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.     

Nucleophilic Substitution at Tricoordinate Sulfur—Alkaline Hydrolysis of Optically Active Dialkoxysulfonium Salts: Stereochemistry,Mechanism and Reaction Energetics

Optically active dialkoxyisopropylsulfonium salts were obtained by methylation (ethylation) of optically active alkyl isopropanesulfinates using methyl (ethyl) trifluoromethanesulfonate. Alkaline hydrolysis of a series of methoxy(alkoxy)sulfonium salts afforded the two sulfinate products methyl isopropanesulfinate and alkyl isopropanesulfinate, both formed with a slightly prevailing inversion of configuration at the sulfur atom. DFT calculations revealed that this substitution reaction proceeded stepwise according to an addition-elimination (A–E) mechanism involving the formation of high tetracoordinate S^IV sulfurane intermediates. In addition, the DFT calculations showed that recombination of the hydroxy anion with the methoxy(alkoxy)sulfonium cation—leading to the parallel formation of the two most stable primary sulfuranes, with the hydroxy and alkoxy groups in apical positions and their direct decomposition—is the most energetically favorable pathway.     

Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies

Phosphate monoester and anhydride hydrolysis is ubiquitous in biology, being involved in, amongst other things, signal transduction, energy production, and the regulation of protein function. Therefore, this reaction has understandably been the focus of intensive research. Nevertheless, the precise mechanism by which phosphate monoester hydrolysis proceeds remains controversial. Traditionally, it has been assumed and frequently implied that a near‐zero activation entropy is indicative of a dissociative pathway. Herein, we examine free‐energy surfaces for the hydrolysis of the methyl phosphate dianion and the methyl pyrophosphate trianion in aqueous solution. In both cases, the reaction can proceed through either compact or expansive concerted (A_ND_N) transition states, with fairly similar barriers. We have evaluated the activation entropies for each transition state and demonstrate that both associative and dissociative transition states have near‐zero entropies of activation that are in good agreement with experimental values. Therefore, we believe that the activation entropy alone is not a useful diagnostic tool, as it depends not only on bond orders at the transition state, but also on other issues that include (but are not limited to) steric factors determining the configurational volumes available to reactants during the reaction, solvation and desolvation effects that may be associated with charge redistribution upon approaching the transition state and entropy changes associated with intramolecular degrees of freedom as the transition state is approached.     

Reaction Mechanism for the Dual Gold‐Catalyzed Synthesis of Dibenzopentalene: A DFT Study

A wide range of gold‐catalyzed reactions based on a dual activation mechanism has recently been reported in the literature. Herein, we present a computational investigation of the mechanism for the formation of dibenzopentalenes from 1‐ethynyl‐2‐(phenylethynyl)benzene. Transition states have been found, which substantiate the dual activation mechanism previously published and furthermore point towards a continuous presence of two gold moieties throughout the mechanistic cycle, an observation of high importance for all reactions in the field of dual activation. The initial activation of the diyne has been shown to proceed via an intermolecular transfer of a cationic gold catalyst from the thermodynamically preferred geminal‐σ,π‐acetylide complex to the active non‐geminal analogue. Furthermore, the regioselectivity of a 5‐endo versus a 6‐endo cyclization has been addressed, and the 5‐endo cyclization was found to be most favorable both thermodynamically and with regard to the activation barrier.     

异双核配合物金属胶束模拟磷酸酯酶催化磷酸单酯水解

 合成和表征了四种含过渡金属离子Cu(Ⅱ)和Ni(Ⅱ)的草酰胺桥联异双核配合物,并将这些配合物与Brij35表面活性剂胶束构成金属胶束作为金属水解酶模拟物用于催化对硝基苯酚磷酸单酯(NPP)水解. 研究了金属胶束对NPP水解反应的催化机理,建立了异双核配合物催化NPP水解的动力学数学模型. 结果表明,四种草酰胺桥联异双核配合物在NPP水解反应中表现出较高的催化活性,随着胶束溶液pH的增大,配合物催化NPP水解的速率提高. 配合物中的两个金属离子在催化NPP水解过程中表现出较好的协同效应.     

Multinuclear Diffusion NMR Spectroscopy and DFT Modeling: A Powerful Combination for Unraveling the Mechanism of Phosphoester Bond Hydrolysis Catalyzed by Metal‐Substituted Polyoxometalates

A detailed reaction mechanism is proposed for the hydrolysis of the phosphoester bonds in the DNA model substrate bis(4‐nitrophenyl) phosphate (BNPP) in the presence of the Zr^IV‐substituted Keggin type polyoxometalate (Et₂NH₂)₈[{α‐PW₁₁O₃₉Zr(μ‐OH) (H₂O)}₂] ? 7 H₂O (ZrK 2:2) at pD 6.4. Low‐temperature ³¹P DOSY spectra at pD 6.4 gave the first experimental evidence for the presence of ZrK 1:1 in fast equilibrium with ZrK 2:2 in purely aqueous solution. Moreover, theoretical calculations identified the ZrK 1:1 form as the potentially active species in solution. The reaction intermediates involved in the hydrolysis were identified by means of ¹H/³¹P NMR studies, including EXSY and DOSY NMR spectroscopy, which were supported by DFT calculations. This experimental/theoretical approach enabled the determination of the structures of four intermediate species in which the starting compound BNPP, nitrophenyl phosphate (NPP), or the end product phosphate (P) is coordinated to ZrK 1:1. In the proposed reaction mechanism, BNPP initially coordinates to ZrK 1:1 in a monodentate fashion, which results in hydrolysis of the first phosphoester bond in BNPP and formation of NPP. EXSY NMR studies showed that the bidentate complex between NPP and ZrK 1:1 is in equilibrium with monobound and free NPP. Subsequently, hydrolysis of NPP results in P, which is in equilibrium with its monobound form.     

Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′‐Phosphate in Ornithine 4,5‐Aminomutase

A computational study was performed on the experimentally elusive cyclisation step in the cofactor pyridoxal 5′‐phosphate (PLP)‐dependent D ‐ornithine 4,5‐aminomutase (OAM)‐catalysed reaction. Calculations using both model systems and a combined quantum mechanics/molecular mechanics approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor PLP and the active site of the enzyme. The captodative effect of PLP is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff‐base nitrogen atom (N2). Furthermore, electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial “strain” energy on the orientation of the cyclic intermediate to control its trajectory. In addition the “strain” energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state. Our results provide new insights into several aspects of the radical mechanism in aminomutase catalysis and broaden our understanding of cofactor PLP‐dependent reactions.     

Turn‐On Colorimetric Platform for Dual Activity Detection of Acid and Alkaline Phosphatase in Human Whole Blood

The activity detection of acid phosphatase (ACP) and alkaline phosphatase (ALP) is of great importance to the diagnosis and prognosis of related diseases. In this work, we report for the first time a turn‐on colorimetric platform for the activity detection of ACP and ALP, by exploiting Cu(BCDS)₂^2? (BCDS=bathocuproinedisulfonate) as the probe. The presence of ACP or ALP dephosphorylates the substrate ascorbic acid 2‐phosphate to produce ascorbic acid, which then reduces Cu(BCDS)₂^2? into Cu(BCDS)₂^3?, leading to a turn‐on spectral absorption at 484 nm and a dramatic color change of the solution from colorless to orange‐red. The underlying metal‐to‐ligand charge‐transfer mechanism has been demonstrated by quantum mechanical computations. This platform allows a rapid, sensitive readout of ACP and ALP activities within the dynamic range from 0 to 220 mU ml^?1. In addition, it is highly immune to false‐positive results and also highly selective. More importantly, it is applicable in the presence of human serum and even whole blood samples. These results demonstrate that our platform holds great potential in clinical practices and in the point‐of‐care analysis.     

Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism

The methylation of Hg^II(SCH₃)₂ by corrinoid‐based methyl donors proceeds in a concerted manner through a single transition state by transfer of a methyl radical, in contrast to previously proposed reaction mechanisms. This reaction mechanism is a consequence of relativistic effects that lower the energies of the mercury 6p_1/2 and 6p_3/2 orbitals, making them energetically accessible for chemical bonding. In the absence of spin–orbit coupling, the predicted reaction mechanism is qualitatively different. This is the first example of relativity being decisive for the nature of an observed enzymatic reaction mechanism.     

Mechanism of the Aerobic Homocoupling of Phenylboronic Acid on Au20−: A DFT Study

The mechanism of the gold nanocluster‐catalyzed aerobic homocoupling of arylboronic acids has been elucidated by means of DFT calculations with Au₂₀^? as a model cluster for the Au:[poly(N‐vinylpyrrolidin‐2‐one)] catalyst. We found that oxygen affects the adsorption of phenylboronic acid and, by lowering the energy barrier, a water molecule enhances dissociation of the C?B bond, which is probably the rate‐determining step. The key role of oxygen is in activating the surface of the gold cluster by generating Lewis acidic sites for adsorption and activation of the phenylboronic acid, leading to the formation of biphenyl through a superoxo‐like species. Moreover, the oxygen adsorbed on the Au nanocluster can act as an oxidant for phenylboronic acid, giving phenol as a byproduct. As shown by NBO analysis, the basic aqueous reaction medium facilitates the reductive elimination process by weakening the Au?C bond, thereby enhancing the formation of biphenyl. The coupling of phenyl and reductive elimination of biphenyl occur at the top or facet site with low‐energy‐barrier through spillover of phenyl group on Au NC. The present findings are useful for the interpretation or design of other coupling reactions with Au NC.     

The Reaction Pathway of Cellulose Pyrolysis to a Multifunctional Chiral Building Block: The Role of Water Unveiled by a DFT Computational Investigation

LAC (hydroxylactone (1R,5S)‐1‐hydroxy‐3,6‐dioxabicyclo[3.2.1]octan‐2‐one) is one of the most interesting products of the pyrolysis of cellulose and represents a useful chiral building block in organic synthesis. A computational investigation at the DFT level on the mechanism of formation of LAC shows that this species can be obtained following two reaction paths, path A and path B , starting from a well‐known pyrolysis product (ascopyrone P). A series of internal rearrangements involving in all cases a proton transfer leads directly to LAC ( path B ). An alternative path ( path A ) can be also followed. From this path, via a “gate” connecting the two reaction channels, it is possible to reach path B and form LAC. In both cases, the rate‐determining step of the process is the initial keto‐enol isomerization. We found that water, which is present in the reaction mixture, “catalyzes” the reaction by assisting the proton transfers present in all the steps of the process. In particular, water lowers the barrier of the rate‐determining step that becomes 40.9 kcal mol^?1 (79.4 kcal mol^?1 in the absence of water). The corresponding computed rate constant is 4.3×10 s^?1 at 500 °C, a value which is consistent with the presence of LAC in the absence of metal catalysts. The results of this study on the non‐catalyzed process underpin the important role played by water in the formation of pyrolysis products of cellulose where proton transfer is a key mechanistic step.     

DFT Study of the Molybdenum‐Catalyzed Deoxydehydration of Vicinal Diols

The mechanism of the molybdenum‐catalyzed deoxydehydration (DODH) of vicinal diols has been investigated using density functional theory. The proposed catalytic cycle involves condensation of the diol with an Mo^VI oxo complex, oxidative cleavage of the diol resulting in an Mo^IV complex, and extrusion of the alkene. We have compared the proposed pathway with several alternatives, and the results have been corroborated by comparison with the molybdenum‐catalyzed sulfoxide reduction recently published by Sanz et al. and with experimental observations for the DODH itself. Improved understanding of the mechanism should expedite future optimization of molybdenum‐catalyzed biomass transformations.     

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.     

新型金属胶束模拟酶对羧酸酯与磷酸酯的催化水解

报道了三种新的含醇羟基、胺基或咪唑基长链配体与铜锌离子构成的金属胶束对几种羧酸酯与磷酸酯底物催化水解动力学。结果表明,设计的金属胶束N-十四烷基-2-(N-2'-羟乙基氨基甲基)咪唑锌铜(2a,2b)在共胶束CTAB(溴化十六烷基三甲铵)存在下,对强配位羧酸酯对硝基苯酚-2-吡啶甲酸酯具有很强的催化水解能力,对磷酸酯对硫磷具有很高的反应性,2a,2b的醇羟基参与了对弱配位底物羧酸酯及磷酸酯的进攻,对不同电荷性质的羧酸酯底物具有较强的静电选择性。     

Mechanism of the Tyrosine Ammonia Lyase Reaction—Tandem Nucleophilic and Electrophilic Enhancement by a Proton Transfer

Quantum mechanics/molecular mechanics calculations in tyrosine ammonia lyase (TAL) ruled out the hypothetical Friedel–Crafts (FC) route for ammonia elimination from L ‐tyrosine due to the high energy of FC intermediates. The calculated pathway from the zwitterionic L ‐tyrosine‐binding state (0.0 kcal mol^?1) to the product‐binding state ((E)‐coumarate+H₂N? MIO; ?24.0 kcal mol^?1; MIO=3,5‐dihydro‐5‐methylidene‐4H‐imidazol‐4‐one) involves an intermediate (IS, ?19.9 kcal mol^?1), which has a covalent bond between the N atom of the substrate and MIO, as well as two transition states (TS1 and TS2). TS1 (14.4 kcal mol^?1) corresponds to a proton transfer from the substrate to the N1 atom of MIO by Tyr300? OH. Thus, a tandem nucleophilic activation of the substrate and electrophilic activation of MIO happens. TS2 (5.2 kcal mol^?1) indicates a concerted C? N bond breaking of the N‐MIO intermediate and deprotonation of the pro‐S β position by Tyr60. Calculations elucidate the role of enzymic bases (Tyr60 and Tyr300) and other catalytically relevant residues (Asn203, Arg303, and Asn333, Asn435), which are fully conserved in the amino acid sequences and in 3D structures of all known MIO‐containing ammonia lyases and 2,3‐aminomutases.     

Hydrogen Release from Dialkylamine–Boranes Promoted by Mg and Ca Complexes: A DFT Analysis of the Reaction Mechanism

Mg and Ca β‐diketiminato silylamides [HC{(Me)CN(2,6‐iPr₂C₆H₃)}₂M(THF)_n{N(SiMe₃)₂}] (M=Mg, n=0; M=Ca, n=1) were studied as precatalysts for the dehydrogenation/dehydrocoupling of secondary amine–boranes R₂HNBH₃. By reaction with equimolar quantities of amine–boranes, the corresponding amidoborane derivatives are formed, which further react to yield dehydrogenation products such as the cyclic dimer [BH₂?NMe₂]₂. DFT was used here to explore the mechanistic alternatives proposed on the basis of the experimental findings for both Mg and Ca amidoboranes. The influence of the steric demand of amine–boranes on the course of the reaction was examined by performing calculations on the dehydrogenation of dimethylamine–borane (DMAB), pyrrolidine–borane (PB), and diisopropylamine–borane. In spite of the analogies in the catalytic activity of Mg‐ and Ca‐based complexes in the dehydrocoupling of amine–boranes, our theoretical analysis confirmed the experimentally observed lower reactivity of Ca complexes. Differences in catalytic activity of Mg‐ and Ca‐based complexes were examined and rationalized. As a consequence of the increase in ionic radius on going from Mg²⁺ to Ca²⁺, the dehydrogenation mechanism changes and formation of a key metal hydride intermediate becomes inaccessible. Dimerization is likely to occur off‐metal in solution for DMAB and PB, whereas steric hindrance of iPr₂NHBH₃ hampers formation of the cyclic dimer. The reported results are of particular interest because, although amine–borane dehydrogenation is now well established, mechanistic insight is still lacking for many systems.     

Exploring 2-Tetradecanoylimino-3-aryl-4-methyl-1,3-thiazolines Derivatives as Alkaline Phosphatase Inhibitors: Biochemical Evaluation and Computational Analysis

The current study focused on the laboratory approach in conjunction with computational methods for the synthesis and bioactivity assessment of unique 2-tetradecanoylimino-3-aryl-4-methyl-1,3-thiazolines (2a–2k). Processes included cyclizing 1-aroyl-3-arylthioureas with propan-2-one in the presence of trimethylamine and bromine. By using spectroscopic techniques and elemental analyses, structures were elucidated. To assess the electronic properties, density functional theory (DFT) calculations were made, while binding interactions of synthesized derivatives were studied by the molecular docking tool. Promising results were found during the evaluation of bioactivity of synthesized compounds against alkaline phosphatase. The drug likeliness score, an indicator used for any chemical entity posing as a drug, was within acceptable limits. The data suggested that most of the derivatives were potent inhibitors of alkaline phosphatase, which in turn may act as lead molecules to synthesize derivatives having desired pharmacological profiles for the treatment of specific diseases associated with abnormal levels of ALPs.     

The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase

Atomic‐level portrait : The mechanism of the reaction catalyzed by the puzzling enzyme farnesyltransferase is elucidated by using computational methods, allowing the obtainment of the first real detailed atomistic quantum‐chemical transition‐state structure (see figure) for the reaction catalyzed by this enzyme. The results obtained provide an atomic‐level framework for the design of more potent and specific inhibitors for this important enzyme.

     

Mechanism of Thyroxine Deiodination by Naphthyl‐Based Iodothyronine Deiodinase Mimics and the Halogen Bonding Role: A DFT Investigation

This paper deals with a systematic density functional theory (DFT) study aiming to unravel the mechanism of the thyroxine (T4) conversion into 3,3′,5‐triiodothyronine (rT3) by using different bio‐inspired naphthyl‐based models, which are able to reproduce the catalytic functions of the type‐3 deiodinase ID‐3. Such naphthalenes, having two selenols, two thiols, and a selenol–thiol pair in peri positions, which were previously synthesized and tested in their deiodinase activity, are able to remove iodine selectively from the inner ring of T4 to produce rT3. Calculations were performed including also an imidazole ring that, mimicking the role of the His residue, plays an essential role deprotonating the selenol/thiol moiety. For all the used complexes, the calculated potential energy surfaces show that the reaction proceeds via an intermediate, characterized by the presence of a X?I?C (X=Se, S) halogen bond, whose transformation into a subsequent intermediate in which the C?I bond is definitively cleaved and the incipient X?I bond is formed represents the rate‐determining step of the whole process. The calculated trend in the barrier heights of the corresponding transition states allows us to rationalize the experimentally observed superior deiodinase activity of the naphthyl‐based compound with two selenol groups. The role of the peri interactions between chalcogen atoms appears to be less prominent in determining the deiodination activity.     

NH3 Synthesis in the N2/H2 Reaction System using Cooperative Molecular Tungsten/Rhodium Catalysis in Ionic Hydrogenation: A DFT Study

The ionic hydrogenation of N₂ with H₂ to give NH₃ is investigated by means of density functional theory (DFT) computations using a cooperatively acting catalyst system. In this system, N₂ binds to a neutral tungsten pincer complex of the type [(PNP)W(N₂)₃] (PNP=pincer ligand) and is reduced to NH₃. The protons and hydride centers necessary for the reduction are delivered by heterolytic cleavage of H₂ between the N₂–tungsten complex and the cationic rhodium complex [Cp*Rh{2‐(2‐pyridyl)phenyl}(CH₃CN)]⁺. Successive transfer of protons and hydrides to the bound N₂, as well as all N_xH_y units that occur during the reaction, enable the computation of closed catalytic cycles in the gas and in the solvent phase. By optimizing the pincer ligands of the tungsten complex, energy spans as low as 39.3 kcal mol^?1 could be obtained, which is unprecedented in molecular catalysis for the N₂/H₂ reaction system.