the QM system and atomic coordinate constraints. Combined QM and molecular mechanics (QM/MM) methods also have important problems, which can be solved by calculations with very large QM systems (400–1000 atoms). Many studies have been published that reproduce experimentally measured activation energies, but for the wrong reason. We also compare the properties of molybdenum and tungsten and discuss why the active sites of the three families of molybdenum oxo-transfer enzymes are so different.