Reaction mechanism of the vitamin K-dependent glutamate carboxylase: a computational study

In the reaction cycle of glutamate carboxylase, vitamin K epoxidation by O2 has been proposed to generate a very strong base able to remove a proton from the gamma carbon of a Glu residue, thus yielding a Glu-based carbanion that readily reacts with CO2. We have used hybrid density functional theory to study this appealing mechanism. Our calculations show a very exergonic four-step mechanism with the reaction of (triplet) O2 with the singlet vitamin K anion as the rate-limiting step, with a rate similar to the experimental value. Our study also establishes the need to apply continuum models when performing the optimization of minimum-energy crossing points between potential energy surfaces of different multiplicities for enzyme model systems.     

Degradation mechanism of methyl mercury selenoamino acid complexes: a computational study

Density functional theory (DFT) calculations have been carried out on the possible degradation/demethylation mechanism of methyl mercury (CH(3)Hg(+)) complexes with free cysteine and seleonocysteine. The binding of CH(3)Hg(+) ions with one (seleno)amino acid is thermodynamically favorable. However, the binding with another acid molecule is a highly unfavorable process. The CH(3)Hg-(seleno)cysteinate then degrades to bis(methylmercuric)sulphide (selenide for the Se-containing complex) which in turn forms dimethyl mercury and HgS/HgSe, the latter being precipitated out as nanoparticles. The dimethyl mercury interacts with water molecules and regenerates the CH(3)HgOH precursor. The calculated free energies of formation confirm the thermodynamic feasibility of every intermediate step of the degradation cycle and fully support earlier experimental results. In completing the cycle, one unit of mercury precipitates out from two units of sources, and thereby Se antagonizes the Hg toxicity. The degradation of CH(3)Hg-L-cysteinate is thermodynamically more favorable than the formation of CH(3)Hg-L-cysteinate. The preferred degradation of the CH(3)Hg-L-cysteinate suggests that another mechanism for CH(3)Hg to cross the blood-brain barrier should exist.     

The mechanism of guanine alkylation by nitrogen mustards: a computational study

The thermodynamics and kinetics for the monofunctional binding of nitrogen mustard class of anticancer drugs to purine bases of DNA were studied computationally using guanine and adenine as model substrates. Mechlorethamine and melphalan are used as model systems in order to better understand the difference in antitumor activity of aliphatic and aromatic mustards, respectively. In good agreement with experiments that suggested the accumulation of a reactive intermediate in the case of mechlorethamine, our model predicts a significant preference for the formation of corresponding aziridinium ion for mechlorethamine, while the formation of the aziridinium ion is not computed to be preferred when melphalan is used. Two effects are found that contribute to this difference. First, the ground state of the drug shows a highly delocalized lone pair on the amine nitrogen of the melphalan, which makes the subsequent cyclization more difficult. Second, because of the aromatic substituent connected to the amine nitrogen of melphalan, a large energy penalty has to be paid for solvation. A detailed study of energy profiles for the two-step mechanism for alkylation of guanine and adenine was performed. Alkylation of guanine is ～6 kcal mol(-1) preferred over adenine, and the factors contributing to this preference were explained in our previous study of cisplatin binding to purine bases. A detailed analysis of energy profiles of mechlorethamine and melphalan binding to guanine and adenine are presented to provide an insight into rate limiting step and the difference in reactivity and stability of the intermediate in both nitrogen mustards, respectively.     

Sila-Pummerer rearrangement of cyclic sulfoxides: computational study of the mechanism

The sila-Pummerer rearrangement of organosilicon cyclic sulfoxides proceeds via the two transition states, the first one with pentacoordinated Si that connects the reagent and the intermediate ylide and the second one that connects the ylide and the product of rearrangement.     

Reaction mechanism of oxidative desulfurization of heterocyclic organic sulfides: a computational study

The potential energy surfaces of the oxidation of two model heterocyclic organic sulfides thiophene and benzothiophene were examined using H₂O₂ and HCO₃H as oxidants adopting CCSD(T), ωB97X-D, M06-2X and B3LYP at the 6-311+G (d,p) level of theory. Stationary points on the potential energy surfaces for the first and second oxidation reaction were fully optimized and characterized. The natural orbital population analysis was also performed to understand the charge distribution. The results suggest that the oxidation of benzothiophene is faster than that of thiophene using both oxidants, and HCO₃H is more efficient than H₂O₂ in oxidation of both sulfides, which are in accordance with the experimental observation. Such results may assist in understanding the reaction mechanism of the oxidative desulfurization of sulfides.     

Hydrogenation of acetylene–ethylene mixtures on Pd catalysts: study of the surface mechanism by computational approaches. Metal dispersion and catalytic activity

The hydrogenation mechanism of acetylene–ethylene mixtures on Pd catalysts under different experimental conditions was studied by employing a time-dependent Monte Carlo approach set to use a fixed series of event probabilities. The dependence of the catalyst activity and selectivity on the sizes of the metal particles was simulated at microscopic level and the results, also refined by fitting procedures, suggested proper explanations for the apparent nonuniformity of the related experimental findings. The use of the steric hindrance parameter of the surface species and the available surface energy on the metallic catalyst sites was decisive for reproducing the experimental results. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 2 May 2000     

A computational approach to understanding the mechanism of aromatic bromination using quaternary ammonium tribromides

Quaternary ammonium tribromides (QATBs) have garnered interest for nearly a century now. Various types of tribromides have been synthesized over the years and their diverse applications have been extensively reported. However, despite the fact that these reagents are touted as safer alternatives to the very poisonous bromine, there is insufficient information on the structure of Br₃^? in QATB systems and there is still no clear explanation for how the tribromide ion (Br₃^?) participates in bromination reactions. This paper reports a through structural assessment of Br₃^?, followed by an attempt was made to fully understand the mechanistic behaviour of tribromide during bromination of aromatic compounds.     

Alkanoylation of quinazoline by nucleophilic aromatic substitution: Combined experimental and computational study

A combined experimental and computational study on the key intermediates of NHC-catalyzed acylation reaction, Breslow intermediates (BIs), has been conducted in order to achieve a direct nucleophilic alkanoylation of N-heterocycles. Various BI precursors are alternatively prepared and used in the reaction with 4-chloroquinazoline. The present study reveals that the intermediates having benzimidazole moiety serve as acylating agents for the introduction of straight-chain alkanoyl groups. Natural bond orbital analysis indicates that the reactivity of intermediates partly correlates to the occupancy of the π_C-C bonds of the hydroxyl enamine moieties. The putative rate-determining step of the acylation reaction has been theoretically investigated. Several new 4-alkanoylquinazolines are synthesized using the BI precursors.     

Insight into detailed mechanism of the atmospheric reaction of imidogen with hydroxyl: a computational study

The details of reaction mechanism of imidogen (NH) and hydroxyl radicals are explored at the UMP2(FC)/cc–pVDZ and PMP4(FC,SDTQ)/cc–pVQZ//UMP2 + ZPE levels, theoretically. The initial association between NH and OH radicals leads to the formation of the intermediates, NH…OH, HN…HO, cis HNOH, and trans HNOH, through the barrierless and exothermic processes. By starting from the initial intermediates, all possible paths for the formation of H + HNO, H₂ + NO, H₂O + ⁴N, H₂N + ³O, and H + ³HON products are investigated on potential energy surface. The results reveal that H₂O + ⁴N is the main product involved in the mechanism of hydrogen atom abstraction of NH by OH radical through the intermediate NH…OH.     

A computational study on the amine-oxidation mechanism of monoamine oxidase: insight into the polar nucleophilic mechanism

The proposed polar nucleophilic mechanism of MAO was investigated using quantum chemical calculations employing the semi-empirical PM3 method. In order to mimic the reaction at the enzyme's active site, the reactions between the flavin and the p-substituted benzylamine substrate analogs were modeled. Activation energies and rate constants of all the reactions were calculated and compared with the published experimental data. The results showed that electron-withdrawing groups at the para position of benzylamine increase the reaction rate. A good correlation between the log of the calculated rate constants and the electronic parameter (sigma) of the substituent was obtained. These results agree with the previous kinetic experiments on the effect of p-substituents on the reduction of MAO-A by benzylamine analogs. In addition, the calculated rate constants showed a correlation with the rate of reduction of the flavin in MAO-A. In order to verify the results obtained from the PM3 method single-point B3LYP/6-31G*//PM3 calculations were performed. These results demonstrated a strong reduction in the activation energy for the reaction of benzylamine derivatives having electron-withdrawing substituents, which is in agreement with the PM3 calculations and the previous experimental QSAR study. PM3 and B3LYP/6-31G* energy surfaces were obtained for the overall reaction of benzylamine with flavin. Results suggest that PM3 is a reasonable method for studying this kind of reaction. These theoretical findings support the proposed polar nucleophilic mechanism for MAO-A.     

A general acid-base mechanism for the stabilization of a tetrahedral adduct in a serine-carboxyl peptidase: a computational study

The QM/MM MD and free energy simulations show that serine-carboxyl peptidases (sedolisins) may stabilize the tetrahedral intermediates and tetrahedral adducts primarily through a general acid-base mechanism involving Asp (Asp164 for kumamolisin-As) rather than the oxyanion-hole interactions as in the cases of serine proteases.     

Catalytic mechanism of yeast cytosine deaminase: an ONIOM computational study

The complete path for the deamination reaction catalyzed by yeast cytosine deaminase (yCD), a zinc metalloenzyme of significant biomedical interest, has been investigated using the ONIOM method. Cytosine deamination proceeds via a sequential mechanism involving the protonation of N(3), the nucleophilic attack of C(4) by the zinc-coordinated hydroxide, and the cleavage of the C(4)-N(4) bond. The last step is the rate determining step for the generation of the zinc bound uracil. Uracil is liberated from the Zn atom by an oxygen exchange mechanism that involves the formation of a gem-diol intermediate from the Zn bound uracil and a water molecule, the C(4)-O(Zn) cleavage, and the regeneration of the Zn-coordinated water. The rate determining step in the oxygen exchange is the formation of the gem-diol intermediate, which is also the rate determining step for the overall yCD-catalyzed deamination reaction.     

Metallacarbenes from diazoalkanes: an experimental and computational study of the reaction mechanism

PCP ligand (1,3-bis-[(diisopropyl-phosphanyl)-methyl]-benzene), and PCN ligand ([3-[(di-tert-butyl-phosphanyl)-methyl]-benzyl]-diethyl-amine) based rhodium dinitrogen complexes (1 and 2, respectively) react with phenyl diazomethane at room temperature to give PCP and PCN-Rh carbene complexes (3 and 5, respectively). At low temperature (-70 degrees C), PCP and PCN phenyl diazomethane complexes (4 and 6, respectively) are formed upon addition of phenyl diazomethane to 1 and 2. In these complexes, the diazo moiety is eta(1) coordinated through the terminal nitrogen atom. Decomposition of complexes 4 and 6 at low temperatures leads only to a relatively small amount of the corresponding carbene complexes, the major products of decomposition being the dinitrogen complexes 1 and 2 and stilbene. This and competition experiments (decomposition of 6 in the presence of 1) suggests that phenyl diazomethane can dissociate under the reaction conditions and attack the metal center through the diazo carbon producing a eta(1)-C bound diazo complex. Computational studies based on a two-layer ONIOM model, using the mPW1K exchange-correlation functional and a variety of basis sets for PCP based systems, provide mechanistic insight. In the case of less bulky PCP ligand bearing H-substituents on the phosphines, a variety of mechanisms are possible, including both dissociative and nondissociative pathways. On the other hand, in the case of i-Pr substituents, the eta(1)-C bound diazo complex appears to be a critical intermediate for carbene complex formation, in good agreement with the experimental results. Our results and the analysis of reported data suggest that the outcome of the reaction between a diazoalkane and a late transition metal complex can be anticipated considering steric requirements relevant to eta(1)-C diazo complex formation.     

Metal ion shuttling mechanism through thiacalix[4]crown: a computational study

The first computational study on the alkali metal ion shuttling mechanism through thiacalix[4]biscrown-5 has been performed using density functional theory (MPWB1K/6-31G(d)//B3LYP/6-31G(d)). The activation free energy for K⁺ ion shuttling through the calix tube of thiacalix[4]biscrown-5 is computed to be 12.7 kcal/mol which is in good agreement with the experimental value. Throughout the shuttling process, K⁺ ion maintains the maximum electrostatic interactions with ether oxygens of crown rings, which contributes to lower the activation barrier of the shuttling process.     

Monosilicon-substituted cyanoacetylene: a computational study

A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.     

Complexes of C60 fullerene with simple donor molecules: Theoretical study

The complex formation between fullerene C60 and simple donor molecules such as dimethyl ether, dimethylamine, dimethylsulfide, furan, pyrrole, and thiophene has been studied applying the hybrid MP2/6‐31G(d′):PM3 ONIOM approach for geometry optimization. Local implementation of Møller–Plesset perturbation theory in combination with 6‐31G(d) and 6‐311G(d,p) basis sets was used for binding energies estimation of fullerene complexes. Two factors were found to contribute most to the complex stability: the polarizability and molecular volume of donor molecule. As follows from positive stabilization energies at the Hartree–Fock level, the stabilization of fullerene complexes is entirely due to dispersion interactions in accordance with available experimental data. The calculations show that for donors of similar molecular volume the binding energy of molecular complex increases with polarizability of donor molecules. Similarly, for such complexes the partial charges on molecules increase with decreasing of ionization potentials of donor molecules. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Aminolysis of a model nerve agent: a computational reaction mechanism study of o,s-dimethyl methylphosphonothiolate

The mechanism for the aminolysis of a model nerve agent, O,S-dimethyl methylphosphonothiolate, is investigated both at density functional level using M062X method with 6-311++G(d,p) basis set and at ab initio level using the second-order M?ller-Plesset perturbation theory (MP2) with the 6-311+G(d,p) basis set. The catalytic role of an additional NH(3) and H(2)O molecule is also examined. The solvent effects of acetonitrile, ethanol, and water are taken into account employing the conductor-like screening model (COSMO) at the single-point M062X/6-311++G(d,p) level of theory. Two possible dissociation pathways, methanethiol and methyl alcohol dissociations, along with two different neutral mechanisms, a concerted one and a stepwise route through two neutral intermediates, for each pathway are investigated. Hyperconjugation stabilization that has an effect on the stability of generated transition states are investigated by natural bond order (NBO) approach. Additionally, quantum theory of atoms in molecules analysis is performed to evaluate the bond critical (BCP) properties and to quantify strength of different types of interactions. The calculated results predict that the reaction of O,S-dimethyl methylphosphonothiolate with NH(3) gives rise to parallel P-S and P-O bond cleavages, and in each cleavage the neutral stepwise route is always favorable than the concerted one. The mechanism of NH(3) and H(2)O as catalyst is nearly similar, and they facilitate the shuttle of proton to accelerate the reaction. The steps involving the H(2)O-mediated proton transfer are the most suitable ones. The first steps for the stepwise process, the formation of neutral intermediate, are the rate-determining step. It is observed that in the presence of catalyst the reaction in the stepwise path possesses almost half the activation energy of the uncatalyzed one. A bond-order analysis using Wiberg bond indexes obtained by NBO calculation predicts that usually all individual steps of the reactions occur in a concerted fashion showing equal progress along different reaction coordinates.     

A computational study of interactions between acetic acid and water molecules

Density functional theory calculations were performed for the title reactions to elucidate the difference between the strong cyclic hydrogen bond of (Me-COOH)(2) and the electrolytic dissociation, MeCOOH <==> Me-COO(-) + H(+), as a weak acid. The association of water clusters with acetic acid dimers strengthens the cyclic hydrogen bond. A nucleophilic attack of the carboxylic carbon by a water cluster leads to a first zwitterionic intermediate, MeCOO(-) + H(3)O(+) + (HO)(3)C-Me. The intermediate is unstable and is isomerized to a neutral interacting system, MeCOOH...(HO)(3)C-Me + H(2)O. The ethanetriol, (HO)(3)-CMe is transformed to an acetic acid monomer. The monomer may be dissociated to give a second zwitterionic intermediate with reasonable proton-relay patterns and energy changes. In proton relay reaction channels, H in MeCOOH is not an acidic proton but is always a hydroxy proton.     

Modelling of the association mechanism of a series of rodenticide molecules with lipid membrane investigated by computational chemistry and biochromatography

The increase of pest rodents population in urban and rural areas is tackled by dissemination of baits poisoned with anticoagulant compounds. In order to modelize the cell membrane transport of these rodenticides, which have toxic effect on human keratynocytes and break the vitamin K cycle, a new general model based on the perturbation method was developed to describe the association process between these rodenticide and an immobilized artificial membrane (IAM). The thermodynamic functions of the rodenticide transfer from the bulk solvent to the IAM surface were also determined. The variation plots of the solute transfer data versus the salt concentration (x) in the bulk solvent allow to demonstrate that the rodenticides—IAM surface association mechanism was governed by both the hydrophobic effect and the van der Waals interactions/hydrogen bonds between the rodenticide polar groups with the polar headgroups of phospholipid monolayers (polar retention effect). This result was also corroborated by a comparison of the number of water molecules surrounded the rodenticide in the medium (obtained by computational chemistry) and the number of water molecule release at the IAM—rodenticide interface (obtained thanks to the Tanford's equation).     

Reaction mechanism and stereoselectivity of ruthenium--porphyrin-catalyzed intramolecular amidation of sulfamate ester: a DFT computational study

The reaction mechanism of the ruthenium--porhyrin complex [Ru(por)(CO)]-catalyzed intramolecular C-H bond amidation was examined using density functional theory (DFT) calculations. The metal-nitrene reactive intermediate, Ru(por)(CO)-NSO3R1 (R1 = 1-methylclohexl-methyl) was found to be highly favorable to generate in terms of the free energy profile from the reaction of the starting materials. Ru(por)(CO)-NSO3R1 may exist in both singlet and triplet states since they are close in energy. In each state, six C-H bond amidation reaction pathways were characterized structurally and energetically. The predicted most probable diastereomeric product out of the four possible diasteromeric products examined in the calculations for the amidation reactions agree well with previously reported experimental results.