Thermodynamics and kinetics of methylboroxine.amine adduct formation: a computational study

Density functional theory (B3LYP//6-311+G*) calculations including Poisson-Boltzmann implicit solvent were applied to study the formation of the trimethylboroxine.amine adduct with respect to methylboronic acid monomers and free amine in solution. Potential intermediates and transition states between intermediates were calculated to assess the thermodynamic and kinetic factors controlling this transformation. Our calculations suggest that the rate-determining steps are condensation reactions to form dimers and trimers, and closure of the boroxine ring. Fast amine exchange is expected throughout the transformation, and the most-stable intermediate is a dimer.amine adduct. Using our calculated barriers for the methyl system as a template, we assess the conversion of phenylboronic acid to the triphenylboroxine.amine adduct and find that the pathway is most likely similar, except that the transformation is thermodynamically and kinetically more favored for the phenyl system in the presence of pyridine.     

Gas-phase stability of tetrahedral multiply charged anions: a conceptual and computational DFT study

Multiply charged anions (MCA's) are unstable relative to electron autoejection; however, the repulsive Coulomb barrier (RCB) provides electronic stability. In view of their interest in biological systems, the behavior of isolated AsO(4)(3-), PO(4)(3-), SO(4)(2-), and SeO(4)(2-) in the gas phase and in solution has been studied. To calculate the RCB values, the electrostatic and point charge model-two methods currently used in the literature-are applied, together with a recently introduced Conceptual Density Functional Theory (DFT) based approach. The relative stability of the above-mentioned MCA's is compared. The trends of the RCB are analyzed by including analogous compounds from the second and third row and by passing from dianionic to trianionic systems. Considering the effect of solvent, using the SCI-PCM solvent model, the evolution of the RCB when passing to higher dielectric constants is evaluated. The RCB is related to the properties of the system as polarizability/softness. Both a numerical and a conceptual correlation between the RCB and the global softness is found.     

A computational foray into the mechanism and catalysis of the adduct formation reaction of guanine with crotonaldehyde

Crotonaldehyde, a common environmental pollutant and product of endogenous lipid peroxidation, reacts with guanine to form DNA adducts with pronounced genotoxicity and mutagenicity. Here, we explore the molecular mechanism of this adduct formation using double-hybrid density functional theory methods. The reaction can be envisaged to occur in a two-step fashion via an aza-Michael addition leading to an intermediate ring-open adduct followed by a cyclization reaction giving the mutagenic ring-closed adduct. We find that (i) a 1,2-type addition is favored over a 1,4-type addition for the aza-Michael addition, and (ii) an initial tautomerization of the guanine moiety in the resulting ring-open adduct significantly reduces the barrier toward cyclization compared to the direct cyclization of the ring-open adduct in its keto-form. Overall, the aza-Michael addition is found to be rate-determining. We further find that participation of a catalytic water molecule significantly reduces the energy barriers of both the addition and cyclization reaction. © 2018 Wiley Periodicals, Inc.     

Hydrogenation of simple aromatic molecules: a computational study of the mechanism

Quantum chemistry calculations have been used to study the metal-free hydrogenation reactions of a variety of simple aromatic, heteroaromatic, and related linear conjugated systems. We find that the barrier for uncatalyzed 1,4-hydrogenation is always substantially lower (by approximately 200 kJ mol-1) than that for 1,2-hydrogenation, despite similar reaction enthalpies. The presence of hydrogen fluoride as a catalyst is found to decrease the 1,2-hydrogenation barriers but, in most cases, to slightly increase the 1,4-hydrogenation barriers when a constrained geometric arrangement is employed. These qualitative observations are consistent with orbital symmetry considerations, which show that both the uncatalyzed 1,4-hydrogenation and the catalyzed 1,2-hydrogenation are formally symmetry-allowed processes. An extreme example of the catalyzed 1,2-hydrogenation of benzene is provided by the involvement of a second molecule of hydrogen, which leads to a substantial lowering of the barrier. The effect of catalysis was further investigated by applying a selection of additional catalysts to the 1,2- and 1,4-hydrogenation of benzene. A decreasing barrier with increasing catalyst acidity is generally observed for the catalytic 1,2-hydrogenation, but the situation is more complex for catalytic 1,4-hydrogenation. For the uncatalyzed 1,4-hydrogenation of aromatic systems containing one or more nitrogen heteroatoms, the barriers for [C,C], [C,N], and [N,N] hydrogenations are individually related to the reaction enthalpies by the Bell-Evans-Polanyi principle. In addition, for a given reaction enthalpy, the barriers for [C,C] hydrogenation are generally lower than those for [C,N] or [N,N] hydrogenation. Finally, we find that the distortion experienced by the reactants in forming the transition structure represents a secondary factor that influences the reaction barrier. The correlation between these quantities allows the 1,4-hydrogenation barriers to be predicted from a ground-state property.     

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.     

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 computational study on the kinetics and mechanism for the unimolecular decomposition of o-nitrotoluene

The kinetics and mechanism for the unimolecular decomposition of o-nitrotoluene (o-CH(3)C(6)H(4)NO(2)) have been studied computationally at the G2M(RCC, MP2)//B3LYP/6-311G(d, p) level of theory in conjunction with rate constant predictions with RRKM and TST calculations. The results of the calculations reveal 10 decomposition channels for o-nitrotoluene and its six isomeric intermediates, among them four channels give major products: CH(3)C(6)H(4) + NO(2), C(6)H(4)C(H)ON (anthranil) + H(2)O, CH(3)C(6)H(4)O (o-methyl phenoxy) + NO, and C(6)H(4)C(H(2))NO + OH. The predicted rate constants in the 500-2000 K temperature range indicate that anthranil production, taking place initially by intramolecular H-abstraction from the CH(3) group by NO(2) followed by five-membered ring formation and dehydration, dominates at temperatures below 1000 K, whereas NO(2) elimination becomes predominant above 1100 K and CH(3)C(6)H(4)O formation by the nitro-nitrite isomerization/decomposition process accounts for only 5-11% of the total product yield in the middle temperature range 800-1300 K. The branching ratio for CH(2)C(6)H(4)NO formation by the decomposition process of CH(2)C(6)H(4)N(O)OH is negligible. The predicted high-pressure-limit rate constants with the rate expression of 4.10 x 10(17) exp[-37000/T] s(-1) for the NO(2) elimination channel and 9.09 x 10(12) exp[-25800/T] s(-1) for the H(2)O elimination channel generally agree reasonably with available experimental data. The predicted high-pressure-limit rate constants for the NO and OH elimination channels are represented as 1.49 x 10(14) exp[-30000/T] and 1.31 x 10(15) exp[-38000/T] s(-1), respectively.     

Exploring the mechanism for the amine-catalyzed isomerization of dimethyl maleate. A computational study

The main objective of this study was to investigate the amine-catalyzed isomerization of dimethyl maleate into dimethyl fumarate in order to utilize the former as a prodrug for the latter. Mechanistic study of this reaction using DFT at B3LYP/6-31G(d,p) level revealed that the reaction is first order in dimethyl maleate, second order in the amine, and overall third order. Moreover, the calculations revealed the existence of a linear correlation between the basicity of the amine catalyst and the isomerization rate.     

Kinetics and mechanism for the CH2O + NO2 reaction: A computational study

The reactants, products, and transition states of the CH₂O + NO₂ reaction on the ground electronic potential energy surface have been searched at both B3LYP/6?311+G(d,p) and MPW1PW91/6?311+G(3df,2p) levels of theory. The forward and reverse barriers are further improved by a modified Gaussian‐2 method. The theoretical rate constants for the two most favorable reaction channels 1 and 2 producing CHO + cis‐HONO and CHO + HNO₂, respectively, have been calculated over the temperature range from 200 to 3000 K using the conventional and variational transition‐state theory with quantum‐mechanical tunneling corrections. The former product channel was found to be dominant below 1500 K, above which the latter becomes competitive. The predicted total rate constants for these two product channels can be presented by k_t (T) = 8.35 × 10^?11 T^6.68 exp(?4182/T) cm³/(mol s). The predicted values, which include the significant effect of small curvature tunneling corrections, are in quantitative agreement with the available experimental data throughout the temperature range studied (390–1650 K). © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 184–190, 2003     

A computational study of the kinetics and mechanism for the reaction of HCO with HNO

The mechanism for the reaction of HCO with HNO has been studied at the G2M level of theory, based on the geometric parameters optimized by the BH&HLYP/6‐311G(d, p) method. There are three direct hydrogen abstraction channels producing (1) H₂CO + NO, (2) H₂NO + CO, and (3) HNOH + CO with barriers of 3.7, 3.9, and 10.4 kcal/mol, respectively. Another important reaction channel, (4), involves an association process forming HN(O)CHO (LM1) with a very small barrier and the subsequent isomerization and decomposition of LM1 producing HNOH + CO as major products. The rate constants of the dominant reaction channels (1), (2), and (4) in the temperature range 200–3000 K have been predicted by the microcanonical RRKM and transition state theory calculations with Eckart tunneling corrections. The theoretical result shows that in the high temperature range ( T > 1500 K), k₁ (H₂CO + NO) and k₂(H₂NO + CO) are preponderant, while in the low temperature range, both k₄(LM1) and k₄(HNOH + CO) appear to be dominant at high and low pressures, respectively. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 205–215, 2004     

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.     

Products and mechanism of acene dimerization. A computational study

The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso-carbon atoms of the central ring of acene blocks the reactivity of this ring but does not efficiently prevent dimerization through other rings.     

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.     

A study on the mechanism of polyvinyl chloride stabilization by lead salts

Infrared spectroscopic and DTA measurements and chemical analysis have shown that during stabilization of PVC with organic and inorganic basic lead salts various reactions occur: (a) binding of the evolved HCl, by these salts with the formation of lead chloride and complexes, including HCl, which catalyze the PVC degradation; (b) complex-forming reaction with the reactive PVC groups, which decreases the intensity of color of the polymer. In addition, with weak-organic-acid basic lead salts, exchange of labile Cl atoms for acid residues in PVC occurs, which results in an increase in inherent polymer stability.     

A computational study of the mechanism for the transmetalation of 2-trimethylstannylbuta-1,3-diene with SnCl4

Electronic structure calculations were performed at the B3LYP/6-31G level to identify the stationary structures on the potential energy surfaces for the transmetalation of 2-trimethylstannylbuta-1,3-diene with SnCl(4). The reaction pathways were characterized by locating the transition states on the intrinsic reaction coordinate. The calculations showed that the reaction between the reactant and SnCl(4), which generates 1-trichlorostannylbuta-2,3-diene via transmetalation, has a low energy barrier of 78.1 kJ.mol(-)(1). The following isomerization process is the rate-controlling step. It turned out that the isomerization process from 1-trichlorostannylbuta-2,3-diene to 2-trichloro-stannylbuta-1,3-diene via transmetalation with SnCl(4) is more energetically favorable than other possible isomerization processes.     

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.