Study of the mechanism of recyclization of furans into thiophenes and selenophenes in conditions of acid catalysis. 5. Direction of protonation of furans

2,5-Dimethyl-3-D-furan was prepared for the first time. Its recyclization into the corresponding thiophene and selenophene was investigated. The possibility of -C-protonation of the furan ring was confirmed by experimental and quantum chemical data.See [1] for Communication 4.Scientific-Research Institute of Chemistry, N. G. Chernyshevskii Saratov State University, Saratov 410026. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1030–1034, August, 1997.     

Study of the mechanism of recyclization of furans into thiophenes and selenophenes in conditions of acid catalysis. 4. study of the effect of the solvent and direction of reactions of hydrolysis and recyclization of 2,5-dimethylfuran

The kinetics of hydrolysis of 2,5-dimethylfuran and its recyclization into the corresponding thiophene were investigated in water-alcohol medium W R I and 50% ethyl alcohol in the presence of HCl. It was found that the rates of these reactions are a function of both the initial concentration of the acid component and the concentration of water in the alcohol. The rate of hydrolysis is a function of the dilution of the alcohol to a greater degree than the rate of recyclization.See [1] for Communication 3.Scientific-Research Institute of Chemistry at N. G. Chernyshevskii Saratov State University, Saratov 410026. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 624-628, May, 1995. Original article submitted January 30, 1995.     

Investigation of the mechanism of the recyclization of furans to thiophenes and selenophenes under acid-catalysis conditions. 3. Investigation of the recyclization of homologs and functional derivatives of furan. Quantum-chemical calculations of the objects of the recyclization

The kinetics of the conversion of di-, tri-, and tetraalkylfurans to the corresponding thiophenes were investigated. A correlation between the reactivities and structures of the investigated furans was established. Quantum-chemical calculations of the objects of the recyclization were made. The calculated and experimental data on the reactivities of the investigated compounds were compared. The most likely pathway of the protonation of furans in their recyclization was determined on the basis of calculations of the total energies of the protonated forms.For Communication 2 see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1614–1620, December, 1993.     

Study of the mechanism of recyclization of furans to thiophenes and selenophenes under theconditions of acid catalysis. 7. The effect of the nature of the nucleophile. The competition constant

Kinetic investigations into the reactions of, 2,5-dimethylfuran with mixtures of hydrogen sulfide and selenide in various quantitative ratios were undertaken, and the competition constant was determined. This made it possible to correlated numerically the nucleophilicity of hydrogen sulfide an selenide in the reaction. For Communication 6, see [1]. I. G. Chernyshevskii Saratov State University, Saratov. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 610–611, May, 1999.     

Mechanism of recyclization of furans to thiophenes and selenophenes under acid catalysis. 1. Kinetic studies of the reaction of 2,5-dialkylfurans with hydrogen sulfide in the presence of hydrochloric acid

The transformation of 2,5-dialkylfurans to thiophenes by reaction with hydrogen sulfide in the presence of hydrochloric acid was studied. The reaction was found to be first order with respect to the furan; the rate of consumption of the furan did not change with increasing length of one of the alkyl substituents. Recyclization in the presence of acid proceeds in two independent directions: through the formation of an intermediate dicarbonyl compound, and by direct conversion of the furan to a thiophene. Kinetic data showed that the reaction occurs mainly by the second route.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1333–1337, October, 1989.     

Mechanism of recyclization of furans to thiophenes and selenophenes under acid-catalysis conditions. 2. Kinetic investigations of the reaction of 2,5-dialkylfurans with hydrogen sulfide and hydrogen selenide in an anhydrous medium

The effect of the concentration of the acidic component on the rates of recyclization of 2,5-dialkylfurans to thiophenes and selenophenes was studied. On the basis of the direct correlation of log k on (H_o)_I and the isotope effect of the solvent it was established that the reaction proceeds via a mechanism of specific acid catalysis. It was shown that the rates of the reactions with the participation of hydrogen sulfide and hydrogen selenide coincide at equal acidities and temperatures. A scheme for the mechanism of the reaction that includes a step involving the formation of the doubly protonated form of the substrate is proposed.See [1] Communication 1.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1458–1462, November, 1989.     

Quantum chemical study of the reaction mechanism of ozone and methane with fluorine and chlorine atoms

Ab initio calculations of the potential energy surface for the F + O₃ and Cl + O₃ reactions have been performed using the G3 and G3MP2 methods, which optimize the geometry configuration of reactants, products, intermediates, and transition states. The results show that fluorine atoms react with ozone as violently as chlorine atoms. At the same time, we have studied the reaction mechanisms of F atoms and Cl atoms with methane. It is found that fluorine atoms prefer to react with methane and chlorine atoms with ozone when there is competition between ozone and methane. Therefore, we can reasonably explain why chlorine atoms play the main role of reactants depleting ozone, while the more active fluorine atoms deplete less ozone. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/qua.10119     

Insights into the mechanism and catalysis of the native chemical ligation reaction

Native chemical ligation of unprotected peptide segments involves reaction between a peptide-alpha-thioester and a cysteine-peptide, to yield a product with a native amide bond at the ligation site. Peptide-alpha-thioalkyl esters are commonly used because of their ease of preparation. These thioalkyl esters are rather unreactive so the ligation reaction is catalyzed by in situ transthioesterification with thiol additives. The most common thiol catalysts used to date have been either a mixture of thiophenol/benzyl mercaptan, or the alkanethiol MESNA. Despite the use of these thiol catalysts, ligation reactions typically take 24-48 h. To gain insight into the mechanism of native chemical ligaton and in order to find a better catalyst, we investigated the use of a number of thiol compounds. Substituted thiophenols with pK(a) > 6 were found to best combine the ability to exchange rapidly and completely with thioalkyl esters, and to then act as effective leaving groups in reaction of the peptide-thioester with the thiol side chain of a cysteine-peptide. A highly effective and practical catalyst was (4-carboxylmethyl)thiophenol ('MPAA'), a nonmalodorous, water-soluble thiol. Use of MPAA gave an order of magnitude faster reaction in model studies of native chemical ligation and in the synthesis of a small protein, turkey ovomucoid third domain (OMTKY3). MPAA should find broad use in native chemical ligation and in the total synthesis of proteins.     

Kinetic and theoretical studies on the mechanism of intramolecular catalysis in phenyl ester hydrolysis

The kinetic study of the hydrolysis reaction of Z-substituted phenyl hydrogen maleates (Z = H, m-CH3, p-CH3, m-Cl, p-Cl and m-CN) was carried out in aqueous solution, and the results were complemented with theoretical studies. Under some experimental conditions, two kinetic processes were observed. One of them was ascribed to maleic anhydride formation and the other to the anhydride hydrolysis. The Br?nsted-type plot for the leaving-group dependence was linear with slope beta(lg) = -1. The experimental results are consistent with a mechanism that involves significant bond breaking in the rate-limiting transition state (alpha(lg) = 0.64). Theoretical results for the reaction in the gas phase showed an excellent Br?nsted-type dependence with a beta(lg) of -1.03. A tetrahedral intermediate (TI) could not be found through DFT gas-phase studies (B3LYP/6-311+G*). Calculations carried out within a continuous solvation model or with discrete water molecules failed to find a stable TI. With both models, a flat region on the potential-energy surface is found and a tight optimization of the structures led back to starting materials. The theoretical results do not discard the possible existence of an unstable intermediate on the free-energy surface, but the analysis of the whole body of results compared with other acyl transfer reactions lead us to suggest that an enforced concerted mechanism is the most appropriate to describe these reactions.     

Quantum chemical study of the products and hypothetical intermediates in the dehydrobromination of bromobullvalene in furan

Equilibrium structural parameters of didehydrobullvalene, its adducts with furan, and tris(didehydrobullvalene) and bullvalenophenol tautomers have been determined by DFT M06-2X/cc-pVTZ quantum chemical calculations. The energies of the assumed Diels-Alder adducts are considerably higher than the energies of the isolated products, and the energy barriers separating them are fairly low. Interconversion of enantiomers of the major adduct via two sequential Cope rearrangements with calculated barriers of 17.2 and 15.0 kcal/mol, respectively, may be regarded as an example of truly degenerate mediated tautomerism.     

Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg(2)ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp(166), as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp(166) is short and dynamically stable, whereas the QM study indicates that an Asp(166)-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.     

Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis

A model based on classical concepts is derived to describe the effect of the nitro group on proton chemical shifts. The calculated chemical shifts are then compared to ab initio (GIAO) calculated chemical shifts. The accuracy of the two models is assessed using proton chemical shifts of a set of rigid organic nitro compounds that are fully assigned in CDCl3 at 700 MHz. The two methods are then used to evaluate the accuracy of different popular post-SCF methods (B3LYP and MP2) and molecular mechanics methods (MMX and MMFF94) in calculating the molecular structure of a set of sterically crowded nitro aromatic compounds. Both models perform well on the rigid molecules used as a test set, although when using the GIAO method a general overestimation of the deshielding of protons near the nitro group is observed. The analysis of the sterically crowded molecules shows that the very popular B3LYP/6-31G(d,p) method produces very poor twist angles for these, and that using a larger basis set [6-311++G(2d,p)] gives much more reasonable results. The MP2 calculations, on the other hand, overestimate the twist angles, which for these compounds compensates for the deshielding effect generally observed for protons near electronegative atoms when using the GIAO method at the B3LYP/6-311++G(2d,p) level. The most accurate results are found when the structures are calculated using B3LYP/6-311++G(2d,p) level of theory, and the chemical shifts are calculated using the CHARGE program based on classical models.     

Kinetics and mechanism of intramolecular carboxylic acid participation in the hydrolysis of N-methoxyphthalamic acid

The rate of formation and disappearance of phthalic anhydride (PAn) intermediate in the aqueous cleavage of N-methoxyphthalamic acid (NMPA) under acidic pH was studied spectrophotometrically in mixed CH3CN-H2O solvents. The rate of formation of PAn from NMPA is almost independent of the change in acetonitrile content from 20 to 70% v/v in mixed aqueous solvents. The rate constants for the formation of PAn from NMPA are approximately 10-fold smaller than the corresponding rate constants for the formation of PAn from o-carboxybenzohydroxamic acid (OCBA). These observations are ascribed to the consequence of the occurrence of slightly different mechanisms in these reactions.     

Quantum chemical calculations of the NHA bound nitric oxide synthase active site: O2 binding and implications for the catalytic mechanism

Density functional theory has been employed to model the binding of the intermediate substrate NHA, by nitric oxide synthases. In particular, the orientation and interactions of possibly catalytically important substrate hydrogens, with and without molecular oxygen bound to the active site heme group, are considered. Without O(2), three possible conformers have been found, with the energetically most favored structure being that in which both protons of the -NHOH moiety of NHA are directed toward the heme group. With oxygen bound, four different structures were found. The energetically lowest structure is again found to have both hydrogens of the -NHOH group pointing toward the heme group, thus forming hydrogen bonds between -NH- and the terminal oxygen, and between -OH and the inner oxygen of the heme-O(2) group. In addition, unprotonated structures of the substrate bound to the active site are considered and the proton affinity calculated.