577-71-9Relevant academic research and scientific papers
Biochemical identification of the catalytic residues of a glycoside hydrolase family 120 β-xylosidase, involved in xylooligosaccharide metabolisation by gut bacteria
Cecchini, Davide A.,Faur, Rgis,Laville, Elisabeth,Potocki-Veronese, Gabrielle
, p. 3098 - 3106 (2015/10/19)
The β-xylosidase B from Bifidobacterium adolescentis ATCC15703 belongs to the newly characterized family 120 of glycoside hydrolases. In order to investigate its catalytic mechanism, an extensive kinetic study of the wild-type enzyme and mutants targeting the three highly conserved residues Asp393, Glu416 and Glu364 was performed. NMR analysis of the xyloside hydrolysis products, the change of the reaction rate-limiting step for the Glu416 mutants, the pH dependency of E416A activity and its chemical rescue allowed to demonstrate that this GH120 enzyme uses a retaining mechanism of glycoside hydrolysis, Glu416 playing the role of acid/base catalyst and Asp393 that of nucleophile.
Leaving-group substituent controls reactivity and reaction mechanism in aminolysis of phenyl y-substituted-phenyl carbonates
Kang, Ji-Sun,Song, Yoon-Ju,Um, Ik-Hwan
, p. 2023 - 2028 (2013/09/02)
A kinetic study is reported for the nucleophilic substitution reactions of phenyl Y-substituted-phenyl carbonates (5a-5k) with piperidine in 80 mol % H2O/20 mol % DMSO at 25.0 ± 0.1 °C. The plots of k obsd vs. [piperidine] for the reactions of substrates possessing a strong electron-withdrawing group (EWG) in the leaving group (i.e., 5a-5i) are linear and pass through the origin. In contrast, the plots for the reactions of substrates bearing a weak EWG or no substituent (i.e., 5j or 5k) curve upward, indicating that the electronic nature of the substituent Y in the leaving group governs the reaction mechanism. Thus, it has been suggested that the reactions of 5a-5i proceed through a stepwise mechanism with a zwitterionic tetrahedral intermediate (i.e., T±) while those of 5j and 5k proceed through a stepwise mechanism with two intermediates (i.e., T± and its deprotonated form T-). The slope of the Bronsted-type plot for the second-order rate constants (i.e., kN or Kk2) changes from -0.41 to -1.89 as the leaving-group basicity increases, indicating that a change in the rate-determining step (RDS) occurs. The reactions of 5a-5k with piperidine result in larger k1 values than the corresponding reactions with ethylamine. Copyright
A kinetic study on ethylaminolysis of phenyl y-substituted-phenyl carbonates: Effect of leaving-group substituents on reactivity and reaction mechanism
Song, Yoon-Ju,Kim, Min-Young,Um, Ik-Hwan
, p. 1722 - 1726 (2013/07/26)
A kinetic study on nucleophilic substitution reactions of phenyl Y-substituted-phenyl carbonates (5a-5j) with ethylamine in 80 mol % H2O/20 mol % DMSO at 25.0 ± 0.1 oC is reported. The plots of kobsd vs. [amine] are linear for the reactions of substrates possessing a strong electron-withdrawing group (EWG) but curve upward for those of substrates bearing a weak EWG, indicating that the electronic nature of the substituent Y in the leaving group governs the reaction mechanism. The reactions have been concluded to proceed through a stepwise mechanism with one or two intermediates (a zwitterionic tetrahedral intermediate T± and its deprotonated form T-) depending on the nature of the substituent Y. Analysis of Bronsted-type plots and dissection of kobsd into microscopic rate constants have revealed that the reactions of substrates possessing a strong EWG (e.g., 5a-5f) proceed through T± with its formation being the rate-determining step, while those of substrates bearing a weak EWG (e.g., 5g-5j) proceed through T± and T-.
The α-effect in nucleophilic substitution reactions of Y-substituted-Phenyl X-substituted-cinnamates with Butane-2,3-dione monoximate
Kim, Min-Young,Son, Yu-Jin,Um, Ik-Hwan
, p. 2877 - 2882 (2014/01/06)
Second-order rate constants (kOx-) have been measured spectrophotometrically for nucleophilic substitution reactions of 4-nitrophenyl X-substituted-cinnamates (7a-7e) and Y-substituted-phenyl cinnamates (8a-8e) with butane-2,3-dione monoximate (Ox-) in 80 mol % H2O/20 mol % DMSO at 25.0 ± 0.1 °C. The Hammett plot for the reactions of 7a-7e consists of two intersecting straight lines while the Yukawa-Tsuno plot exhibits an excellent linearity with ρX = 0.85 and r = 0.58, indicating that the nonlinear Hammett plot is not due to a change in the rate-determining step but is caused by resonance stabilization of the ground state (GS) of the substrate possessing an electron-donating group (EDG). The Bronsted-type plot for the reactions of Y-substituted-phenyl cinnamates (8a-8e) is linear with βlg = - 0.64, which is typical of reactions reported previously to proceed through a concerted mechanism. The a-nucleophile (Ox-) is more reactive than the reference normalnucleophile (4-ClPhO-). The magnitude of the α-effect (i.e., the kOx-/k4-ClPhO- ratio) is independent of the electronic nature of the substituent X in the nonleaving group but increases linearly as the substituent Y in the leaving group becomes a weaker electron-withdrawing group (EWG). It has been concluded that the difference in solvation energy between Ox- and 4-ClPhO - (i.e., GS effect) is not solely responsible for the α-effect but stabilization of transition state (TS) through a cyclic TS structure contributes also to the Y-dependent a-effect trend (i.e., TS effect).
Chemoselective amide formation using O-(4-nitrophenyl)hydroxylamines and pyruvic acid derivatives
Kumar, Sonali,Sharma, Rashi,Garcia, Megan,Kamel, Joseph,McCarthy, Caroline,Muth, Aaron,Phanstiel, Otto
, p. 10835 - 10845 (2013/02/23)
A series of O-(4-nitrophenyl)hydroxylamines were synthesized from their respective oximes using a pulsed addition of excess NaBH3CN at pH 3 in 65a-75% yield. Steric hindrance near the oxime functional group played a key role in both the ease by which the oxime could be reduced and the subsequent reactivity of the respective hydroxylamine. Reaction of the respective hydroxylamines with pyruvic acid derivatives generated the desired amides in good yields. A comparison of phenethylamine systems bearing different leaving groups revealed significant differences in the rates of these systems and suggested that the leaving group ability of the Na-OR substituent plays an important role in determining their reactivity with pyruvic acid. Competition experiments (in 68% DMSO/phosphate buffered saline) using 1 equiv of N-phenethyl-O-(4-nitrophenyl)hydroxylamine and 2 equiv of pyruvic acid in the presence of other nucleophiles such as glycine, cysteine, phenol, hexanoic acid, and lysine demonstrated that significant chemoselectivity is present in this reaction. The results suggest that this chemoselective reaction can occur in the presence of excess α-amino acids, phenols, acids, thiols, and amines.
Probing synergy between two catalytic strategies in the glycoside hydrolase O-GlcNAcase using multiple linear free energy relationships
Greig, Ian R.,Macauley, Matthew S.,Williams, Ian H.,Vocadlo, David J.
supporting information; experimental part, p. 13415 - 13422 (2010/01/16)
Human O-GlcNAcase plays an important role in regulating the post-translational modification of serine and threonine residues with β-O-linked N-acetylglucosamine monosaccharide unit (O-GlcNAc). The mechanism of O-GlcNAcase involves nucleophilic participation of the 2-acetamido group of the substrate to displace a glycosidically linked leaving group. The tolerance of this enzyme for variation in substrate structure has enabled us to characterize O-GlcNAcase transition states using several series of substrates to generate multiple simultaneous free-energy relationships. Patterns revealing changes in mechanism, transition state, and rate-determining step upon concomitant variation of both nucleophilic strength and leaving group abilities are observed. The observed changes in mechanism reflect the roles played by the enzymic general acid and the catalytic nucleophile. Significantly, these results illustrate how the enzyme synergistically harnesses both modes of catalysis; a feature that eludes many small molecule models of catalysis. These studies also suggest the kinetic significance of an oxocarbenium ion intermediate in the O-GlcNAcase-catalyzed hydrolysis of glucosaminides, probing the limits of what may be learned using nonatomistic investigations of enzymic transition-state structure and offering general insights into how the superfamily of retaining glycoside hydrolases act as efficient catalysts.
Structure-reactivity correlations in nucleophilic substitution reactions of Y-substituted phenyl X-substituted benzoates with anionic and neutral nucleophiles
Um, Ik-Hwan,Lee, Ji-Youn,Fujio, Mizue,Tsuno, Yuho
, p. 2979 - 2985 (2008/02/11)
A kinetic study is reported for the reactions of 4-nitrophenyl X-substituted benzoates (1a-l) and Y-substituted phenyl benzoates (2a-l) with two anionic nucleophiles (OH- and CN-) and three amines (piperidine, hydrazine, and glycylglycine) in 80 mol% H2O-20 mol% dimethyl sulfoxide (DMSO) at 25.0 ± 0.1 °C. Each Hammett plot exhibits two intersecting straight lines for the reactions of 1a-l with the anionic nucleophiles and piperidine, while the Yukawa-Tsuno plots for the same reactions are linear. The Hammett plots for the reactions of 2a-l with hydrazine and glycylglycine demonstrate much better linear correlations with σ- constants than with σ° or σ constants, indicating that the leaving group departure occurs at the rate determining step (RDS). On the contrary, σ- constants result in poorer Hammett correlation than σ° constants for the corresponding reactions with OH- and CN-, indicating that the leaving group departure occurs after the RDS for the reactions with the anionic nucleophiles. The large ρX value (1.7 ± 0.1) obtained for the reactions of 1a-l with the anionic nucleophiles supports the proposal that the reactions proceed through an addition intermediate with its formation being the RDS. The Royal Society of Chemistry 2006.
Elucidation of the mechanism of polysaccharide cleavage by chondroitin AC lyase from Flavobacterium heparinum
Rye, Carl S.,Withers, Stephen G.
, p. 9756 - 9767 (2007/10/03)
Chondroitin AC lyase from Flavobacterium heparinum degrades chondroitin sulfate glycosaminoglycans via an elimination mechanism resulting in disaccharides or oligosaccharides with Δ4,5-unsaturated uronic acid residues at their nonreducing end. Mechanistic details concerning the ordering of the bond-breaking and -forming steps of this enzymatic reaction are nonexistent, mainly due to the inhomogeneous nature of the polymeric substrates. The creation of a new class of synthetic substrates for this enzyme has allowed the measurement of defined and reproducible kcat and Km values and has expanded the range of mechanistic studies that can be performed. The primary deuterium kinetic isotope effect upon kcat/Km for the abstraction of the proton α to the carboxylic acid was measured to be 1.67 ± 0.07, showing that deprotonation occurs in a rate-limiting step. Using substrates with leaving groups of differing reactivity, a flat linear free energy relationship was produced, indicating that the C4-O4 bond is not broken in a rate-determining step. Taken together, these results strongly suggest a stepwise mechanism. Consistent with this was the measurement of a secondary deuterium kinetic isotope effect upon kcat/Km of 1.01 ± 0.03 on a 4-{2H}-substrate, indicating that no sp2 character is developed at C4 during the rate-limiting step, thereby ruling out a concerted syn-elimination.
Synthesis of aryl 3-O-β-cellobiosyl-β-D-glucopyranosides for reactivity studies of 1,3-1,4-β-glucanases
Planas, Antoni,Abel, Mireia,Millet, Oscar,Palasi, Josep,Pallares, Cristina,Viladot, Josep-Lluis
, p. 53 - 64 (2007/10/03)
A series of substituted aryl β-glycosides derived from 3-O-β-cellobiosyl-D-glucopyranose with different phenol-leaving group abilities as measured by the pK(a) of the free phenol group upon enzymatic hydrolysis has been synthesised. Aryl β-glycosides with a pK(a) of the free phenol leaving group>5 were prepared by phase-transfer glycosidation of the per-O-acetylated α-glycosyl bromide with the corresponding phenol, whereas the 2,4-dinitrophenyl β-glycoside was obtained by condensation of 1-fluoro-2,4-dinitrobenzene with the partially acetylated trisaccharide followed by acid de-O-acetylation. The aryl β-glycosides have been used for reactivity studies of the wild-type Bacillus licheniformis 1,3-1,4-β-d-glucan 4-glucanohydrolase. The Hammett plot log k(cat) versus pK(a) is biphasic with an upward curvature at low pK(a) values suggesting a change in transition-state structure depending on the aglycon. Copyright (C) 1998 Elsevier Science Ltd.
Intrinsic acidity and basicity of 2,2,2-trifluoroethanethiol. The first experimental and theoretical study
Molina,Bouab,Esseffar,Herreros,Notario,Abboud,Mo,Yanez
, p. 5485 - 5491 (2007/10/03)
The gas phase acidity and basicity of 2,2,2-trifluoroethanethiol (TFET), i.e., the standard Gibbs energy changes for the following two reactions have been determined by means of Fourier transform ion cyclotron resonance spectroscopy: CF3CH2SH(g) → CF3CH2S-(g) + H+(g) and CF3CH2SH2+ (g) → CF3CH2SH(g) + H+(g). Also determined were the equilibrium constants for the 1:1 associations in dilute solution between TFET and pyridine N-oxide, 3,4-dinitrophenol (both in cyclohexane), and molecular iodine (in tetrachloromethane). Quantum-mechanical treatments at the G2(MP2) level were carried out on TFET, 2,2,2-trifluoroethanol, ethanethiol, and ethanol as neutral, protonated, and deprotonated species. Topological analyses of the charge densities and the Laplacians thereof were performed on all of them. This combination of experimental and theoretical information leads to a vastly enlarged view of structural effects on the reactivity of alcohols and thiols as well as to a satisfactory rationalization of the reactivity of TFET.
