Ab initio molecular dynamics simulations of elimination reactions in water solution: exploring the borderline region between the E1cb and E2 reaction mechanisms

We report a theoretical study, based on ab initio molecular dynamics simulations in water solution, of the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Recent theoretical and experimental evidence points toward the lack of a net distinction between the E1cb and E2 reaction paths, which seem to merge smoothly into each other in these borderline cases (Alunni, S.; De Angelis, F.; Ottavi, L.; Papavasileiou, M.; Tarantelli, F. J. Am.Chem. Soc. 2005, 127, 15151-15160). In this study, we explore the dynamics on the potential energy surface for the reaction of 2-(2-fluoroethyl)-1-methyl pyridinium with OH- by means of Car-Parrinello simulations in water solution. Our results indicate that the reaction mechanism effectively evolves through the potential energy region of the carbanion: the carbon-fluoride bond breaks only after the carbon-hydrogen bond, confirming the conclusions of a recently reported study of the potential energy surface for this system.     

Kinetics and mechanism of p-isopropenylphenol synthesis via hydrothermal cleavage of bisphenol A

Although bishydroxyarylalkanes are known to be reactive in high-temperature (T > 200 degrees C) liquid water (HTW), no mechanistic insight has been given to explain the reactivity of methylene bridge-containing diaryls under hydrothermal conditions. We examined the kinetics and mechanism of p-isopropenylphenol (IPP) synthesis via bisphenol A (BPA) cleavage in HTW. The cleavage reaction is first order in BPA. Cleavage of BPA in HTW occurs by specific acid catalysis, by specific base catalysis, and by general water catalysis. Under neutral conditions, the dominant mechanism is general base catalysis with water serving as the proton acceptor. We generated a detailed chemical kinetics model for the decomposition reaction based on a base-catalyzed mechanism in the literature. This three-parameter model fit the experimental data for BPA disappearance and formation of IPP and phenol and accurately predicted the yield of the IPP hydrolysis product acetone. Using acid- and base-catalyzed mechanisms, we explain the reactivity in HTW reported for other diaryl groups linked by methylene bridges and propose criteria for assessing the reactivity of methylene bridges under hydrothermal conditions.     

Evidence of a borderline region between E1cb and E2 elimination reaction mechanisms: a combined experimental and theoretical study of systems activated by the pyridine ring

We report a combined experimental and theoretical study to characterize the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Experimentally, the Taft correlation for H/D exchange, in OD(-)/D(2)O with noneliminating substrates (1-methyl-2-(2-Xethyl)pyridinium iodide), is used to predict the expected values of the rate constants for the elimination reactions with N-methylated substrates and F, Cl, Br as the leaving group. The comparison indicates an E1cb irreversible mechanism with F, but the deviation observed with Cl and Br does not allow a conclusive assignment. The theoretical calculations show that for the N-methylated substrate with a fluoride leaving group the elimination proceeds via formation of a moderately stable carbanion. No stable anionic intermediate is instead found when the leaving group is Cl or Br, as well as for any of the nonmethylated species, indicating a concerted elimination. The methylated substrate with Cl shows however only a moderate increase in reactivity compared to the fluorinated substrate, despite the change in mechanism. Very interestingly, our analysis of the computed two-dimensional potential energy surface for the reaction with a F leaving group indeed evidences the lack of a net distinction between the E1cb and E2 reaction paths, which appear to merge smoothly into each other in these borderline cases.     

Mimics of small ribozymes utilizing a supramolecular scaffold

For elucidating the mechanism of the general acid/base catalysis of the hydrolysis of RNA phosphodiester bonds, a number of cleaving agents having two cyclen moieties tethered to a 1,3,5-triazine core have been prepared and their ability to bind and cleave uridylyl-3',5'-uridine (UpU) studied over a wide pH range. Around neutral pH, the cleaving agents form a highly stable ternary complex with UpU and Zn(II) through coordination of the uracil N3 and the cyclen nitrogen atoms to the Zn(II) ions. Under conditions where the triazine core exists in the deprotonated neutral form, hydrolysis of UpU, but not of adenylyl-3',5'-adenosine (ApA), is accelerated by approximately two orders of magnitude in the presence of the cleaving agents, suggesting general base rather than metal ion catalysis. The probable mechanism of the observed catalysis and implications to understanding the general acid/base-catalyzed phosphodiester hydrolysis by ribozymes are discussed.     

Reaction of organosilicon hydrides with solid surfaces: an example of surface-catalyzed self-assembly

The solution-phase reactions of octadecylsilane (C(18)H(37)SiH(3)) with 10 high surface area metal oxides (groups II-VIII) were investigated. C(18)H(37)SiH(3) reacted with most metal oxides at room temperature and produced supported monolayers (self-assembled monolayers, SAMs) with a high grafting density of C(18), approximately 4.5-5 groups/nm(2). According to the FTIR and (29)Si NMR spectra, molecules in the SAMs demonstrated "horizontal" cross-linking (Si-O-Si and Si-OH.HO-Si bonds) and little or no "vertical" bonds with the metal oxide forming an amorphous, yet ordered film. Also, approximately 3 mol of H(2) was formed per each mole of grafted C(18), indicating complete hydrolysis of C(18)H(37)SiH(3) during the reaction. On the basis of the activity of different metal oxides, we concluded that the hydrolysis of C(18)H(37)SiH(3), the key step in the reaction mechanism, is catalyzed by water adsorbed on acidic and basic centers (Lewis and Br?nsted) of the surface of metal oxide. Metal oxides and solids with weak acidic and basic properties, like silica, carbon, and organic polymers, do not react with C(18)H(37)SiH(3). Increasing the temperature of the reaction or doping neutral surfaces with acids or bases greatly increases their activity in the reaction with RSiH(3).     

Intramolecular general base catalyzed ester hydrolysis. The hydrolysis of 2-aminobenzoate esters

Rate constants have been obtained for the hydrolysis of the trifluoroethyl, phenyl, and p-nitrophenyl esters of 2-aminobenzoic acid at 50 degrees C in H(2)O. The pseudo-first-order rate constants, k(obsd), are pH independent from pH 8 to pH 4 (the pK(a) of the amine group conjugate acid). The 2-aminobenzoate esters hydrolyze with similar rate constants in the pH-independent reactions, and these water reactions are approximately 2-fold slower in D(2)O than in H(2)O. The most likely mechanism involves intramolecular general base catalysis by the neighboring amine group. The rate enhancements in the pH-independent reaction in comparison with the pH-independent hydrolysis of the corresponding para substituted esters or the benzoate esters are 50-100-fold. In comparison with the hydroxide ion catalyzed reaction, the enhancement in k(obsd) at pH 4 with the phenyl ester is 10(5)-fold. Intramolecular general base catalyzed reactions are assessed in respect to their relative advantages and disadvantages in enzyme catalysis. A general base catalyzed reaction can be more rapid at low pH than a nucleophilic reaction that has a marked dependence on pH and the leaving group.     

Nucleophilic substitution reactions of N-chloramines: evidence for a change in mechanism with increasing nucleophile reactivity

Third-order rate constants (kNu)H (M-2 s-1) for the hydronium ion catalyzed reactions of a range of nucleophiles with N-chlorotaurine (1) in water at 25 degrees C and I=0.5 (NaClO4) are reported. The solvent deuterium isotope effects on hydronium ion catalysis of the reaction with 1 of bromide and iodide ion are (kBr)H/(kBr)D=0.30 and (kI)H/(kI)D=0.54, respectively. The inverse nature of these isotope effects and the absence of general acid catalysis are consistent with a stepwise mechanism involving protonation of 1 in a fast preequilibrium step. The appearance of strong catalysis by general acids for the reaction of the more nucleophilic SO(3)2- and HOCH2CH2S- with the chloramine indicates a change to a concerted mechanism, with protonation of the chloramine at nitrogen and chlorine transfer to the nucleophile occurring in a single step. A rough estimate of the lifetime of the protonated chloramine in the presence of the thiolate anion suggests that the concerted mechanism is enforced by the absence of a significant lifetime of the protonated substrate in contact with the nucleophile. Theoretical calculations provide evidence against an electron-transfer mechanism for chlorination of the nucleophiles by protonated 1.     

Transition-state analysis of the DNA repair enzyme MutY

The transition state (TS) structure of MutY-catalyzed DNA hydrolysis was solved using multiple kinetic isotope effect (KIE) measurements. MutY is a base excision repair enzyme which cleaves adenine from 8-oxo-G:A mismatches in vivo, and also from G:A mismatches in vitro. TS analysis of G:A-DNA hydrolysis revealed a stepwise S(N)1 (D(N)*A(N)(double dagger)) mechanism proceeding through a highly reactive oxacarbenium ion intermediate which would have a lifetime in solution of <10(-10) s. C-N bond cleavage is reversible; the N-glycoside bond breaks and reforms repeatedly before irreversible water attack on the oxacarbenium ion. KIEs demonstrated that MutY uses general acid catalysis by protonating N7. It enforces a 3'-exo sugar ring conformation and other sugar ring distortions to stabilize the oxacarbenium ion. Combining the experimental TS structure with the previously reported crystal structure of an abortive Michaelis complex elucidates the step-by-step catalytic sequence.     

Modeling the chemical step utilized by human alkyladenine DNA glycosylase: a concerted mechanism AIDS in selectively excising damaged purines

Human alkyladenine DNA glycosylase (AAG) initiates the repair of a wide variety of (neutral or cationic) alkylated and deaminated purines by flipping damaged nucleotides out of the DNA helix and catalyzing the hydrolytic N-glycosidic bond cleavage. Unfortunately, the limited number of studies on the catalytic pathway has left many unanswered questions about the hydrolysis mechanism. Therefore, detailed ONIOM(M06-2X/6-31G(d):AMBER) reaction potential energy surface scans are used to gain the first atomistic perspective of the repair pathway used by AAG. The lowest barrier for neutral 1,N(6)-ethenoadenine (εA) and cationic N(3)-methyladenine (3MeA) excision corresponds to a concerted (A(N)D(N)) mechanism, where our calculated ΔG(?) = 87.3 kJ mol(-1) for εA cleavage is consistent with recent kinetic data. The use of a concerted mechanism supports previous speculations that AAG uses a nonspecific strategy to excise both neutral (εA) and cationic (3MeA) lesions. We find that AAG uses nonspecific active site DNA-protein π-π interactions to catalyze the removal of inherently more difficult to excise neutral lesions, and strongly bind to cationic lesions, which comes at the expense of raising the excision barrier for cationic substrates. Although proton transfer from the recently proposed general acid (protein-bound water) to neutral substrates does not occur, hydrogen-bond donation lowers the catalytic barrier, which clarifies the role of a general acid in the excision of neutral lesions. Finally, our work shows that the natural base adenine (A) is further inserted into the AAG active site than the damaged substrates, which results in the loss of a hydrogen bond with Y127 and misaligns the general base (E125) and water nucleophile to lead to poor nucleophile activation. Therefore, our work proposes how AAG discriminates against the natural purines in the chemical step and may also explain why some damaged pyrimidines are bound but are not excised by this enzyme.     

Hydrolysis of schiff bases 2: Intramolecular catalysis of an ortho-hydroxy group in nonionic surfactant systems

The rates of hydrolysis of N-(2&4-hydroxybenzylidene)-2-aminobenzothiazoles has been studied in the pH range 4–13 in a 10% dioxane-water system and in various nonionic surfactant systems. The reaction is found to be due to water mediated intramolecular general base catalysis within the pH range 4.0 to 12.0 and due to nucleophilic catalysis beyond pH 12.0. A ten membered intermediate facilitating transannular attack of a water molecule on the methine carbon forming a naphthalene type transition state has been proposed. The reactivity difference in water and nonionic surfactants has been explained by a suitable entrapment model.     

General base and general acid catalyzed intramolecular aminolysis of esters. Cyclization of esters of 2-aminomethylbenzoic acid to phthalimidine

Plots of log k(0) vs pH for the cyclization of trifluoroethyl and phenyl 2-aminomethylbenzoate to phthalimidine at 30 degrees C in H(2)O are linear with slopes of 1.0 at pH >3. The values of the second-order rate constants k(OH) for apparent OH(-) catalysis in the cyclization reactions are 1.7 x 10(5) and 5.7 x 10(7) M(-)(1) s(-)(1), respectively. These rate constants are 10(5)- and 10(7)-fold greater than for alkaline hydrolysis of trifluoroethyl and phenyl benzoate. The k(OH) for cyclization of the methyl ester is 7.2 x 10(3) M(-)(1) s(-)(1). Bimolecular general base catalysis occurs in the intramolecular nucleophilic reactions of the neutral species. The value of the Bronsted coefficient beta for the trifluoroethyl ester is 0.7. The rate-limiting step in the general base catalyzed reaction involves proton transfer in concert with leaving group departure. The mechanism involving rate-determining proton transfer exemplified by the methyl ester in this series (beta = 1.0) can then be considered a limiting case of the concerted mechanism. General acid catalysis of the neutral species reaction or a kinetic equivalent also occurs when the leaving group is good (pK(a) 相似文献   

Efficient intramolecular general acid catalysis of nucleophilic attack on a phosphodiester

The hydrolysis of methyl 8-dimethylamino-1-naphthyl phosphate 4 and its reactions with a representative range of nucleophiles are catalyzed by the dimethylammonium group at acidic pH with rate accelerations of the order of 106. The reaction persists up to pH 7 because the strong intramolecular hydrogen bond, which is the key to efficient general acid catalysis, is present also in the reactant. The sensitivity to the basicity of the nucleophile (Br?nsted beta(nuc) = 0.29) lies between values measured previously for mono- and triesters. The comparisons suggest that general acid catalyzed reactions of phosphate mono- or diesters with strongly basic oxyanion nucleophiles (like those derived from a serine oxygen or a bound water molecule in an enzyme active site) will be fastest when their negative charges are neutralized by protonation. Reactions with NH2OH and its N-methylated derivatives show an apparent alpha-effect, but NH2OMe reacts no faster than a primary amine of similar basicity. It is suggested that the reaction involving NH2OH as an oxygen nucleophile proceeds through the pre-equilibrium formation of the tautomer H3N+-O- as the active nucleophile: ab initio calculations support this idea.     

Simplified speciation and improved phosphodiesterolytic activity of hydroxo complexes of trivalent lanthanides in aqueous DMSO

Potentiometric titrations of La(III), Nd(III), and Eu(III) perchlorates by Me 4N(OH) in 80% vol aq DMSO revealed formation of predominantly mononuclear complexes M(OH)n(3- n) (n = 1, 2, or 3) and a single binuclear complex M2(OH)(5+). Kinetics of the cleavage of two phosphate diesters, bis (4-nitrophenyl) phosphate (BNPP) and 2-hydroxypropyl 4-nitrophenyl phosphate (HPNPP), and a triester, 4-nitrophenyl diethyl phosphate (paraoxon), were studied as a function of metal and Me4N(OH) concentrations in the same medium. Rate of BNPP cleavage is second-order in metal and is proportional to the product of concentrations of M(OH)2(+) and M(OH)3 species. Rate of HPNPP cleavage is proportional to [M(OH)3](3) for La(III) and Nd(III) and to [M(OH)3](2) for Eu(III). Proposed mechanism for BNPP hydrolysis involves formation of M2(OH)5(diester) intermediate followed by intramolecular nucleophilic attack of hydroxide anion on the phosphoryl group of the substrate. Proposed mechanism for HPNPP cleavage involves formation of M3(OH)9(diester)(-) or M2(OH)6(diester)(-) intermediates followed by the general base-assisted intramolecular cyclization of HPNPP. The latter mechanism is supported by observation of the solvent kinetic isotope effect k H/kD = 2.9 for Eu(III) catalyzed HPNPP cleavage. The efficiency of catalysis in 80% DMSO is much higher than in water. The reaction rate observed in the presence of 1 mM metal in neutral solution surpasses the rate of background hydrolysis by a factor of 10(12)-10(13) for BNPP and 10(10) for HPNPP. The increased catalytic activity is attributed principally to the preferable solvation of lanthanide ions by DMSO, which creates an anhydrous microenvironment favorable for reaction in the coordination sphere of the catalyst. The catalytic activity of lanthanides in paraoxon hydrolysis is much lower with the estimated efficiency of catalysis about 10(5) for 1 mM La(III).     

The role of metal ions in phosphate ester hydrolysis

Many phosphatases make use of metal ions to aid catalysis of phosphate ester hydrolysis. Here, we investigate the impact of metal ions on the potential energy surface (PES), and hence the preferred reaction mechanism, for a simple model for hydrolysis of phosphate ester monoanions. We show that, while both associative (A(N) + D(N)) and dissociative (D(N) + A(N)) mechanisms are represented on the potential energy surfaces both in the presence and absence of metal ions, the D(N) + A(N) process is favoured when there are no metal ions present and the A(N) + D(N) process is favoured in the presence of two metal ions. A concerted (A(N)D(N)) process is also available in the presence of two metal ions, but proceeds via a high-energy transition state. In the presence of only a single metal ion the A(N)D(N) process is the most favoured, but still proceeds via a high-energy transition state. Thus, we conclude that metallo-enzyme phosphatases are likely to utilise an associative process, while those that function without metal ions may well follow a dissociative process.     

Intramolecular reaction and intramolecular catalysisd̊ II. Mechanism of intramolecular catalysis in hydrolysis of 2-(2'-benzimidazolyl)phenyl acetate by benzimidazolyl group

As a model for acetyl-α-chymotrypsin, 2-(2'-benzimidazolyl)phenyl acetate was synthesized in a good yield and its hydrolytic kinetics has been studied in buffer solutions at 45'C within a wide pH range (0.65–8.80). The measured pseudo-first-order rate constants (k_obs) at different pH values conform well with the data derived from the proposed theoretical model. It is shown that in an acidic solution of medium strength (pH = 2.0–3.0), the ester is hydrolyzed via intramolecular general acid catalysis by benzimidazolium cation; while at pH values near neutrality (pH = 5.5–7.0), this ester is hydrolyzed via intramolecular general base catalysis by neutral benzimidazole. These findings are discussed and the activation parameters of the hydrolysis reaction were also determined.     

Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters

The mechanism of the hydrolysis reaction of the unprotonated methyl triphosphate (MTP) ester in water clusters has been modeled. The effective fragment potential based quantum mechanical-molecular mechanical (QM/MM) approach has been applied in the simulations. It is shown that the minimum energy reaction path is consistent with an assumption of a two-step dissociative-type process similar to the case of the guanosine triphosphate (GTP) hydrolysis in the Ras-GAP protein complex (Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Cachau, R. E.; Burt, S. K. Proteins: Struct., Funct., Bioinf. 2005, 60, 495). At the first stage, a unified action of environmental molecular groups and the catalytic water molecule leads to a substantial spatial separation of the gamma-phosphate group from the rest of the molecule. At the second stage, inorganic phosphate H2PO4- is formed from water and the metaphosphate anion PO3- through the chain of proton transfers along hydrogen bonds. The estimated activation barriers for MTP in aqueous solution at both stages (20 and 14 kcal/mol) are substantially higher than the corresponding barriers for the GTP hydrolysis in the protein.     

Catalysis by [Ga4L6]12− Metallocage on the Nazarov Cyclization: The Basicity of Complexed Alcohol is Key

The Nazarov cyclization is investigated in solution and within K₁₂[Ga₄L₆] supramolecular organometallic cage by means of computational methods. The reaction needs acidic condition in solution but works at neutral pH in the presence of the metallocage. The reaction steps for the process are analogous in both media: (a) protonation of the alcohol group, (b) water loss and (c) cyclization. The relative Gibbs energies of all the steps are affected by changing the environment from solvent to the metallocage. The first step in the mechanism, the alcohol protonation, turns out to be the most critical one for the acceleration of the reaction inside the metallocage. In order to calculate the relative stability of protonated alcohol inside the cavity, we propose a computational scheme for the calculation of basicity for species inside cavities and can be of general use. These results are in excellent agreement with the experiments, identifying key steps of catalysis and providing an in-depth understanding of the impact of the metallocage on all the reaction steps.     

Hydrolysis of acetals in water under hydrothermal conditions

A simple method for the hydrolysis of acetals and ketals was accomplished in neutral water or aqueous media by hydrothermal treatment without using acidic reagents. The deacetalization reaction was effectively accelerated in the presence of calcium chloride. Because no acidic catalysts were employed, neutralization of the reaction mixture was not necessary after the reaction. This sequence was successfully applied to the hydrolysis of chitosan, a biodegradable polyaminosaccharide.     

Hydrolysis on transition metal oxide clusters and the stabilities of M-O-M bridges

Water addition to molecular single, double and triple M-O-M bridges (M = Sc, Ti, V, Cr, and Mn) were considered, and the stabilities toward stepwise hydrolysis of the oxygen bridges were studied by means of quantum chemistry. The M-O bond distances for the studied systems were compared to experiment for demonstration of the applicability of the B3LYP functional to the investigated systems. While substantial exothermicities were found for the hydrolysis of double and triple M-O-M bridges, addition of water to a single bridge was generally found to be slightly endothermic. The lack of enthalpy drive for the (OH)yOxM-O-MOx(OH)y + H2O-->2MOx-1(OH)y+2 reaction was taken to suggest that entropy increase and the formation of mononuclear water complexe, would be decisive factors for the dissociation. A mechanism was proposed for the observed erosion of the protective chromium oxide scale on high-temperature alloys at elevated temperatures and high humidities, based on the formation of CrO2(OH)2(g).