Evolution of function in the crotonase superfamily: the stereochemical course of the reaction catalyzed by 2-ketocyclohexanecarboxyl-CoA hydrolase

Members of the mechanistically diverse enoyl-CoA hydratase (crotonase) superfamily catalyze reactions that involve stabilization of an enolate anion derived from an acyl thioester of coenzyme A. 2-Ketocyclohexanecarboxyl-CoA hydrolase (BadI), found in a pathway for anaerobic degradation of benzoate by Rhodopseudomonas palustris, is a member of the crotonase superfamily that catalyzes a reverse Dieckmann reaction in which the substrate is hydrolyzed to pimelyl-CoA. The substrate is the configurationally labile 2S-ketocyclohexanecarboxyl-CoA, and in 2H2O solvent hydrogen is incorporated into the 2-proS position of the pimelyl-CoA product. Therefore, the stereochemical course of the BadI-catalyzed reaction is inversion. This information is important for understanding the roles of active-site functional groups in the active site of BadI as well as in the active sites of the homologous 1,4-dihydroxynaphthoyl-CoA synthases that catalyze a forward Dieckmann reaction.     

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

Ab initio and density functional theory studies of the catalytic mechanism for ester hydrolysis in serine hydrolases

We present results from ab initio and density functional theory studies of the mechanism for serine hydrolase catalyzed ester hydrolysis. A model system containing both the catalytic triad and the oxyanion hole was studied. The catalytic triad was represented by formate anion, imidazole, and methanol. The oxyanion hole was represented by two water molecules. Methyl formate was used as the substrate. In the acylation step, our computations show that the cooperation of the Asp group and oxyanion hydrogen bonds is capable of lowering the activation barrier by about 15 kcal/mol. The transition state leading to the first tetrahedral intermediate in the acylation step is rate limiting with an activation barrier (ΔE₀) of 13.4 kcal/mol. The activation barrier in the deacylation step is smaller. The double-proton-transfer mechanism is energetically unfavorable by about 2 kcal/mol. The bonds between the Asp group and the His group, and the hydrogen bonds in the oxyanion hole, increase in strength going from the Michaelis complex toward the transition state and the tetrahedral intermediate. In the acylation step, the tetrahedral intermediate is a very shallow minimum on the energy surface and is not viable when molecular vibrations are included. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 89–103, 1998     

Discussion of the catalytic pathway of cysteine proteases based on AM1 calculations

The deacylation reaction of the cysteine protease papain was examined by AM1 reaction-coordinate calculations. The transition-state (TS) structure was extracted from the reaction pathway as corresponding to the maximum point along this minimum-energy pathway. Consistent with experimental kinetic data revealing that deacylation is about 60 times faster for thioester (---C(O)---S---) than dithioester (---C(S)---S---) intermediates, calculated E_a values are about 10 kcal mol⁻¹ lower for the former than the latter. The calculated partial atomic charges indicate that the C=O carbon in the thioester is a good site for nucleophilic attack whereas the corresponding C=S carbon in the dithioester is a poor site. The present calculations reveal that the enzyme's oxyanion hole contributes about 9 kcal mol⁻¹ toward reducing E_a for the anionic tetrahedral intermediate and TS structure. On the other hand, the presence of Asn in the putative Asn-His-Cys catalytic triad contributes only about l kcal mol⁻¹ toward reducing their E_a value. The presence of this Asn, however, did appear to stabilize His in its protonated form (ImH⁺) over its unprotonated form (Im). Two novel mechanisms are introduced to explain the unusual effect of a remote X substituent on the deacylation kinetics of the substrate family under consideration. The first mechanism invokes a “field effect” while the second mechanism embodies the concepts of induction and homoconjugation. The unique feature of these two mechanisms is that, unlike other proposed models, they circumvent the requirement for a close N…S interaction which has stimulated controversy.     

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K

Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.     

两价钯催化下烯醇钯中间体和亲电试剂的反应研究

根据在两价钯催化的亲核试剂－炔烃－α,β-不饱和羰基化合物的串联加成反应中所假设的烯醇钯中间体的机理,研究了炔酸烯丙酯化合物1和亲电试剂在两价钯催化下的反应。使用乙酰氮作为亲电试剂得到了β－乙酰氧基烯基－γ－丁丙酯3,这一结果为烯醇钯中间体的机理提供了一个实验证据。     

Semiempirical Molecular Orbital Studies of the Acylation Step in the Lipase‐Catalyzed Ester Hydrolysis

In this study, we present the results from the semiempirical molecular orbital calculations for the acylation step in the lipase‐catalyzed ester hydrolysis. The results reveal that the lowest energy path for the formation of the tetrahedral intermediate is for the serine residue of the catalytic triad to attack the substrate, followed by coupling heavy atom movement and proton transfer. The calculations of four active site models show that the cooperation of the aspartate group and the oxyanion hole is capable of lowering the activation energy by about 16 kcalmol^?1. Our results further suggest that the lipase‐catalyzed ester hydrolysis adopts the single proton transfer mechanism.     

Mass spectrometric interrogation of thioester-bound intermediates in the initial stages of epothilone biosynthesis

Direct detection of thioester intermediate mixtures bound to EpoC, a 195 kDa polyketide synthase, has been achieved using limited proteolysis and Fourier-transform mass spectrometry (FTMS). Incubation with various N-acetylcysteamine thioester (S-NAC) substrate mimics produced mass shifts on the EpoC ACP domain consistent with their condensation with an enzyme-bound carbanion produced by the decarboxylation of methylmalonyl-S-EpoC. Reconstitution of EpoA-ACP, EpoB, and EpoC gave a +165.0 Da mass shift consistent with the formation of the methylthiazolyl-methacrylyl product by incorporation of acetyl-CoA, cysteine, and methylmalonyl-CoA. Thioester-templated reaction intermediates and products are typically characterized by quantifying radioactive substrates, either enzyme bound or chemically hydrolyzed. In contrast, the MS-based methodology described here provides semiquantifiable ratios of free enzyme, intermediate, and product occupancy and reveals that certain substrates result in a >50% formation of nonproductive intermediates.     

Diastereoselective Total Synthesis of (±)‐Schindilactone A,Part 3: The Final Phase and Completion

The final phase for the total synthesis of (±)‐schindilactone A ( 1 ) is described herein. Two independent synthetic approaches were developed that featured Pd–thiourea‐catalyzed cascade carbonylative annulation reactions to construct intermediate 3 and a RCM reaction to make intermediate 4 . Other important steps that enabled the completion of the synthesis included: 1) A Ag‐mediated ring‐expansion reaction to form vinyl bromide 17 from dibromocyclopropane 30 ; 2) a Pd‐catalyzed coupling reaction of vinyl bromide 17 with a copper enolate to synthesize ketoester 16 ; 3) a RCM reaction to generate oxabicyclononenol 10 from diene 11 ; 4) a cyclopentenone fragment in substrate 8 was constructed through a Co–thiourea‐catalyzed Pauson–Khand reaction (PKR); 5) a Dieckmann‐type condensation to successfully form the A ring of schindilactone A ( 1 ). The chemistry developed for the total synthesis of schindilactone A ( 1 ) will shed light on the synthesis of other family members of schindilactone A.     

Michael addition of stannyl ketone enolate to alpha,beta-unsaturated esters catalyzed by tetrabutylammonium bromide and an ab initio theoretical study of the reaction course

Michael addition of stannyl ketone enolates to alpha,beta-unsaturated esters was accomplished in the presence of a catalytic amount of tetrabutylammonium bromide (Bu(4)NBr). Other typical systems using lithium enolate or silyl enolate with catalysts (TiCl(4) or Bu(4)NF) failed to give the desired products. The bromide anion from Bu(4)NBr coordinates to the tin center in enolate to accelerate the conjugate addition where a five-coordinated tin species was generated. The coordination of the bromide anion significantly raises the HOMO level of tin enolate and enhances its nucleophilicity. The conjugate addition provides the intermediate Michael adduct, which has an ester enolate moiety, and the adduct immediately transforms to alpha-stannyl gamma-ketoester by keto-enol tautomerization. This step contributes to the stabilization of the product system and leads to a thermodynamically favorable reaction course. An ab initio calculation reveals that the activation energy in the reaction using the bromide anion is lower than that of the reaction without using it. The transition state in either reaction course has a linear structure, not a cyclic one. This system can be applied to a variety of tin enolates and alpha,beta-unsaturated carbonyls involving enoates, enones, and unsaturated amides.     

Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin

Understanding the mechanisms by which beta-lactamases destroy beta-lactam antibiotics is potentially vital in developing effective therapies to overcome bacterial antibiotic resistance. Class A beta-lactamases are the most important and common type of these enzymes. A key process in the reaction mechanism of class A beta-lactamases is the acylation of the active site serine by the antibiotic. We have modeled the complete mechanism of acylation with benzylpenicillin, using a combined quantum mechanical and molecular mechanical (QM/MM) method (B3LYP/6-31G+(d)//AM1-CHARMM22). All active site residues directly involved in the reaction, and the substrate, were treated at the QM level, with reaction energies calculated at the hybrid density functional (B3LYP/6-31+Gd) level. Structures and interactions with the protein were modeled by the AM1-CHARMM22 QM/MM approach. Alternative reaction coordinates and mechanisms have been tested by calculating a number of potential energy surfaces for each step of the acylation mechanism. The results support a mechanism in which Glu166 acts as the general base. Glu166 deprotonates an intervening conserved water molecule, which in turn activates Ser70 for nucleophilic attack on the antibiotic. This formation of the tetrahedral intermediate is calculated to have the highest barrier of the chemical steps in acylation. Subsequently, the acylenzyme is formed with Ser130 as the proton donor to the antibiotic thiazolidine ring, and Lys73 as a proton shuttle residue. The presented mechanism is both structurally and energetically consistent with experimental data. The QM/MM energy barrier (B3LYP/ 6-31G+(d)//AM1-CHARMM22) for the enzymatic reaction of 9 kcal mol(-1) is consistent with the experimental activation energy of about 12 kcal mol(-1). The effects of essential catalytic residues have been investigated by decomposition analysis. The results demonstrate the importance of the "oxyanion hole" in stabilizing the transition state and the tetrahedral intermediate. In addition, Asn132 and a number of charged residues in the active site have been identified as being central to the stabilizing effect of the enzyme. These results will be potentially useful in the development of stable beta-lactam antibiotics and for the design of new inhibitors.     

Aerobic oxidation of methanol to formic acid on Au20-: a theoretical study on the reaction mechanism

The aerobic oxidation of methanol to formic acid catalyzed by Au(20)(-) has been investigated quantum chemically using density functional theory with the M06 functional. Possible reaction pathways are examined taking account of full structure relaxation of the Au(20)(-) cluster. The proposed reaction mechanism consists of three elementary steps: (1) formation of formaldehyde from methoxy species activated by a superoxo-like anion on the gold cluster; (2) nucleophilic addition by the hydroxyl group of a hydroperoxyl-like complex to formaldehyde resulting in a hemiacetal intermediate; and (3) formation of formic acid by hydrogen transfer from the hemiacetal intermediate to atomic oxygen attached to the gold cluster. A comparison of the computed energetics of various elementary steps indicates that C-H bond dissociation of the methoxy species leading to formation of formaldehyde is the rate-determining step. A possible reaction pathway involving single-step hydrogen abstraction, a concerted mechanism, is also discussed. The stabilities of reactants, intermediates and transition state structures are governed by the coordination number of the gold atoms, charge distribution, cooperative effect and structural distortion, which are the key parameters for understanding the relationship between the structure of the gold cluster and catalytic activity in the aerobic oxidation of alcohols.     

A theoretical study of the mechanism of phosphine-catalyzed hydroalkoxylation of methyl vinyl ketone

The mechanism of phosphine-catalyzed hydroalkoxylation of the methyl vinyl ketone has been investigated by the second-order M?ller-Plesset perturbation theory and the conductor-like polarized continuum model. The free energy reaction profiles of the reaction in both gas phase and solution phase are explored and compared. Our results suggest that the first stage of the studied reaction is the generation of the base (the methoxide anion) with the help of trialkylphosphine, and the second stage is the hydroalkoxylation of the methyl vinyl ketone catalyzed by this base. In the first stage, trialkylphosphine first adds to the methyl vinyl ketone to form a phosphonium enolate intermediate and then this species deprotonates a methanol molecule to generate a methoxide anion. Both steps involve free energy barriers of about 20 kcal/mol. In the second stage, both the addition of the methoxide anion to the methyl vinyl ketone and the proton transfer process from methanol to the methoxyl enolate anion intermediate have activation free energies of about 16 kcal/mol. The reaction in the second stage is exothermic by 10.2 kcal/mol at room temperature. A comparison of the free energy reaction profiles in the gas phase and the solution phase demonstrated that the generation of the methoxide anion could only occur in the presence of the polar solvents. The mechanism proposed in the present work is in reasonable agreement with the known experimental facts.     

Novel synthesis of highly functionalized 14-beta-hydroxysteroids related to batrachotoxin and ouabain

The use of anionic polycyclization was investigated in an effort to develop a versatile and convergent synthesis of advanced tetracyclic intermediates of batrachotoxin and ouabain analogues. Two new 5-(trialkylsilyl)-2-cyclohexenones as A ring precursors and a new Nazarov intermediate (D ring precursor) were prepared for this purpose. The reaction of the unsaturated beta-keto aldehyde A ring precursor with the enolate of the Nazarov intermediate afforded, after subsequent transformations, a 14-beta-hydroxysteroid with complete control of stereochemistry.     

Insight into Isothiourea‐Catalyzed Enantioselective Addition of Saturated Esters to Iminium Ions

The possible mechanisms and origin of the selectivities of isothiourea‐catalyzed addition of saturated esters to iminium ions have been investigated by density functional theory. The favorable reaction pathway includes three stages: formation of an ammonium enolate intermediate, enantioselective addition of the ammonium enolate intermediate to the iminium ion, and dissociation of the catalyst to form the product. The enantioselective addition process is the stereoselectivity‐determining step, while the chemoselectivity‐determining step is included in the formation of the final product. The calculated energy barriers show that the chemoselectivity is thermodynamically controlled, and it depends on the polarities of the products and the nucleophilicities of the N atoms of the enamine reactant moieties of the intermediates. The origin of the stereoselectivity was investigated by non‐covalent interaction analysis of the key transition states. Hydrogen bonding interactions were identified as the determining factor for controlling the stereoselectivity. The obtained insight will be valuable for rational design of novel Lewis base organocatalyst‐promoted enantioselective addition reactions with special chemoselectivities.     

Mechanism of Formation of Aromatic Vinylphosphonium Salts via the Peterson Olefination

The mechanism of the reaction of tributyl[(trimethylsilyl)methylene]phosphorane with benzaldehyde and its p‐substituted analogues has been examined. It has been found that the electronic nature of the p‐substituents in aromatic aldehydes strongly influences the stereochemical and kinetic outcome of the Peterson olefination whereas temperature substantially affects their Hammett correlation. This indicates that the Peterson olefination is a multistep reaction involving the formation of at least an oxyanion/betaine and a carbanion as intermediates. In turn, moderate Z‐selectivity might be the result of “steric approach intermediate control”; however, E‐selectivity seems to result from the silicon–oxygen interaction and interactions of steric substituents in competing erythro‐ and threo‐betaines.     

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study

The initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) has been studied by a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach. The reaction proceeds through the nucleophilic addition of the Ser203 O to the carbonyl C of acetylcholine, and the reaction is facilitated by simultaneous proton transfer from Ser203 to His447. The calculated potential energy barrier at the MP2(6-31+G) QM/MM level is 10.5 kcal/mol, consistent with the experimental reaction rate. The third residue of the catalytic triad, Glu334, is found to be essential in stabilizing the transition state through electrostatic interactions. The oxyanion hole, formed by peptidic NH groups from Gly121, Gly122, and Ala204, is also found to play an important role in catalysis. Our calculations indicate that, in the AChE-ACh Michaelis complex, only two hydrogen bonds are formed between the carbonyl oxygen of ACh and the peptidic NH groups of Gly121 and Gly122. As the reaction proceeds, the distance between the carbonyl oxygen of ACh and NH group of Ala204 becomes smaller, and the third hydrogen bond is formed both in the transition state and in the tetrahedral intermediate.     

Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD)

Extensive combined quantum mechanical (B3LYP/6‐31G*) and molecular mechanical (QM/MM) molecular dynamics simulations have been performed to elucidate the hydrolytic deamination mechanism of cytosine to uracil catalyzed by the yeast cytosine deaminase (yCD). Though cytosine has no direct binding to the zinc center, it reacts with the water molecule coordinated to zinc, and the adjacent conserved Glu64 serves as a general acid/base to shuttle protons from water to cytosine. The overall reaction consists of several proton‐transfer processes and nucleophilic attacks. A tetrahedral intermediate adduct of cytosine and water binding to zinc is identified and similar to the crystal structure of yCD with the inhibitor 2‐pyrimidinone. The rate‐determining step with the barrier of 18.0 kcal/mol in the whole catalytic cycle occurs in the process of uracil departure where the proton transfer from water to Glu64 and nucleophilic attack of the resulting hydroxide anion to C2 of the uracil ring occurs synchronously. © 2016 Wiley Periodicals, Inc.     

Experimental and theoretical studies on radical trifluoromethylation of titanium ate and lithium enolates

The radical trifluoromethylation of Ti ate and Li enolates has been investigated by both experiments and density functional (UB3LYP/6-311+G//UB3LYP/6-31+G*) calculations. Radical CF3 addition to the enolates proceeds in a highly exothermic manner without significant reaction barriers in both Ti ate and Li enolates. There are two possible reaction paths after the addition of CF3 radical in the case of Ti ate enolate; one is the elimination of Ti(III) from the ketyl radical intermediate and the other is the direct reaction of the ketyl radical intermediate with CF3I. However, in the case of Li enolate, only the latter path is possible due to the high energy barrier of the elimination of the Li radical. This analysis provides an explanation of the experimental observation that the Li enolate could form the radical cycle efficiently but the Ti ate enolate could not. To make the radical cycle complete, I- has to be extracted from CF3I itself or the radical anion of CF3I. In the case of Li, formation of Li-I bond could be the driving force for the extraction of I- and regeneration of CF3 radical. However, Ti does not give exothermic Ti-I formation and thus regeneration of CF3 radical is less likely.     

Gas-phase base-catalyzed Claisen—Schmidt reactions of the acetone enolate anion with various para-substituted benzaldehydes

Substituent effects were determined for the gas-phase base-catalyzed Claisen-Schmidt reaction of the acetone enolate anion and various para-substituted benzaldehydes. Under chemical ionization conditions, the adduct for the reaction was detected and the fraction of adduct that is tetrahedral was determined. The Hammett constants for the substituents correlate the fraction of the adduct population that is tetrahedral. The fraction of tetrahedral intermediate is greatest for those systems in which the negative charge is most highly stabilized. The structures of the adducts are determined on the basis of collisionally activated decomposition mass spectra. These spectra show that both the adducts of the ion-molecule reactions and deprotonated reference compounds, which have a structure that is similar to the tetrahedral intermediate, decompose by elimination of water and by a retro-aldol reaction. The adducts formed from the ion-molecule reactions show a greater propensity to reform the acetone enolate, whereas the deprotonated reference compounds eliminate H₂O readily. The reaction constant ρ from the Hammett correlation is +1.6, which substantiates that the production of tetrahedral intermediates is facilitated by electron-withdrawing substituents.