首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 46 毫秒
1.
We model the hydrolytic cleavage of dimethylphosphate by hydroxide ion and water in the gas phase and in implicit water using density functional theory. In all cases the rate-determining step is the nucleophilic attack. The barrier for this nucleophilic attack in vacuum is much larger for the hydroxide than for the neutral nucleophile. However, in water the barriers are similar. The rate-determining step in the attack by the neutral nucleophile involves the concerted transfer of a proton from the water molecule to the phosphate ion and the formation of the P–O bond.  相似文献   

2.
Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4-dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous SN2(P) reactions of F with the monoanion of the monoester 2,4-dinitrophenyl phosphate and its diester analogue, methyl 2,4-dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH and F can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving-group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (βlg=−0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pKa<11 are involved, as in alkaline phosphatase, then the SN2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of βlg (−0.95) is predicted for the substrate-assisted catalysis mechanism.  相似文献   

3.
Hydrolyses of p‐nitrophenyl picolinate (PNPP) and p‐nitrophenyl acetate (PNPA) mediated by the micellar catalytic systems of two types of cationic surfactants [cetyltrimethylammonium bromide (CTAB), Gemini dimethylene‐1,2‐bis(cetyltrimethylammonium bromide) (16‐2‐16, 2Br?)] were investigated spectrophotometrically in the pH range of 7.0–9.0 and 25°C. Also, the effects of several kinds of additives, such as ethanol, cyclodextrins (CDs), on the hydrolytic reactions of PNPP and PNPA were studied systematically. It is noteworthy that: (1) double chain Gemini surfactant micellar system enhanced the hydrolyses of carboxylic acid esters notably compared with single chain surfactant (CTAB) micellar solutions under the same reaction conditions; (2) the apparent rate constants (k obsd) of PNPP and PNPA hydrolyses increased with the increasing in pH values of reaction media; (3) as additives, ethanol has effect on both PNPP and PNPA hydrolyses, and moreover, the k obsd for hydrolyses decreased with the increasing contents of ethanol (≤5%) at 25°C and pH 9.00; (4) the presence of CDs [α‐cyclodextrin (α‐CD), β‐cyclodextrin (β‐CD), γ‐cyclodextrin (γ‐CD)], as additives, showed different effects on PNPP and PNPA hydrolyses in different reaction systems.  相似文献   

4.
The reaction mechanism of the gold(I)-phosphine-catalyzed hydroamination of 1,3-dienes was analyzed by means of density functional methods combined with polarizable continuum models. Several mechanistic pathways for the reaction were considered and evaluated. It was found that the most favorable series of reaction steps include the ligand substitution reaction in the catalytically active Ph3PAuOTf species between the triflate and the substrate, subsequent nucleophile attack of the N-nucleophile (benzyl carbamate) on the activated double bond, which is followed by proton transfer from the NH2 group to the unsaturated carbon atom. The latter step, the most striking one, was analyzed in detail, and a novel pathway involving tautomerization of benzyl carbamate nucleophile assisted by triflate anion acting as a proton shuttle was characterized by the lowest barrier, which is consistent with experimental findings.  相似文献   

5.
Isotope effects in the nucleophile and in the leaving group were measured to gain information about the mechanism and transition state of the hydrolysis of methyl p-nitrophenyl phosphate complexed to a dinuclear cobalt complex. The complexed diester undergoes hydrolysis about 1011 times faster than the corresponding uncomplexed diester. The kinetic isotope effects indicate that this rate acceleration is accompanied by a change in mechanism. A large inverse 18O isotope effect in the bridging hydroxide nucleophile (0.937 +/- 0.002) suggests that nucleophilic attack occurs before the rate-determining step. Large isotope effects in the nitrophenyl leaving group (18Olg = 1.029 +/- 0.002, 15N = 1.0026 +/- 0.0002) indicate significant fission of the P-O ester bond in the transition state of the rate-determining step. The data indicate that in contrast to uncomplexed diesters, which undergo hydrolysis by a concerted mechanism, the reaction of the complexed diester likely proceeds via an addition-elimination mechanism. The rate-limiting step is expulsion of the p-nitrophenyl leaving group from the intermediate, which proceeds by a late transition state with extensive bond fission to the leaving group. This represents a substantial change in mechanism from the hydrolysis of uncomplexed aryl phosphate diesters.  相似文献   

6.
Understanding the chemical step in the catalytic reaction of DNA polymerases is essential for elucidating the molecular basis of the fidelity of DNA replication. The present work evaluates the free energy surface for the nucleotide transfer reaction of T7 polymerase by free energy perturbation/empirical valence bond (FEP/EVB) calculations. A key aspect of the enzyme simulation is a comparison of enzymatic free energy profiles with the corresponding reference reactions in water using the same computational methodology, thereby enabling a quantitative estimate for the free energy of the nucleotide insertion reaction. The reaction is driven by the FEP/EVB methodology between valence bond structures representing the reactant, pentacovalent intermediate, and the product states. This pathway corresponds to three microscopic chemical steps, deprotonation of the attacking group, a nucleophilic attack on the P(alpha) atom of the dNTP substrate, and departure of the leaving group. Three different mechanisms for the first microscopic step, the generation of the RO(-) nucleophile from the 3'-OH hydroxyl of the primer, are examined: (i) proton transfer to the bulk solvent, (ii) proton transfer to one of the ionic oxygens of the P(alpha) phosphate group, and (iii) proton transfer to the ionized Asp654 residue. The most favorable reaction mechanism in T7 pol is predicted to involve the proton transfer to Asp654. This finding sheds light on the long standing issue of the actual role of conserved aspartates. The structural preorganization that helps to catalyze the reaction is also considered and analyzed. The overall calculated mechanism consists of three subsequent steps with a similar activation free energy of about 12 kcal/mol. The similarity of the activation barriers of the three microscopic chemical steps indicates that the T7 polymerase may select against the incorrect dNTP substrate by raising any of these barriers. The relative height of these barriers comparing right and wrong dNTP substrates should therefore be a primary focus of future computational studies of the fidelity of DNA polymerases.  相似文献   

7.
Abstract

In this paper, two oximato complexes, mononuclear [Cu(Hdmg)2] and binuclear [Cu2(Hdmg)2(H2dmg)]ClO4 · H2O (H2dmg: dimethylglyoxime), were synthesized and characterized. Hydrolyses of carboxyl acid esters, p‐nitrophenyl picolinate (PNPP) and p‐nitrophenyl acetate (PNPA), catalyzed by these two complexes were investigated in different micellar systems in the pH range from 6.58–8.65 at 25°C. The results obtained indicate that these two complexes exhibit good catalytic function. It also appears that both complexes accelerate the hydrolytic cleavage of PNPP and PNPA in cationic CTAB micellar solution faster than that in nonionic Brij35 micellar solution, which may be due to the different coordinating ability of substrates to complexes and electrostatic interaction between micelles and complexes. For binuclear Cu(II), the rate constant (k N) for the hydrolysis of PNPA is about two times larger than that for PNPP in CTAB micellar solution, while in Brij35 micellar solution, the k N values for PNPA and PNPP are roughly the same. This small difference may be ascribed to the configurations of intermediates formed during the reaction and electrostatic interaction between micelles and reactants.  相似文献   

8.
9.
Metal‐catalyzed C?H activation not only offers important strategies to construct new bonds, it also allows the merge of important research areas. When quinoline N‐oxide is used as an arene source in C?H activation studies, the N?O bond can act as a directing group as well as an O‐atom donor. The newly reported density functional theory method, M11L, has been used to elucidate the mechanistic details of the coupling between quinoline N?O bond and alkynes, which results in C?H activation and O‐atom transfer. The computational results indicated that the most favorable pathway involves an electrophilic deprotonation, an insertion of an acetylene group into a Rh?C bond, a reductive elimination to form an oxazinoquinolinium‐coordinated RhI intermediate, an oxidative addition to break the N?O bond, and a protonation reaction to regenerate the active catalyst. The regioselectivity of the reaction has also been studied by using prop‐1‐yn‐1‐ylbenzene as a model unsymmetrical substrate. Theoretical calculations suggested that 1‐phenyl‐2‐quinolinylpropanone would be the major product because of better conjugation between the phenyl group and enolate moiety in the corresponding transition state of the regioselectivity‐determining step. These calculated data are consistent with the experimental observations.  相似文献   

10.
The effect of substituents on nucleophilic addition at the C=O bond, which occurs by the mechanism of intramolecular proton transfer, has been studied by the quantum-chemical MNDO/H method. The effect of nucleophiles and substituents at the carbonyl C atom in the gas phase is opposite to that in solution. Strengthening of the bond between the nucleophile and the carbonyl compound as the result of the transfer of electron density to the carbonyl C atom results in the stabilization of the tetrahedral bipolar adduct. In the formation of an adduct with a strong nucleophile the geometry of the transition state (TS) is closer to that of the reaction product, whereas in the case of a weak nucleophile it is similar to that of the initial reagents. Attack by a weak nucleophile and electron-donating groups at the carbonyl C atom favor the situation in which the reaction system achieves a TS earlier and proton transfer occurs with a low activation barrier.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 227–230, February, 1994.  相似文献   

11.
In connection with the synthesis of guanosine‐capped oligodeoxynucleotides on polymer supports, we found an unprecedented Si O bond cleavage reaction, which occurred when polymer‐linked oligodeoxynucleotides having unprotected internucleotidic phosphate groups were allowed to react with the guanosine 5′‐phosphorimidazolide derivative 18 in the presence of 4‐nitro‐6‐(trifluoromethyl)‐1H‐benzotriazol‐1‐ol (Ntbt‐OH) as an effective activator in pyridine. This side reaction was confirmed by the fact that the liquid‐phase reaction of DMTrTpT O Si(iPr2)OEt 42 with a simpler model compound, methyl phosphorimidazolide 34 , in the presence of Ntbt‐OH gave DMTrTpT 43 . It turned out that the side reaction hardly occurs without unprotected internucleotidic phosphate groups on oligodeoxynucleotides. The detailed study of this side reaction disclosed that Ntbt‐OH directly attacks the Si‐atom to release oligonucleotides from the resin. It is likely that Ntbt‐OH serves as a very strong nucleophile in pyridine, especially to the Si‐atom of the linker.  相似文献   

12.
D‐glucosamine Schiff base N‐(2‐deoxy‐β‐D‐glucopyranosyl‐2‐salicylaldimino) and its Cu(II) and Zn(II) complexes were synthesized and characterized. The hydrolysis of p‐nitrophenyl picolinate (PNPP) catalyzed by ligand and complexes was investigated kinetically by observing the rates of the release of p‐nitrophenol in the aqueous buffers at 25°C and different pHs. The scheme for reaction acting mode involving a ternary complex composed of ligand, metal ion, and substrate was established and the reaction mechanisms were discussed by metal–hydroxyl and Lewis acid mechanisms. The experimental results indicated that the complexes, especially the Cu(II) complex, efficiently catalyzed the hydrolysis of PNPP. The catalytic reactivity of the Zn(II) complex was much smaller than the Cu(II) complex. The rate constant kN showing the catalytic reactivity of the Cu(II) complex was determined to be 0.299 s?1 (at pH 8.02) in the buffer. The pKa of hydroxyl group of the ternary complex was determined to be 7.86 for the Cu(II) complex. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 345–350, 2002  相似文献   

13.
Two polyether bridged dihydroxamic acids and their mono-and binuclear manganese(Ⅱ), zinc(Ⅱ) complexes have been synthesized and employed as models to mimic hydrolase in catalytic hydrolysis of p-nitrophenyl picolinate (PNPP). The reaction kinetics and the mechanism of hydrolysis of PNPP have been investigated. The kinetic mathematical model for PNPP cleaved by the complexes has been proposed. The effects of the different central metal ion, mono-and binuclear metal, the pseudo-macrocyclic polyether constructed by polyethoxy group of the complexes, and reactive temperature on the rate for catalytic hydrolysis of PNPP have been examined. The results showed that the transition metal dthydroxamates exhibited high catalytic activity to the hydrolysis of PNPP, the catalytic activity of binuclear complexes was higher than that of mononuclear ones, and the pseudo-macrocyclic polyether might synergetically activate H20 coordinated to metal ion with central metal ion together and promote the catalytic hydrolysis of PNPP.  相似文献   

14.
A copper(Ⅱ) complex 1 of a novel macrocyclic polyamine ligand with hydroxylethyl pendant groups, 4,11-bis(hydroxylethyl)-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane (L) has been synthesized and characterized. Rate enhancement for hydrolysis of p-nitrophenyl picolinate (PNPP) catalyzed by 1 was studied kinetically under Brij35 micellar condition. For comparision, the catalytic activity of corresponding copper(Ⅱ) complex 2 of non-substituted macrocyclic polyamine ligand, 5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraaza-cyclotetradecane (L') toward the hydrolysis of PNPP was also investigated. The results indicate that the macrocyclic polyamine copper(Ⅱ) complex 1 effectively catalyzed the hydrolysis of PNPP, and the pendant ligand hydroxyl group or deprotonated pendant ligand hydroxyl group can act as catalytically active species in the reaction. A ternary Complex kinetic model involving metal ion, ligand and substrate has been proposed, and the results confirmed the reasonability of such kinetic model.  相似文献   

15.
Ab initio MO -LCAO -SCF calculations using an STO -3G basis set were performed to find the most stable conformations of L -serine phosphate and hydrated L -serine phosphate. The most favorable conformation of L -serine phosphate is found to be one where the bond sequence O? C? C? C is trans and P? O? C? C gauche, and a very short hydrogen bond is formed between an oxygen atom of the phosphate group and a hydrogen atom of the ammonium group. For hydrated L -serine phosphate, a bridge-type hydration in which a water molecule links a phosphate oxygen and an ammonium hydrogen displays particularly low energy. In the four-hydrated L -serine phosphate anion, the most favorable conformation is such a bridged one having a rather extended configuration with regard to the bond sequences O? C? C? C and P? O? C? C.  相似文献   

16.
β1,6‐GlcNAc‐transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O‐glycans. The catalytic mechanism of this metal‐ion‐independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme–substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted SN2‐like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously. The transition state for the proposed reaction mechanism at the M06‐2X/6‐31G** (with diffuse functions on the O1′, O5′, OGlu, and O6 atoms) level was located at C1? O6=1.74 Å and C1? O1=2.86 Å. The activation energy for this mechanism was estimated to be between 20 and 29 kcal mol?1, depending on the method used. These calculations also identified a low‐barrier hydrogen bond between the nucleophile O6H and the catalytic base Glu320, and a hydrogen bond between the N‐acetamino group and the glycosidic oxygen of the donor in the TS. It is proposed that these interactions contribute to a stabilization of TS and participate in the catalytic mechanism.  相似文献   

17.
Iron(IV)–oxo intermediates are involved in oxidations catalyzed by heme and nonheme iron enzymes, including the cytochromes P450. At the distal site of the heme in P450 Compound I (FeIV–oxo bound to porphyrin radical), the oxo group is involved in several hydrogen‐bonding interactions with the protein, but their role in catalysis is currently unknown. In this work, we investigate the effects of hydrogen bonding on the reactivity of high‐valent metal–oxo moiety in a nonheme iron biomimetic model complex with trigonal bipyramidal symmetry that has three hydrogen‐bond donors directed toward a metal(IV)–oxo group. We show these interactions lower the oxidative power of the oxidant in reactions with dehydroanthracene and cyclohexadiene dramatically as they decrease the strength of the O? H bond (BDEOH) in the resulting metal(III)–hydroxo complex. Furthermore, the distal hydrogen‐bonding effects cause stereochemical repulsions with the approaching substrate and force a sideways attack rather than a more favorable attack from the top. The calculations, therefore, give important new insights into distal hydrogen bonding, and show that in biomimetic, and, by extension, enzymatic systems, the hydrogen bond may be important for proton‐relay mechanisms involved in the formation of the metal–oxo intermediates, but the enzyme pays the price for this by reduced hydrogen atom abstraction ability of the intermediate. Indeed, in nonheme iron enzymes, where no proton relay takes place, there generally is no donating hydrogen bond to the iron(IV)–oxo moiety.  相似文献   

18.
The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐CoII derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear CoII center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.  相似文献   

19.
From enzyme kinetics, 4‐nitrophenyl‐N‐substituted carbamates 1 are characterized as pseudo‐substrate inhibitors of acetylcholinesterase. However, the activity of the carbamyl enzyme does not recover in the presence of a competitive inhibitor, edrophonium. Therefore, carbamates 1 should be called as the “pseudo‐pseudo‐substrate” inhibitors of the enzyme. Moreover, the ‐logKi, logkc, and logki values are linearly correlated with Taft‐Ingold equation, log (k/ko) = ρ*σ* + δ Es. A three‐step AChE inhibition mechanism by carbamates 1 is proposed. The first step is the pre‐equilibrium protonations of carbamates 1 with ρ* value of ?1.4 from pKa‐σ*‐correlation. The second step is the enzyme‐carbamates 1 tetrahedral intermediate formation from nucleophilic attack of the active site Ser200 on the protonated carbamates 1 . The ρ* value for the ‐logKi‐σ*‐Es‐correlation indicates that the true ρ* value for the second step is 0.5 [= ?0.9 ‐ (‐1.4)]. The δ value of 0.56 for the ‐logKi‐σ*‐Es‐correlation indicates that carbamates 1 with bulky substituents retarded the formation of enzyme‐inhibitor tetrahedral intermediates. The third step (kc step) is the carbamylation step and is the carbamyl enzyme conjugate formation from the enzyme‐carbamates 1 tetrahedral intermediate. The ρ* value of 0.21 for the logkc‐correlation indicates that the transition state for the carbamylation step is more negative charge than the enzyme‐carbamates 1 tetrahedral intermediate. Moreover, the kc step is insensitive to substituent effects since there is a cancellation of electronic demands for bond‐making and bond‐breaking components, like SN2 reactions. The δ value of 0.00 for the logkc‐correlation indicates that the kc step is independent of substituent steric effect. Therefore, the product of this step carbamyl enzyme conjugate is as crowded as the enzyme‐carbamates 1 tetrahedral intermediate and is likely bound to the leaving group, p‐nitrophenol.  相似文献   

20.
The reactions of diethyl 4‐nitrophenyl phosphate ( 1 ) with a series of nucleophiles: phenoxides, secondary alicyclic (SA) amines, and pyridines are subjected to a kinetic study. Under excess of nucleophile, all the reactions obey pseudo‐first‐order kinetics and are first order in the nucleophile. The nucleophilic rate constants (kN) obtained are pH independent for all the reactions studied. The Brønsted‐type plot (log kN vs. pKa nucleophile) obtained for the phenolysis is linear with slope β=0.21; no break was found at pKa 7.5, consistent with a concerted mechanism. The Brønsted‐type plots for the SA aminolysis and pyridinolysis are linear with slopes β=0.39 and 0.43, respectively, also suggesting concerted processes. The concerted mechanisms for the latter reactions are proposed on the basis of the lack of break in the Brønsted‐type plots and the instability of the hypothetical pentacoordinate intermediates formed in these reactions. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 43: 708–714, 2011  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号