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.     

A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase

The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two‐layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn‐bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate‐determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn‐bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate‐determining step is the proton transfer from Zn‐OH to 6‐NH₂ of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

A theoretical study of the mechanism for the homogeneous catalytic reversible dehydrogenation-hydrogenation of nitrogen heterocycles

A mechanism for the dehydrogenation reaction of 1,2,3,4-tetrahydroquinoline to quinoline derivatives, catalyzed by a Cp*Ir complex containing a 2-pyridonate ligand, is proposed and supported by theoretical calculations at the B3LYP level. The proposed mechanism involves two stages which are all thermodynamically unfavorable (endothermic by 36.3 kcal mol(-1) and 18.4 kcal mol(-1), respectively). The apparent activation energies of the first and second stages of the reaction are 30.8 kcal mol(-1) and 34.0 kcal mol(-1), respectively, and are considered overestimates of the entropy change of reaction. Owing to a decrease in the oxidative ability of iridium(III) coordinated to large electronegative nitrogen and chlorine, ligand promoted hydrogen abstraction is crucial at both stages of dehydrogenation, in which the oxidation state of iridium(III) does not change, and the ligand 2-pyridonate is converted to 2-hydroxypyridine. Cp*Ir(C(5)NH(4)OH)ClH, an important intermediate, releases hydrogen through an energy barrier of 23.5 kcal mol(-1).     

Hydride transfer mechanism in the catalytic allylation of norbornadiene with allyl formate

Russian Chemical Bulletin - Allylation of norbornadiene with allyl formate in the presence of the palladium catalytic systems is characterized by several peculiarities associated with the new...     

Evidence for the formation of a mo-h intermediate in the catalytic cycle of formate dehydrogenase

DFT/BP86/TZVP and DFT/B3LYP/TZVP have been used to investigate systematically the reaction pathways associated with the H-transfer step, which is the rate-determining step of the reaction HCOO(-) ? CO(2) + H(+) + 2e(-), as catalyzed by metalloenzyme formate dehydrogenase (FDH). Actually, the energetics associated with the transfer from formate to all H (proton or hydride) acceptors that are present within the FDH active site have been sampled. This study points to a viable intimate mechanism in which the metal center mediates H transfer from formate to the final acceptor, i.e. a selenocysteine residue. The Mo-based reaction pathway, consisting of a β-H elimination to metal with concerted decarboxylation, turned out to be favored over previously proposed routes in which proton transfer occurs directly from HCOO(-) to selenocysteine. The proposed reaction pathway is reminiscent of the key step of metal-based catalysis of the water-gas shift reaction.     

A theoretical study of catalytic hydration reactions of ethylene

The hydration reaction of ethylene, C₂H₄+H₂O → C₂H₅OH, catalyzed by oxoacids (H₃PO₄, H₂SO₄, and HClO₄) and metal cations (B³⁺, Al³⁺, Sc³⁺, Ga³⁺, La³⁺, Be²⁺, Mg²⁺, Ca²⁺, Zn²⁺, and Sr²⁺) are studied systematically by density functional theory with a BLYP functional. The reaction profiles of the main reaction and some side reactions, such as ester formation, dimerization of ethylene, and dehydrogenation of ethanol, have been determined with a variety of catalysts. In each case, the intermediate states, the transition states, and their energetics are calculated. Metal cations react more efficiently for the main reaction than oxoacids, but they also make the dehydrogenation reaction active. While the dimerization reaction is strongly affected by the acidity of the catalyst, both the acidity and basicity of the catalyst are important for the dehydrogenation reaction. Efficient formation of ethanol from ethylene over a catalyst is suggested. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1292–1304, 2000     

A theoretical study of malonate and formate calcium binding by ab initio techniques

Ab initio calculations at the STO—3G level have been performed on the binding of CA(II) ion to malonate and formate with and without d orbitals in the basis set for the CA(II) ion. The malonate and formate binding results with CA(II) are similar. The addition of d orbitals to CA(II) has little effect on the conformational minimum. The results are qualitatively similar to those from our previous calculations on the Mg²⁺—malonate interaction: a single carboxyl interaction with the metal ion appears to be preferred over a conformation in which two carboxyl groups bind to Ca(II). Moreover, the single carboxyl group interaction with CA(II) appears to be favored over the binding of CA(II) to a single oxygen of a carboxyl group.     

A theoretical study on the decomposition mechanism of artemisinin

A theoretical study on the artemisinin decomposition mechanism is reported. The suggested pathways have been reproduced and the appearance of the final products can be explained in a satisfactory way. In addition, several intermediates and radicals have been found as relatively stable species, thus giving support to the current hypothesis that some of these species can be responsible for the antimalarial action of artemisinin and its derivatives.     

A theoretical study on the mechanism of boron metathesis

The mechanism of the boron metathesis reaction of the transition-metal-aminoborylene complex Cp(CO)(2)FeBN(CH(3))(2+) (8) with EX, where EX = H(3)PO (9ap), H(3)AsO (9bp), H(3)PS (9aq), H(3)AsS (9bq), CH(3)CHCH(2) (9cr), (NH(2))(2)CCH(2) (9dr), H(2)CO (9ep), and (NH(2))(2)CO (9dp) is investigated at the B3LYP/LANL2DZ level. The analysis of bonding and charge distribution shows that the Fe-borylene complex (8) is a Fischer-type carbene analogue. The attack of the olefin takes place at the metal end of the M=C bond of the metal-carbene complex in olefin metathesis and proceeds via [2 + 2] cycloaddition, while in boron metathesis, the initial attack of the substrates takes place at the positively charged B atom of the Fe-borylene complex and forms the preferred acyclic intermediate. The energetics of boron metathesis is comparable to that of the olefin metathesis. Substrates that are polar and a have low-lying sigma* molecular orbital (weak sigma bond) prefer the boron metathesis reaction. The relative stability of the metathesis products is controlled by the strength of the Fe-E and B-X bonds of the products 13 and 14, respectively. We have also investigated the possibility of a beta-hydride-transfer reaction in the Fe-borylene complex.     

Copper-zinc superoxide dismutase: theoretical insights into the catalytic mechanism

The mechanism for the toxic superoxide radical disproportionation to molecular oxygen and hydrogen peroxide by copper-zinc superoxide dismutase (CuZnSOD) has been studied using the B3LYP hybrid density functional. On the basis of the X-ray structure of the enzyme, the molecular system investigated includes the first-shell protein ligands of the two metal centers as well as the second-shell ligand Asp122. The substrates of the model reaction are two superoxide radical anions, approaching the copper center at the beginning of two half-reactions: the first part of the catalytic cycle involving Cu+ oxidation and the second part reducing Cu2+ back to its initial state. The quantitative free energy profile of the reaction is obtained and discussed in connection with the experimental data on the reduction potentials and CuZnSOD kinetics. The optimized structures are analyzed and compared to the experimental ones. The two transition states alternate the protonation state of His61 and correspond to histidine Cu-His61-Zn bridge rupture/reformation. Modifications applied to the initial model allow the importance of Asp122 for catalysis to be estimated.     

A theoretical study of the chelation complex comprising formate ions, calcium ion and water of hydration

Ab initio calculations at the STO-3G level have been performed on the binding of Ca(II) ion to two formate ions. Two logical chelation structures have been studied with and without water of solvation. Differential solvation effects are found to be sufficiently large to invert the order of energetically favored structures.     

Catalytic mechanism of 6-phosphogluconate dehydrogenase: a theoretical investigation

Density functional calculations are employed to theoretically explore the mechanism of all elementary reaction steps involved in the catalytic reaction of 6-phosphogluconate dehydrogenase (6PGDH). The model systems we choose for the enzyme contain the essential parts of the cofactor (NADP+), the substrate 6-phosphogluconate (6PG), and some key residues (Lys183 and Glu190) in the active site of sheep liver 6PGDH. The effect of the apoenzyme electrostatic environment on the studied reaction is treated by the self-consistent reaction-field method. Our calculations demonstrate that the first step of the catalytic reaction is the formation of a 3-keto 6PG intermediate, which proceeds through a concerted transition state involving a hydride transfer from 6PG to NADP+, and a proton transfer from 6PG to Lys183. The second step is the elimination of a CO2 molecule from 6-PG, concomitant with a proton transfer from Lys183 to 6-PG. In the final step, a concerted double proton transfer (one from Glu190 to the substrate, another from the substrate to Lys183) results in the final product, the keto form of ribulose 5-phosphate (Ru5P). The rate-limiting step is the formation of a 3-keto 6PG intermediate, with a free energy barrier of 22.7 kcal/mol at room temperature in the protein environment, and all three steps are calculated to be thermodynamically favorable. These results are in good agreement with the general acid/general base mechanism suggested from previous experiments for the 6PGDH reaction.     

A theoretical study on the mechanism of the cyclopolymerization of diallyl monomers

The cyclization and intermolecular propagation steps of the cyclopolymerization mechanism are studied with density functional theory. In addition to standard cyclization and intermolecular propagation reactions of cyclopolymerization, competing reactions that lead to chain transfer and termination are also discussed. The mechanistic study of the cyclopolymerization reaction of two representative monomers, N,N-diallylamine (1) and N,N-dimethyl-N,N-diallylamonium (2), was carried out with B3LYP/6-31G computations. Monomer 1 has almost the same activation barriers for homopolymerization and cyclization. In monomer 2, cyclization is much more facile than homopolymerization, leading to the higher cyclopolymerization efficiency. In the case of 2, methyl substituents on nitrogen inhibit hydrogen abstraction, whereas in 1, hydrogen abstraction reactions from the neutral monomer yield stabilized products leading to chain transfer. Calculations show that facile competing reactions of monomer 1 lower the polymerization efficiency. Monomer 2 displays a stronger preference for cyclization relative to other processes.     

Inactivation of formate dehydrogenase at pH 8

The first-order inactivation rate constant as a function of the phosphate buffer concentration has been studied for recombinant formate dehydrogenases from plants Arabidopsis thaliana and soybean and for mutant formate dehydrogenase from bacterium Pseudomonas sp. 101 (PseFDH GAV). Both stabilization and destabilization of the enzyme can be observed depending on the ionic strength of the buffer.     

纤维素热解形成左旋葡聚糖机理的理论研究

采用密度泛函理论UB3LYP/6-31G(d)方法,对模型化合物纤维二糖热解反应机理进行了量子化学理论计算研究。设计了三种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化,计算了不同温度下热解反应的标准热力学和动力学参数。计算结果表明,糖苷键均裂而形成两个自由基中间体IM₁a和IM₁b,吸收热量为321.26kJ/mol,中间体IM₁a经过渡态TS₁a进一步形成左旋葡聚糖P₁,反应势垒为202.72kJ/mol;与分步反应相比,纤维二糖经过渡态TS₂协同反应直接形成左旋葡聚糖P₁和吡喃葡萄糖P₂的反应势垒低于分步反应的总势垒,其反应势垒为377.54kJ/mol;H⁺的加入有利于糖苷键的断裂,断裂形成的中间体IM₃很难进一步反应形成左旋葡聚糖。     

A theoretical study on the substrate deacylation mechanism of class C beta-lactamase

The whole reaction of the deacylation of class C beta-lactamase was investigated by performing quantum chemical calculations under physiological conditions. In this study, the X-ray crystallographic structure of the inhibitor moxalactam-bound class C beta-lactamase (Patera et al. J. Am. Chem. Soc. 2000, 122, 10504-10512.) was utilized and moxalactam was changed into the substrate cefaclor. A model for quantum chemical calculations was constructed using an energy-minimized structure of the substrate-bound enzyme obtained by molecular mechanics calculation, in which the enzyme was soaked in thousands of TIP3P water molecules. It was found that the deacylation reaction consisted of two elementary processes. The first process was formation of a tetrahedral intermediate, which was initiated by the activation of catalytic water by Tyr150, and the second process was detachment of the hydroxylated substrate from the enzyme, which associated with proton transfer from the side chain of Lys67 to Ser64O(gamma). The first process is a rate-determining process, and the activation energy was estimated to be 30.47 kcal/mol from density functional theory calculations considering electron correlation (B3LYP/6-31G**). The side chain of Tyr150 was initially in a deprotonated state and was stably present in the active site of the acyl-enzyme complex, being held by Lys67 and Lys315 cooperatively.     

A theoretical study on the mechanism of the reductive half-reaction of xanthine oxidase

On the basis of the crystal structure of an aldehyde oxidoreductase, Huber et al. proposed a catalytic mechanism for the reductive half-reaction of xanthine oxidase which involves nucleophilic addition of Mo-bound hydroxide (Moco 1) to the substrate and hydride transfer from the substrate to sulfido group (Mo=S). Density functional theory calculations have been carried out for the oxidation of formaldehyde, acetaldehyde, formamide, and formamidine with Moco 2 to understand more detailed catalytic pathways. Our calculation results indicate that the anionic catalyst model acts as a nucleophile and is reactive for the oxidation of aldehyde substrates, which are reactive for nucleophilic addition. In these cases, a concerted mechanism is found to be more favorable than a stepwise mechanism. The concerted mechanism is further shown to be promoted by the presence of a nearby water molecule, in the active site, which serves as a Lewis acid for the nucleophilic addition of hydroxide. For less reactive formamide and formamidine (a model for xanthine) substrates, the calculated activation energies with the above mechanisms are high. These reactions also do not benefit from the presence of the water molecule. The results indicate that different catalyst forms might be responsible for the oxidation of different substrates, which could be regulated by the enzyme active site environment.     

A theoretical study of the comonomer effect in the ethylene polymerization with zirconocene catalytic systems

The PM3(tm) semiempirical method has been used to optimize the structures for the reactants and transition states of the first and second ethylene insertion processes into zirconocene catalytic systems. The results obtained for these reactions are compared with calculations published in the literature performed at different ab-initio theoretical levels. The agreement between our calculations and those reported in the literature is satisfactory. Taking advantage of the reduced computational effort required in semiempirical calculations two additional processes related with the so-called comonomer effect were also studied: ethylene/1-hexene copolymerization, and chain termination reaction, both in the homopolymerization and in copolymerization of ethylene with 1-hexene comonomer. The calculated activation energies support some experimental findings such as the higher polymerization activities in the presence of comonomers and also the molecular weight reduction of the copolymers due to the more favorable β-elimination reactions. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1157–1167, 1998     

A theoretical study on the mechanism and diastereoselectivity of the Kulinkovich hydroxycyclopropanation reaction

A detailed mechanism for the Kulinkovich hydroxycyclopropanation reaction has been explored with density functional theory calculations on the reactions between R(1)COOMe and Ti(OMe)(2)(CH(2)CHR(2)) (R(1) and R(2) are hydrogen and alkyl groups). Addition of ester to titanacyclopropane is found to be fast, exothermic, and irreversible. It has a preference for the alpha-addition manifold over the beta-addition manifold in which its cycloinsertion transition states suffer from the steric repulsion between the R(2) and ester. The following intramolecular methoxy migration step is also exothermic with reasonable activation energy. The cyclopropane-forming step is the rate-determining step, which affords the experimentally observed cis-R(1)/R(2) diastereoselectivity in the alpha-addition manifold by generating cis-R(1)/R(2) 1,2-disubstituted cyclopropanol when R(1) is primary alkyl groups. On the contrary, the unfavored beta-addition manifold offers the diastereoselectivity contradicting the experimental observations. The effects of R(1) and R(2) on the regio- and stereoselectivity are also discussed.