Triesterase and Promiscuous Diesterase Activities of a Di‐CoII‐Containing Organophosphate Degrading Enzyme Reaction Mechanisms

The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐Co^II derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear Co^II center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.     

团簇CrPS4催化性质研究

为了探究团簇CrPS₄的催化反应活性,研究其在催化方面的潜能,本文根据拓扑学原理,利用密度泛函理论,采用B3LYP泛函和def2-tzvp基组,分析了该团簇16种稳定构型的贡献率、费米能级、能隙差、态密度等方面的数据,得出以下结论：在这16种构型中,构型5^（2）的能隙差最小,电子最容易发生跃迁。构型5^（2）和构型4^（2）的催化反应活性较强,值得深入研究。团簇CrPS₄失电子能力要略强于得电子能力,S对HOMO-LUMO轨道的贡献率最大,分别为66.98%和63.93%,Cr、P原子次之,S为此团簇潜在的反应活性位点。本文丰富了团簇CrPS₄在催化方面的研究内容,为以后的应用提供了理论基础。     

The Catalytic Mechanism of the Retaining Glycosyltransferase Mannosylglycerate Synthase

To protect their intracellular proteins, extremophile microorganisms synthesize molecules called compatible solutes. These molecules are the result of the attachment of a small negatively charged molecule to a sugar molecule. It has been found that these molecules, not only protect the microorganism against osmotic stress but also against other extreme conditions. They can also confer protection against extreme conditions to isolated enzymes from different organisms making them an exciting prospect for potential biotechnological applications. One of the most widespread compatible solute in hyperthermophile organisms is the molecule 2-O-α-D-mannosyl-D-glycerate (MG). In addition to confer protection to proteins against extreme conditions, MG was found to prevent Alzheimer's β-amyloid aggregation and reduce α-synuclein fibril formation in Parkinson's disease. In this work we studied, using computational methods, the catalytic mechanism of the synthesis of MG by the enzyme mannosylglycerate synthase (MGS) from the thermophilic bacteria Rhodothermus marinus.     

The Site‐Assembly Determines Catalytic Activity of Nanoparticles

Heterogeneous catalysts are often designed as metal nanoparticles supported on oxide surfaces. Here, the relation between particle morphology and reaction kinetics is investigated by scaling relation kinetic Monte Carlo simulations using CO oxidation over Pt nanoparticles as a model reaction. We find that different particle morphologies result in vastly different catalytic activities. The activity is strongly affected by kinetic couplings between sites, and a wide site distribution generally enhances the activity. The present study highlights the role of site‐assemblies as a concept that, in addition to isolated active sites, can be used to understand catalytic reactions over nanoparticles.     

烯酰基-辅酶A水合酶催化机理的理论研究

采用DFT方法研究了烯酰基-辅酶A （ECH）催化的4-（N,N-二甲氨基）-肉桂酰-辅酶A （DAC-CoA）和巴豆酰基-辅酶A （Crotonyl-CoA）水合反应.计算表明：水合反应以分步机理进行,经历一个烯醇负离子中间体.Glu164残基作为唯一的催化碱/酸参与水合反应,而Glu144虽然没有直接参与反应,但是它能通过氢键作用诱使水分子以合适的朝向活化底物.Crotonyl-CoA底物的水加成活性高于DAC-CoA.Ala98和Gly141与底物羰基之间的氢键作用既有利于底物的准确结合,也能有效稳定反应中形成的过渡态和中间体.另外,Glu144和Glu164周围的氢键网络对于合理维持活性位点排布进而有效促进底物活化也很重要.     

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1–2 kcal ⋅ mol⁻¹. Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal ⋅ mol⁻¹ and −6.3 to +3.8 kcal ⋅ mol⁻¹ depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. The results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.     

The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations

In order to elucidate the catalytic mechanism of the Mn–Mn containing serine/threonine protein phosphatase 5 (PP5), we present a density functional theory study with a cluster model approach. According to our results, the reaction occurs through an in‐line concerted transition state with an energy of 15.8 kcal mol^?1, and no intermediates are formed. The important role played by His304 and Asp274 as stabilizers of the leaving group has been shown, whereas the role played by the metal ions seems to be mostly electrostatic. The indispensable requirement of having a neutral active center has been demonstrated by testing different protonation states of the cluster model. We have shown also the importance of describing properly the electronic configuration of the Mn–Mn binuclear centers.     

The Catalytic Mechanism of Human Transketolase

We have computationally determined the catalytic mechanism of human transketolase (hTK) using a cluster model approach and density functional theory calculations. We were able to determine all the relevant structures, bringing solid evidences to the proposed experimental mechanism, and to add important detail to the structure of the transition states and the energy profile associated with catalysis. Furthermore, we have established the existence of a crucial intermediate of the catalytic cycle, in agreement with experiments. The calculated data brought new insights to hTK′s catalytic mechanism, providing free-energy values for the chemical reaction, as well as adding atomistic detail to the experimental mechanism.     

The Unexpected Mechanism Underlying the High‐Valent Mono‐Oxo‐Rhenium(V) Hydride Catalyzed Hydrosilylation of CN Functionalities: Insights from a DFT Study

In this study, we theoretically investigated the mechanism underlying the high‐valent mono‐oxo‐rhenium(V) hydride Re(O)HCl₂(PPh₃)₂ ( 1 ) catalyzed hydrosilylation of C?N functionalities. Our results suggest that an ionic S_N2‐Si outer‐sphere pathway involving the heterolytic cleavage of the Si?H bond competes with the hydride pathway involving the C?N bond inserted into the Re?H bond for the rhenium hydride ( 1 ) catalyzed hydrosilylation of the less steric C?N functionalities (phenylmethanimine, PhCH=NH, and N‐phenylbenzylideneimine, PhCH=NPh). The rate‐determining free‐energy barriers for the ionic outer‐sphere pathway are calculated to be ～28.1 and 27.6 kcal mol^?1, respectively. These values are slightly more favorable than those obtained for the hydride pathway (by ～1–3 kcal mol^?1), whereas for the large steric C?N functionality of N,1,1‐tri(phenyl)methanimine (PhCPh=NPh), the ionic outer‐sphere pathway (33.1 kcal mol^?1) is more favorable than the hydride pathway by as much as 11.5 kcal mol^?1. Along the ionic outer‐sphere pathway, neither the multiply bonded oxo ligand nor the inherent hydride moiety participate in the activation of the Si?H bond.     

The Mechanism of Copper-Catalyzed Trifunctionalization of Terminal Allenes

A highly selective copper-catalyzed trifunctionalization of allenes has been established based on diborylation/cyanation with bis(pinacolato)diboron (B₂pin₂) and N-cyano-N-phenyl-p-toluenesulfonamide (NCTS). The Cu-catalyzed trifunctionalization of terminal allenes is composed of three catalytic reactions (first borocupration, electrophilic cyanation, and second borocupration) that provide a densely functionalized product with regio-, chemo- and diastereoselectivity. Allene substrates have multiple reaction-sites, and the selectivities are determined by the suitable interactions (e.g., electronic and steric demands) between the catalyst and substrates. We employed DFT calculations to understand the cascade copper-catalyzed trifunctionalization of terminal allenes, providing densely-functionalized organic molecules with outstanding regio-, chemo- and diastereoselectivity in high yields. The selectivity challenges presented by cumulated π-systems are addressed by systematic computational studies; these give insight to the catalytic multiple-functionalization strategies and explain the high selectivities that we see for these reactions.     

DFT Calculations Suggest a New Type of Self‐Protection and Self‐Inhibition Mechanism in the Mammalian Heme Enzyme Myeloperoxidase: Nucleophilic Addition of a Functional Water rather than One‐Electron Reduction

The mammalian heme enzyme myeloperoxidase (MPO) catalyzes the reaction of Cl^? to the antimicrobial‐effective molecule HOCl. During the catalytic cycle, a reactive intermediate “Compound I” (Cpd I) is generated. Cpd I has the ability to destroy the enzyme. Indeed, in the absence of any substrate, Cpd I decays with a half‐life of 100 ms to an intermediate called Compound II (Cpd II), which is typically the one‐electron reduced Cpd I. However, the nature of Cpd II, its spectroscopic properties, and the source of the additional electron are only poorly understood. On the basis of DFT and time‐dependent (TD)‐DFT quantum chemical calculations at the PBE0/6‐31G* level, we propose an extended mechanism involving a new intermediate, which allows MPO to protect itself from self‐oxidation or self‐destruction during the catalytic cycle. Because of its similarity in electronic structure to Cpd II, we named this intermediate Cpd II′. However, the suggested mechanism and our proposed functional structure of Cpd II′ are based on the hypothesis that the heme is reduced by charge separation caused by reaction with a water molecule, and not, as is normally assumed, by the transfer of an electron. In the course of this investigation, we found a second intermediate, the reduced enzyme, towards which the new mechanism is equally transferable. In analogy to Cpd II′, we named it Fe^II′. The proposed new intermediates Cpd II′ and Fe^II′ allow the experimental findings, which have been well documented in the literature for decades but not so far understood, to be explained for the first time. These encompass a) the spontaneous decay of Cpd I, b) the unusual (chlorin‐like) UV/Vis, circular dichroism (CD), and resonance Raman spectra, c) the inability of reduced MPO to bind CO, d) the fact that MPO‐Cpd II reduces SCN^? but not Cl^?, and e) the experimentally observed auto‐oxidation/auto‐reduction features of the enzyme. Our new mechanism is also transferable to cytochromes, and could well be viable for heme enzymes in general.     

Unsymmetrical Binding Modes of the HOPNO Inhibitor of Tyrosinase: From Model Complexes to the Enzyme

The deciphering of the binding mode of tyrosinase (Ty) inhibitors is essential to understand how to regulate the tyrosinase activity. In this paper, by combining experimental and theoretical methods, we studied an unsymmetrical tyrosinase functional model and its interaction with 2‐hydroxypyridine‐N‐oxide (HOPNO), a new and efficient competitive inhibitor for bacterial Ty. The tyrosinase model was a dinuclear copper complex bridged by a chelated ring with two different complexing arms (namely (bis(2‐ethylpyridyl)amino)methyl and (bis(2‐methylpyridyl)amino)methyl). The geometrical asymmetry of the complex induces an unsymmetrical binding of HOPNO. Comparisons have been made with the binding modes obtained on similar symmetrical complexes. Finally, by using quantum mechanics/molecular mechanics (QM/MM) calculations, we studied the binding mode in tyrosinase from a bacterial source. A new unsymmetrical binding mode was obtained, which was linked to the second coordination sphere of the enzyme.     

On the Mechanism of Au-Catalyzed Enynamide-yne Dehydro-Diels-Alder Reactions: An Experimental and Computational Study

Gold-catalyzed dehydro-Diels-Alder reactions of ynamide derivatives allow efficient access to a variety of N-containing aromatic heterocycles. A dual gold catalysis mechanism was postulated for transformations involving the formation of C−C bonds by reaction between a terminal alkyne and an enynamide fragment. In this article, complete experimental and computational investigations into the mechanism of such a transformation are reported. Support for a dual gold catalysis was found and it was shown that the concerted or stepwise nature of the cyclization event depends on the substitution of the ynamide moiety. The reaction was found to proceed in three stages: 1) formation of a σ,π-digold complex from the terminal alkyne, 2) cyclization to produce a gem-diaurated aryl complex, and 3) catalyst transfer to free the product and regenerate the σ,π-digold complex.     

Catalytic Activities of Au6, , and Clusters for CO oxidation: A density functional study

We have studied the CO oxidation over neutral, anionic, and cationic gold hexamer clusters using density functional theory which elucidates the effect of cluster charge state on the catalytic activity. Herein, we have considered the conventional bimolecular Langmuir–Hinshelwood mechanism with coadsorbed CO and O₂ at the neighboring sites in all the clusters. Among the three clusters, entails lower barriers during the various steps of the oxidation mechanism. The stability of all the species including the transition states with respect to the interacting species in indicates no thermal activation. Our study suggests better catalytic activity of as compared to the neutral and cationic counterparts. © 2014 Wiley Periodicals, Inc.     

Experimental and Computational Evidence for the Mechanism of Intradiol Catechol Dioxygenation by Non‐Heme Iron(III) Complexes

Catechol intradiol dioxygenation is a unique reaction catalyzed by iron‐dependent enzymes and non‐heme iron(III) complexes. The mechanism by which these systems activate dioxygen in this important metabolic process remains controversial. Using a combination of kinetic measurements and computational modelling of multiple iron(III) catecholato complexes, we have elucidated the catechol cleavage mechanism and show that oxygen binds the iron center by partial dissociation of the substrate from the iron complex. The iron(III) superoxide complex that is formed subsequently attacks the carbon atom of the substrate by a rate‐determining C?O bond formation step.     

Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study

Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.     

How Absorbed Hydrogen Affects the Catalytic Activity of Transition Metals

Heterogeneous catalysis is commonly governed by surface active sites. Yet, areas just below the surface can also influence catalytic activity, for instance, when fragmentation products of catalytic feeds penetrate into catalysts. In particular, H absorbed below the surface is required for certain hydrogenation reactions on metals. Herein, we show that a sufficient concentration of subsurface hydrogen, H^sub, may either significantly increase or decrease the bond energy and the reactivity of the adsorbed hydrogen, H^ad, depending on the metal. We predict a representative reaction, ethyl hydrogenation, to speed up on Pd and Pt, but to slow down on Ni and Rh in the presence of H^sub, especially on metal nanoparticles. The identified effects of subsurface H on surface reactivity are indispensable for an atomistic understanding of hydrogenation processes on transition metals and interactions of hydrogen with metals in general.     

Reaction mechanism of molybdoenzyme formate dehydrogenase

Formate dehydrogenase is a molybdoenzyme of the anaerobic formate hydrogen lyase complex of the Escherichia coli microorganism that catalyzes the oxidation of formate to carbon dioxide. The two proposed mechanisms of reaction, which differ in the occurrence of a direct coordination or not of a SeCys residue to the molybdenum metal during catalysis were analyzed at the density functional level in both vacuum and protein environments. Some DF functionals, in addition to the very popular B3LYP one, were employed to compute barrier heights. Results revealed the role played by the SeCys residue in performing the abstraction of the proton from the formate substrate. The computation of the energetic profiles for both mechanisms indicated that the reaction barriers are higher when the selenium is directly coordinated to the metal, whereas less energy is required when SeCys is not a ligand at the molybdenum site.