The nonheme diiron toluene/o-xylene monooxygenase (ToMO) is the most studied toluene monooxygenase that mediates an aromatic hydroxylation reaction. In this work, QM/MM calculations were performed to understand the reaction mechanism. It is revealed that the μ-η :η peroxodiferric species is the reactive intermediate after the binding of the O molecule to the reduced diferrous center. Subsequently, both a stepwise and a concerted mechanism involving the critical O-O bond cleavage and C-O bond formation were considered. The latter was calculated to be more favorable, suggesting that the formation of a high-valent diferryl Q intermediate is not needed. The isomeric formation of the phenol product was found very facile. The first step was calculated to be rate-limiting, with a barrier of 17.6 kcal/mol for the ortho-hydroxylation.
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http://dx.doi.org/10.1002/asia.202200490 | DOI Listing |
Biochem Biophys Res Commun
January 2025
Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina. Electronic address:
The interest in chemical interactions between inorganic sulfur species and heme compounds has grown significantly in recent years due to their physiological relevance. The model system ferric N-acetyl microperoxidase 11 (NAcMP11Fe) enables the exploration of the mechanistic aspects of the interaction between the ferric heme group and binding sulfur ligands, without the constraints imposed by a protein matrix and the stabilizing effects of distal amino acids. In this study, we investigated the coordination of disulfane (HSSH) and its conjugate base hydrodisulfide (HSS) to NAcMP11Fe.
View Article and Find Full Text PDFJ Phys Chem Lett
January 2025
Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, Vienna 1190, Austria.
In the past decade, machine-learned potentials (MLP) have demonstrated the capability to predict various QM properties learned from a set of reference QM calculations. Accordingly, hybrid QM/MM simulations can be accelerated by replacement of expensive QM calculations with efficient MLP energy predictions. At the same time, alchemical free-energy perturbations (FEP) remain unachievable at the QM level of theory.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.
We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudobond treatment of the QM/MM boundary. We demonstrate that our method has well-controlled errors, stable self-consistent QM convergence, and energy-conserving dynamics. We further describe an application to the catalytic kinetics of chorismate mutase.
View Article and Find Full Text PDFChembiochem
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 PDFPhys Chem Chem Phys
January 2025
UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, OX11 0FA, UK.
Methanol adsorption isotherms of fresh f-ZSM-5 and steamed s-ZSM-5 (Si/Al ≈ 40) are investigated experimentally at room temperature under equilibrium and by grand canonical Monte Carlo (GCMC) simulations with the aim of understanding the adsorption capacity, geometry and sites as a function of steam treatment (at 573 K for 24 h). Methanol adsorption energies calculated by GCMC are complemented by density functional theory (DFT) employing both periodic and quantum mechanics/molecular mechanics (QM/MM) techniques. Physical and textural properties of f-ZSM-5 and s-ZSM-5 are characterised by diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS) and N-physisorption, which form a basis to construct models for f-ZSM-5 and s-ZSM-5 to simulate methanol adsorption isotherms by GCMC.
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