Trigonal Prismatic or not Trigonal Prismatic? On the Mechanisms of Oxygen‐Atom Transfer in Molybdopterin‐Based Enzymes

Kaupp, Martin

doi:10.1002/anie.200301690

Cited by 30 publications

(20 citation statements)

References 23 publications

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“…7,10-15, 17,18 In particular, the importance of the trigonal prismatic structure has been emphasized, 61 as well as the fact that the enzyme seems to destabilize the product by avoiding a octahedral structure.…”

Section: Structuresmentioning

confidence: 99%

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

Mata

Ryde

2013

J. Chem. Theory Comput.

105

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The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention by both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations that what has previously been appreciated. Basis sets of at least triplezeta quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and non-polar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a pre-formed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration towards local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.

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Section: Structuresmentioning

confidence: 99%

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

Mata

Ryde

2013

J. Chem. Theory Comput.

105

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“…[62] Enzymes of the xanthine oxidase family catalyze hydroxylation reactions of several substrates, and the mechanism proposed implies a trigonal-prismatic intermediate in which the substrate is coordinated to a molybdenum atom, [63] whose geometry is supported by computational studies. [64] Several copper sites present coordination environments that are described as intermediate between the trigonal prism and the octahedron, including a copper amine oxidase, [65] copper-substituted human lactoferrin, [66] and superoxide dismutases, [67] although their deviations from the Bailar pathway are quite large. Also the environment of the Fe atom in enterobactin has a twisted geometry that, however, is closer to the octahedron than to the trigonal prism (see the Supporting Information), while the vanadium(IV) enterobactin complex [68] is practically midway between the octahedron and the trigonal prism (f OC!TP = 54 %).…”

Section: Occurrence and Relevance Of The Trigonal Prism As A Coordinamentioning

confidence: 99%

The Trigonal Prism in Coordination Chemistry

Cremades

Echeverría

Álvarez

2010

Chemistry A European J

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Herein we analyze the accessibility of the trigonal-prismatic geometry to metal complexes with different electron configurations, as well as the ability of several hexadentate ligands to favor that coordination polyhedron. Our study combines i) a structural database analysis of the occurrence of the prismatic geometry throughout the transition-metal series, ii) a qualitative molecular orbital analysis of the distortions expected for a trigonal-prismatic geometry, and iii) a computational study of complexes of several transition-metal ions with different hexadentate ligands. Also the tendency of specific electron configurations to present a cis bond-stretch Jahn-Teller distortion is analyzed.

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“…A second-shell residue, Glu869, forms one hydrogen bond to the oxygen species bound to Mo. The reaction mechanisms of Mo-AOR [34], xanthine oxidase [35][36][37][38][39][40][41][42][43][44], and other related Modependent enzymes [45][46][47][48][49][50][51][52][53] have been studied using quantum chemical methods. Recent QM/MM calculations of Mo-AOR suggested that the Glu869 residue functions as a general base to take a proton from the Mo-OH and to facilitate nucleophilic attack on the substrate aldehyde carbonyl carbon to form a tetrahedral intermediate [34].…”

Section: Introductionmentioning

confidence: 99%

Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations

Liao

Himo

2011

Journal of Inorganic Biochemistry

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Trigonal Prismatic or not Trigonal Prismatic? On the Mechanisms of Oxygen‐Atom Transfer in Molybdopterin‐Based Enzymes

Cited by 30 publications

References 23 publications

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

The Trigonal Prism in Coordination Chemistry

Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations

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