The stereospecific cytochrome P450-catalyzed hydroxylation of the C(5)-H((5-exo)) bond in camphor has been studied theoretically by a combined quantum mechanical/molecular mechanical (QM/MM) approach. Density functional theory is employed to treat the electronic structure of the active site (40-100 atoms), while the protein and solvent environment (ca. 24,000 atoms) is described by the CHARMM force field. The calculated energy profile of the hydrogen-abstraction oxygen-rebound mechanism indicates that the reaction takes place in two spin states (doublet and quartet), as has been suggested earlier on the basis of calculations on simpler models ("two-state reactivity"). While the reaction on the doublet potential energy surface is nonsynchronous, yet effectively concerted, the quartet pathway is truly stepwise, including formation of a distinct intermediate substrate radical and a hydroxo-iron complex. Comparative calculations in the gas phase demonstrate the effect of the protein environment on the geometry and relative stability of intermediates (in terms of spin states and redox electromers) through steric constraints and electronic polarization.
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http://dx.doi.org/10.1021/ja039847w | DOI Listing |
Chembiochem
January 2025
Renmin University of China, Chemistry, No.59 Zhongguangcun Street, Haidian District, 100872, Beijing, CHINA.
BTG13, a non-heme iron-dependent enzyme with a distinctive coordination environment of four histidines and a carboxylated lysine, has been found to catalyze the cleavage of the C4a-C10 bond in anthraquinone. Contrary to typical dioxygenase mechanisms, our quantum mechanical/molecular mechanical (QM/MM) calculations reveal that BTG13 functions more like a monooxygenase. It selectively inserts an oxygen atom into the C10-C4a bond, creating a lactone species that subsequently hydrolyzes, leading to the formation of a ring-opened product.
View Article and Find Full Text PDFJ Phys Condens Matter
January 2025
Physics, Xiamen University, Wulijidian Building 358, Haiyun campus, Xiamen University, Xiamen, Fujian, 361005, CHINA.
Newly-synthesized structure T (sT) hydrate show promising practical applications in hydrogen storage and transport, yet the properties remain poorly understood. Here, we develop a machine learning potential (MLP) of sT hydrogen hydrate derived from quantum-mechanical molecular dynamics (MD) simulations. Using this MLP forcefield, the structural, hydrogen diffusion, mechanical and thermal properties of sT hydrogen hydrate are extensively explored.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585, Japan.
The light-harvesting complex II (LHCII) in green plants exhibits highly efficient excitation energy transfer (EET). A comprehensive understanding of the EET mechanism in LHCII requires quantum chemical, molecular dynamics (MD), and statistical mechanics calculations that can adequately describe pigment molecules in heterogeneous environments. Herein, we develop MD simulation parameters that accurately reproduce the quantum mechanical/molecular mechanical energies of both the ground and excited states of all chlorophyll (Chl) molecules in membrane embedded LHCII.
View Article and Find Full Text PDFBiochemistry
January 2025
Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, United States.
The target DNA (tDNA) cleavage catalyzed by the CRISPR Cas9 enzyme is a critical step in the Cas9-based genome editing technologies. Previously, the tDNA cleavage from an active SpyCas9 enzyme conformation was modeled by Palermo and co-workers (Nierzwicki et al., , 912) using ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulations, where the free energy barrier was found to be more favorable than that from a pseudoactive enzyme conformation.
View Article and Find Full Text PDFJ Am Chem Soc
December 2024
Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
Non-heme iron (Fe), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of Fe/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others.
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