The effect of restricted intramolecular energy flow on the rate of one-substrate enzyme catalyzed reaction

We assume that the free intramolecular energy flow (intramolecular vibrational energy redistribution—IVR) between bonded substrate and enzyme can be restricted due to the presence of a metal atom near the binding site of enzyme. This restriction can represent one of the factors of enzyme catalysis. The concentration of energy evolved during the formation of enzyme-substrate complex in the bonded substrate enhances the reaction rate by several orders of magnitude in comparison with the case of free dissipation of evolved energy into the enzyme.     

The isomerization of methoxy radical: intramolecular hydrogen atom transfer mediated through acid catalysis

The catalytic ability of water, formic acid, and sulfuric acid to facilitate the isomerization of the CH(3)O radical to CH(2)OH has been studied. It is shown that the activation energies for isomerization are 30.2, 25.7, 4.2, and 2.3 kcal mol(-1), respectively, when the reaction is carried out in isolation and with water, formic acid, or sulfuric acid as a catalyst. The formation of a doubly hydrogen bonded transition state is central to lowering the activation energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. The changes in the rate constant for the CH(3)O-to-CH(2)OH isomerization with acid catalysis have also been calculated at 298 K. The largest enhancement in the rate, by over 12 orders of magnitude, is with sulfuric acid. The results of the present study demonstrate the feasibility of acid catalysis of a gas-phase radical isomerization reaction that would otherwise be forbidden.     

Intramolecular, intermolecular, and heterogeneous nonadiabatic dissociative electron transfer to peresters

The electron transfer to peresters was studied by electrochemical means in N,N-dimethylformamide. The reduction was carried out by three independent methods: (i) heterogeneously, by using glassy carbon electrodes, (ii) homogeneously, by using electrogenerated radical anions as the donors, and (iii) intramolecularly, by using purposely synthesized donor-spacer-acceptor (D-Sp-A) systems. Convolution analysis of the heterogeneous data led to results in excellent agreement with the dissociative electron transfer theory. The homogeneous redox catalysis data also confirmed the reduction mechanism. The cyclic voltammetries of the D-Sp-A molecules could be simulated, leading to determination of the corresponding intramolecular dissociative rate constants. Analysis of the results showed that, regardless of the way by which the acceptor is reduced, the investigated dissociative electron transfers are strongly nonadiabatic and, particularly, that the experimental rates are several orders of magnitude smaller than the adiabatic limit. A possible mechanism responsible for the observed behavior is discussed.     

Synthesis of functionalized tetrahydropyridones by the tandem Knoevenagel—Michael—intramolecular ammonolysis—alkylation reaction

Russian Chemical Bulletin - The tandem Knoevenagel—Michael—intramolecular ammonolysis—alkylation reaction was used to synthesize functionalized tetrahydropyridones. The molecular...     

Palladium(II) extraction by sulfur-containing calix[4,6]arenes from hydrochloric acid solutions

The comparison of the extraction properties of calixarenes, thiacalixarenes, and calix[4,6]arene thioethers showed that methyl(thiamethyl)calix[4,6]arenes 3a and 4a have the highest extraction abilities. These extractants rapidly and completely extract palladium from hydrochloric acid solutions; regarding distribution factors achieved in the kinetic mode, they three to four orders of magnitude exceed their monodentate analogue, octylbenzyl sulfide (OBnS). Approaches are considered to enhance palladium extraction via generating mixed palladium species in low-acidity solutions and via intramolecular catalysis by the protonated oxygen atoms of alkoxy groups in the lower rim. For 1 M HCl, the kinetic order of diluent effects on palladium extraction was established. The substitution of sulfur atoms for bridging CH₂ groups was discovered to enhance palladium extraction by calix[4]arene thioether 3c.     

Models for intramolecular triplet exciton migration applied to vinyl aromatic polymers

Models for intramolecular triplet exciton migration have been developed for vinyl aromatic polymers. A one-dimensional model which allows only neighbor-to-neighbor migrations yields frequencies which are several orders of magnitude smaller than those predicted either by exchange or dipole-dipole mechanisms. An intramolecular model permitting three translational degrees of freedom predicts triplet exciton hop frequencies on the order of 10⁴ s⁻ in reasonable agreement with either exchange or dipole-dipole mechanisms.     

Kinetics and mechanisms of hydrolysis and aminolysis of thioxocephalosporins

The effect of replacing the beta-lactam carbonyl oxygen in cephalosporins by sulfur on their reactivity has been investigated. The second-order rate constant for alkaline hydrolysis of the sulfur analogue is 2-fold less than that for the natural cephalosporin. The thioxo derivative of cephalexin, with an amino group in the C7 side chain, undergoes beta-lactam ring opening with intramolecular aminolysis by a reaction similar to that for cephalexin itself. However, the rate of intramolecular aminolysis for the S-analogue is 3 orders of magnitude greater than that for cephalexin. Furthermore, unlike cephalexin, intramolecular aminolysis in the S-analogue occurs up to pH 14 with no competitive hydrolysis. The rate of intermolecular aminolysis of natural cephalosporins is dominated by a second-order dependence on amine concentration, whereas that for thioxocephalosporins shows only a first-order term in amine. The Bronsted beta(nuc) for the aminolysis of thioxo-cephalosporin is +0.39, indicative of rate-limiting formation of the tetrahedral intermediate with an early transition state with relatively little C-N bond formation.     

Photochemical properties of the naphthol-styrylquinoline dyad in neutral and ionic forms

The photochemical properties of the naphthol-styrylquinoline dyad 2-(E)-{4-[4-(3-hydroxynaphthalen-2-yloxy)butoxy]styryl}quinoline (SQ4Np) have been investigated. It has been found that the excited-state acidity of the styrylquinoline (SQ) moiety is reduced by six orders of magnitude and that of the naphthol (Np) moiety increases by four orders of magnitude. As part of the dyad in the neutral and protonated forms, the SQ moiety retains a high photoisomerization quantum yield characteristic of model styrylquinoline. Deprotonation of the Np moiety of the dyad reduces the SQ photoisomerization quantum yields, presumably because of the formation of intramolecular complexes (exciplexes) or energy transfer to the Np anion.     

Fluorescence enhancements of benzene-cored luminophors by restricted intramolecular rotations: AIE and AIEE effects

Photoluminescence of simple arylbenzenes with ready synthetic accessibility is enhanced by two orders of magnitude through aggregate formation; viscosity and temperature effects indicate that the emission enhancement is due to the restriction of their intramolecular rotations in the solid state.     

Synthesis of polyhydroxylated 7-aminopyrrolizidines and 8-aminoindolizidines

The ammonolysis of a lactone moiety in tricyclic cycloadducts derived from non-racemic five-membered cyclic nitrone and 2(5H)-furanones furnishes an amido function, which after subsequent Hofmann rearrangement, leads to a protected amino group attached to the bicyclic isoxazolidine skeleton. A successive simple transformation, involving cleavage of N-O bond followed by intramolecular N-alkylation, provides an access to the polyhydroxylated 7-aminopyrrolizidines and 8-aminoindolizidines, potential glycosidases inhibitors.     

Reactivity of ethyl acetate and its derivatives toward ammonolysis: ramifications for ammonolysis‐based microencapsulation process

The reactivity of three ester organic solvents toward ammonolysis was examined in relation to the development of an ammonolysis‐based microencapsulation process. Ethyl acetate, ethyl chloroacetate, and ethyl fluoroacetate were chosen as ester organic solvents. Progesterone was considered as a model drug to be encapsulated into poly‐D , L ‐lactide‐co‐glycolide microspheres. A polymeric dispersed phase was emulsified in an aqueous phase, to which ammonia was added to initiate ammonolysis. The polarization status of a carbonyl group in the backbone of the ester was found to decide the magnitude of the ester reactivity. In fact, the simple ester ethyl acetate hardly reacted with ammonia, while ethyl chloroacetate and ethyl fluoroacetate showed greater reactivity toward ammonolysis. The rapid completion of ammonolysis led to the conversion of the water‐immiscible solvents into water‐soluble solvents, thereby providing an efficient tool for microsphere solidification. Among microencapsulation parameters, the type of dispersed solvent, the molar ratio of ammonia to a dispersed solvent, and the percentage of the progesterone payload decisively influenced the characteristics of the microspheres. Subsequently, variations in such parameters accompanied considerable influence on microsphere morphology, incorporation efficiency, thermal behavior, the degree of residual solvents, and the physical status of progesterone. Optimization of the process parameters would not only contribute to improving the ammonolysis‐based microencapsulation process, but would also permit the tailoring of microsphere properties to specific demands. Copyright © 2008 John Wiley & Sons, Ltd.     

Solvent polarity effects and limited acid catalysis in rearrangements of model radicals for the methylmalonyl-CoA mutase- and isobutyryl-CoA mutase-catalyzed isomerization reactions

The kinetics of reactions of models for the intermediate radicals formed in the methylmalonyl-CoA mutase- and isobutyryl-CoA mutase-catalyzed rearrangements were studied by laser flash photolysis methods. The aldehyde-containing model analogous to the propanal-3-yl radical reacted via 3-exo cyclization with rate constants that varied with solvent polarity (k in the range 2 x 105 to 1 x 107 s-1). The analogous methyl ketone-containing radical reacted 2 orders of magnitude less rapidly, and the ethylthiocarbonyl-containing radical analogue reacted too slowly for kinetic measurements. No acid catalysis was observed in acetic acid, but the CF3CO2H-complexed radicals reacted 1 order of magnitude faster than the uncomplexed radicals. The results indicate that catalysis of the 3-exo radical cyclizations of the radicals formed in the enzymes by hydrogen bonding to an acid, so-called "partial protonation", is not adequate for acceleration of the reactions to the point of kinetic competence. A dissociative mechanism for the radical rearrangements in nature is considered as an alternative.     

Setting the stage for new catalytic functions in designed proteins--exploring the imine pathway in the efficient decarboxylation of oxaloacetate by an Arg-Lys site in a four-helix bundle protein scaffold

Fourteen 42-residue polypeptides have been designed to identify reactive sites for the catalysis of the decarboxylation of oxaloacetate, a chemical transformation that proceeds through the formation of an imine intermediate. The sequences fold into helix-loop-helix motifs and dimerize to four-helix bundles. The catalytically active lysine residues were incorporated in several surface exposed positions, but also in positions characterised by hydrophobic properties to reduce their pKa values. The molecular environments of the Lys residues were systematically varied, to find which residues were able to stabilise and bind the imine intermediate in the decarboxylation reaction. A two-residue Arg-Lys site formed the main component of the reactive site of the helix-loop-helix dimer Decarb-K34_R33, which obeyed saturation kinetics in catalysing the reaction with a kcat/KM of 0.59 M-1S-1. The rate constant measured was nearly three orders of magnitude larger than the second-order rate constant of the butylamine-catalysed reaction (0.0011 M-1S-1), and four orders of magnitude larger than the pseudo first-order rate constant of the uncatalyzed reaction (1.3 x 10(-5) s(-1)). The sequence of Decarb-K34_R33 contained only a single lysine residue. It was flanked by an arginine in the preceding position in the sequence. A flanking Arg residue provided more efficient catalysis than a flanking Lys or Gln residue. Arginines in flanking positions in the helix, in positions four residues before or after the Lys in the sequence, are not as important in catalysis as the Arg of the Arg-Lys pair. The effect of pKa on the catalytic efficiency of the Lys residue in the decarboxylation reaction is well known. The identification of the role of the flanking Arg residue in catalysing decarboxylation, its optimal position, and the importance of conformational stability reported here sets the stage for developing a number of catalytic systems that depend on the formation of imine intermediates, but that lead to different reaction products.     

Steric desolation enhances the effective molarities of intramolecular H-bonding interactions

Free energy contributions due to intramolecular phosphonate diester-phenol H-bonds have been measured for 20 different supramolecular architectures in cyclohexanone solution. High throughput UV/Vis titrations were used in combination with chemical double mutant cycles to dissect out the contributions of different functional group interactions to the stabilities of over 100 different zinc porphyrin-pyridine ligand complexes. These complexes have previously been characterised in toluene and in 1,1,2,2-tetrachloroethane (TCE) solution. Intramolecular ester-phenol H-bonds that were measured in these less polar solvents are too weak to be detected in cyclohexanone, which is a more competitive solvent. The stability of the intermolecular phosphonate diester-phenol H-bond in cyclohexanone is an order of magnitude lower than in TCE and two orders of magnitude lower than in toluene. As a consequence, only seven of the twenty intramolecular phosphonate diester-phenol interactions that were previously measured in toluene and TCE could be detected in cyclohexanone. The effective molarities (EM) for these intramolecular interactions are different in all three solvents. Determination of the EM accounts for solvent effects on the strengths of the individual H-bonding interactions and the zinc porphyrin-pyridine coordination bond, so the variation in EM with solvent implies that differences in the solvation shells make significant contributions to the overall stabilities of the complexes. The results suggest that steric effects lead to desolvation of bulky polar ligands. This increases the EM values measured in TCE, because ligands that fail to replace the strong interactions made with this solvent are unusually weakly bound compared with ligands that make intramolecular H-bonds.     

Insights into the free-energy dependence of intramolecular dissociative electron transfers

To study the relationship between rate and driving force of intramolecular dissociative electron transfers, a series of donor-spacer-acceptor (D-Sp-A) systems has been devised and synthesized. cis-1,4-Cyclohexanedyil and a perester functional group were kept constant as the spacer and acceptor, respectively. By changing the aryl substituents of the phthalimide moiety, which served as the donor, the driving force could be varied by 0.74 eV. X-ray diffraction crystallography and ab initio conformational calculations pointed to D-Sp-A molecules having the cis-(cyclohexane) equatorial(phthalimido)-axial(perester) conformation and the same D/A orientation. The intramolecular dissociative electron-transfer process was studied by electrochemical means in N,N-dimethylformamide, in comparison with thermodynamic and kinetic information obtained with models of the acceptor and the donor. The intramolecular process consists of the electron transfer from the electrochemically generated phthalimide-moiety radical anion to the peroxide functional group. The electrochemical analysis provided clear evidence of a concerted dissociative electron-transfer mechanism, leading to the cleavage of the O-O bond. Support for this mechanism was obtained by ab initio MO calculations, which provided information about the LUMO of the acceptor and the SOMO of the donor. The intramolecular rate constants were determined and compared with the corresponding intermolecular values, the latter data being obtained by using the model molecules. As long as the effective location of the centroid of the donor SOMO does not vary significantly by changing the aryl substituent(s), the intramolecular dissociative electron transfer obeys the same main rules already highlighted for the corresponding intermolecular process. On the other hand, introduction of a nitro group drags the SOMO away from the acceptor, and consequently, the intramolecular rate drops by as much as 1.6 orders of magnitude from the expected value. Therefore, a larger solvent reorganization than for intermolecular electron transfers and the effective D/A distance and thus electronic coupling must be taken into account for quantitative predictions of intramolecular rates.     

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   

Iridium-catalyzed silylation of unactivated C–H bonds

The functionalization of primary C–H bonds has been a longstanding challenge in catalysis. Our group has developed a series of silylations of primary C–H bonds that occur with site selectivity and diastereoselectivity resulting from an approach to run the reactions as intramolecular processes. These reactions have become practical by using an alcohol or amine as a docking site for a hydrosilyl group, thereby leading to intramolecular silylations of C–H bonds at positions dictated by the presence common functional groups in the reactants. Oxidation of the C–Si bond leads to the introduction of alcohol functionality at the position of the primary C–H bond of the reactant. The development, scope, and applications of these functionalization reactions is described in this minireview.     

Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4)

The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fast (ms-μs) intramolecular ET in an electrochemical environment has recently been achieved by controlling the molecular orientation of the protein assembled on a gold electrode surface. In this work we have performed computational modeling of the intramolecular ET process by a combination of density functional theory (DFT) and quantum mechanical charge transfer theory to disclose reasons for this difference. We first address the electronic structures of the model heme core with histidine and methionine axial ligands in both low- and high-spin states by structure-optimized DFT. The computations enable estimating the intramolecular reorganization energy of the ET process for different combinations of low- and high-spin heme couples. Environmental reorganization free energies, work terms ("gating") and driving force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe-Fe separations. The reactivity of low- and high-spin heme groups was notably different. The ET rate is exceedingly low for the crystallographic equilibrium orientation but increases by several orders of magnitude for thermally accessible non-equilibrium configurations. Deprotonation of the propionate carboxyl group was also found to enhance the ET rate significantly. The results are discussed in relation to the observed surface immobilization effect and support the notion of conformationally gated ET.     

DNA-based asymmetric catalysis: sequence-dependent rate acceleration and enantioselectivity

This study shows that the role of DNA in the DNA-based enantioselective Diels-Alder reaction of azachalcone with cyclopentadiene is not limited to that of a chiral scaffold. DNA in combination with the copper complex of 4,4'-dimethyl-2,2'-bipyridine (Cu-L1) gives rise to a rate acceleration of up to 2 orders of magnitude compared to Cu-L1 catalysis alone. Furthermore, both the enantioselectivity and the rate enhancement prove to be dependent on the DNA-sequence. These features are the main reasons for the efficient and enantioselective catalysis observed with salmon testes DNA/Cu-L1 in the Diels-Alder reaction. The fact that absolute levels of stereocontrol can be achieved with a simple and weak DNA-binding complex like Cu-L1 is a clear demonstration of the power of the supramolecular approach to hybrid catalysis.     

Iron catalyzed CO2 hydrogenation to formate enhanced by Lewis acid co-catalysts

A family of iron(ii) carbonyl hydride complexes supported by either a bifunctional PNP ligand containing a secondary amine, or a PNP ligand with a tertiary amine that prevents metal–ligand cooperativity, were found to promote the catalytic hydrogenation of CO₂ to formate in the presence of Brønsted base. In both cases a remarkable enhancement in catalytic activity was observed upon the addition of Lewis acid (LA) co-catalysts. For the secondary amine supported system, turnover numbers of approximately 9000 for formate production were achieved, while for catalysts supported by the tertiary amine ligand, nearly 60 000 turnovers were observed; the highest activity reported for an earth abundant catalyst to date. The LA co-catalysts raise the turnover number by more than an order of magnitude in each case. In the secondary amine system, mechanistic investigations implicated the LA in disrupting an intramolecular hydrogen bond between the PNP ligand N–H moiety and the carbonyl oxygen of a formate ligand in the catalytic resting state. This destabilization of the iron-bound formate accelerates product extrusion, the rate-limiting step in catalysis. In systems supported by ligands with the tertiary amine, it was demonstrated that the LA enhancement originates from cation assisted substitution of formate for dihydrogen during the slow step in catalysis.