A Reaction‐Induced Localization of Spin Density Enables Thermal C−H Bond Activation of Methane by Pristine FeC4+

The reactivity of the cationic metal‐carbon cluster FeC4+ towards methane has been studied experimentally using Fourier‐transform ion cyclotron resonance mass spectrometry and computationally by high‐level quantum chemical calculations. At room temperature, FeC4H+ is formed as the main ionic product, and the experimental findings are substantiated by labeling experiments. According to extensive quantum chemical calculations, the C−H bond activation step proceeds through a radical‐based hydrogen‐atom transfer (HAT) mechanism. This finding is quite unexpected because the initial spin density at the terminal carbon atom of FeC4+, which serves as the hydrogen acceptor site, is low. However, in the course of forming an encounter complex, an electron from the doubly occupied sp‐orbital of the terminal carbon atom of FeC4+ migrates to the singly occupied π*‐orbital; the latter is delocalized over the entire carbon chain. Thus, a highly localized spin density is generated in situ at the terminal carbon atom. Consequently, homolytic C−H bond activation occurs without the obligation to pay a considerable energy penalty that is usually required for HAT involving closed‐shell acceptor sites. The mechanistic insights provided by this combined experimental/computational study extend the understanding of methane activation by transition‐metal carbides and add a new facet to the dizzying mechanistic landscape of hydrogen‐atom transfer.DFG, 53182490, EXC 314: Unifying Concepts in CatalysisTU Berlin, Open-Access-Mittel - 201

Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations.

There are three families of mononuclear molybdenum enzymes that catalyze oxygen atom transfer (OAT) reactions, named after a typical example from each family, viz., dimethyl sulfoxide reductase (DMSOR), sulfite oxidase (SO), and xanthine oxidase (XO). These families differ in the construction of their active sites, with two molybdopterin groups in the DMSOR family, two oxy groups in the SO family, and a sulfido group in the XO family. We have employed density functional theory calculations on cluster models of the active sites to understand the selection of molybdenum ligands in the three enzyme families. Our calculations show that the DMSOR active site has a much stronger oxidative power than the other two sites, owing to the extra molybdopterin ligand. However, the active sites do not seem to have been constructed to make the OAT reaction as exergonic as possible, but instead to keep the reaction free energy close to zero (to avoid excessive loss of energy), thereby making the reoxidation (SO and XO) or rereduction of the active sites (DMSOR) after the OAT reaction facile. We also show that active-site models of the three enzyme families can all catalyze the reduction of DMSO and that the DMSOR model does not give the lowest activation barrier. Likewise, all three models can catalyze the oxidation of sulfite, provided that the Coulombic repulsion between the substrate and the enzyme model can be overcome, but for this harder reaction, the SO model gives the lowest activation barrier, although the differences are not large. However, only the XO model can catalyze the oxidation of xanthine, owing to its sulfido ligand

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

The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated Basis sets of at least triple-zeta 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 nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed 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 toward local CCSD (T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBEO, 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

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular, the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerization reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site

Highly regioselective hydride transfer, oxidative dehydrogenation, and hydrogen-atom abstraction in the thermal gas-phase chemistry of [Zn(OH)](+)/C3H8

The thermal reactions of [Zn(OH)]+ with C3H8 have been studied by means of gas-phase experiments and computational investigation. Two types of C–H bond activation are observed in the experiment, and pertinent mechanistic features include inter alia: (i) the metal center of [Zn(OH)]+ serves as active site in the hydride transfer to generate [i-C3H7]+ as major product, (ii) generally, a high regioselectivity is accompanied by remarkable chemoselectivity: for example, the activation of a methyl C–H bond results mainly in the formation of water and [Zn(C3,H7)]+. According to computational work, this ionic product corresponds to [HZn(CH3CH[double bond, length as m-dash]CH2)]+. Attack of the zinc center at a secondary C–H bond leads preferentially to hydride transfer, thus giving rise to the generation of [i-C3H7]+; (iii) upon oxidative dehydrogenation (ODH), liberation of CH3CH2[double bond, length as m-dash]CH2 occurs to produce [HZn(H2O)]+. Both, ODH as well as H2O loss proceed through the same intermediate which is characterized by the fact that a methylene hydrogen atom from the substrate is transferred to the zinc and one hydrogen atom from the methyl group to the OH group of [Zn(OH)]+. The combined experimental/computational gas-phase study of C–H bond activation by zinc hydroxide provides mechanistic insight into related zinc-catalyzed large-scale processes and identifies the crucial role that the Lewis-acid character of zinc plays.DFG, EXC 314, Unifying Concepts in Catalysi

Experiment and Theory Clarify: Sc+ Receives One Oxygen Atom from SO2 to Form ScO+, which Proves to be a Catalyst for the Hidden Oxygen-Exchange with SO2

[EN] Using Fourier-transform ion cyclotron resonance mass spectrometry, it was experimentally determined that Sc+ in the highly diluted gas phase reacts with SO2 to form ScO+ and SO. By O-18 labeling, ScO+ was shown to play the role of a catalyst when further reacting with SO2 in a Mars-van Krevelen-like (MvK) oxygen exchange process, where a solid catalyst actively reacts with the substrate but emerges apparently unchanged at the end of the cycle. High-level quantum chemical calculations confirmed that the multi-step process to form ScO+ and SO is exoergic and that all intermediates and transition states in between are located energetically below the entrance level. The reaction starts from the triplet surface; although three spin-crossing points with minimal energy have been identified by computational means, there is no evidence that a two-state scenario is involved in the course of the reaction, by which the reactants could switch from the triplet to the singlet surface and back. Pivotal to the oxygen exchange reaction of ScO+ with SO2 is the occurrence of a highly symmetric four-membered cyclic intermediate by which two oxygen atoms become equivalent.The authors thank IZO-SGI SGIker (UPV/EHU), supported by ERDF and ESF European funding programmes, for technical and human assistance with the calculations, and the DIPC for generous allocation of computational resources. Financial support comes from the Spanish Office for Scientific Research (MCIU /AEI /FEDER, UE), Ref.: PGC2018-097529-B-100 and Eusko Jaurlaritza (Basque Government), Ref.: IT1254-19, and the National Natural Science Foundation of China (21773085 and 92161120)

Revisiting the Intriguing Electronic Features of the BeOBeC Carbyne and Some Isomers: A Quantum‐Chemical Assessment

Extensive high‐level quantum‐chemical calculations reveal that the rod‐shaped molecule BeOBeC, which was recently generated in matrix experiments, exists in two nearly isoenergetic states, the 5Σ quintet (56) and the 3Σ triplet (36). Their IR features are hardly distinguishable at finite temperature. The major difference concerns the mode of spin coupling between the terminal beryllium and carbon atoms. Further, the ground‐state potential‐energy surface of the [2Be,C,O] system at 4 K is presented and differences between the photochemical and thermal behaviors are highlighted. Finally, a previously not considered, so far unknown C2v‐symmetric rhombus‐like four‐membered ring 3[Be(O)(C)Be] (35) is predicted to represent the global minimum on the potential‐energy surface.TU Berlin, Open-Access-Mittel – 2020DFG, 390540038, EXC 2008: Unifying Systems in Catalysis "UniSysCat

A quantum-mechanical study of the reaction mechanism of sulfite oxidase.

The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerisation reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site