Ab initio studies of the intramolecular amide hydrolysis in N-methylmaleamic acids

The intramolecular amide hydrolysis reactions of N-methylmaleamic acids (NMMA) are studied at the MP2/6-31G**//RHF/4-31G level of theory as model reactions of peptide bond cleavage by a proteolytic enzyme. In contrast to the previously reported results for a bimolecular reaction model of peptide hydrolysis, the unimolecular reactions studied here proceed via the concerted pathway in which the C–O bond formation and the release of methylamine occur simultaneously in preference to the stepwise one. The determination of an intrinsic reaction coordinate shows that the reaction is facilitated by the intramolecular proton transfer from the undissociated carboxyl group to the nitrogen of the leaving amine group. Mainly because of the increase in activation energy, methyl substitution at the 2-position retards the hydrolysis reaction rate by a factor of 14 compared to the reaction of the unsubstituted molecule. In contrast, additional methyl substitution at 3-position leads to 35-fold increase in the reaction rate. These variations of reactivity are caused by the charge redistributions in the amide group induced by methyl substitutions and the resulting changes in electrophilicity of the aminocarbonyl carbon.     

A catalytic antibody programmed for torsional activation of amide bond hydrolysis

Amidase antibody 312d6, obtained against the sulfonamide hapten 4 a that mimics the transition state for hydrolysis of a distorted amide, accelerates the hydrolysis of the corresponding amides 1 a-3 a by a factor of 10(3) at pH 8. The mechanisms of both the uncatalyzed and antibody-catalyzed reactions were studied. Between pH 8 and 12 the uncatalyzed hydrolysis of N-toluoylindoles 1 a and 3 a shows a simple first-order dependence on [OH(-)], while hydrolysis of 3 a is zeroth-order in [OH(-)] below pH 8. The pH profile for hydrolysis of the corresponding tryptophan amide 2 a is more complex due to the dissociation of the zwitterion into an anion with pK(a) 9.74; hydrolysis of the zwitterionic and the anionic form of 2 a both show simple first-order dependence on [OH(-)]. Absence of (18)O exchange between H(2) (18)O/(18)OH(-) and the substrate, a normal SKIE for both 1 a (k(H)/k(D)=1.12) and 3 a (k(H)/k(D)=1.24) and the value of the Hammett constant rho for hydrolysis of p-substituted amides 3 a-e are consistent with an ester-like mechanism in which formation of the tetrahedral intermediate is rate-determining and the amine departs as anion. The 312d6-catalyzed hydrolysis of 3 a was studied between pH 7.5 and 9, and its independence of pH in this range indicates that water is the reacting nucleophile. Hydrolysis of 3 a is only partially inhibited by the sulfonamide hapten, and this indicates that non-specific catalysis by the protein accompanies the specific process. Only the nonspecific process is observed in the hydrolysis of amides 3 with para substituents other than methyl. Binding studies on the corresponding series of p-substituted sulfonamides 5 a-e confirm the high specificity of antibody 312d6 for p-methyl substituted substrates.     

聚酯-酰胺的水解降解行为

研究了各种条件下聚酯-酰胺的水解降解行为及其与结构之间的关系。结果表明：酯键含量越高,质量损失就越快。聚合物的降解受酸、碱催化。根据SEM观察提出了可能发生的降解机理：表面腐蚀、非晶区腐蚀、晶区破坏到全部降解。     

Synthesis of a transition-state analog for the hydrolysis of the zearalenone lactone

The development of a catalytic antibody for the hydrolysis of the lactone functionality in zearalenone (1) is viewed as a potential solution to animal fertility problems associated with the estrogenic mycotoxin. A phosphonomacrolactone is proposed as a hapten for the generation of such antibodies. A suitably functionalized aryl phosphonic acid 4 was condensed with the racemic aliphatic fragment 5 via a Mitsunobu reaction. Macrocyclic formation was achieved via RCM to give advanced intermediate 23, a phosphonate analog of zearalenone, ready for deprotection and conjugation to a carrier protein.     

Silencing lung cancer genes using miRNAs identified by 7mer-seed matching

Lung cancer (LC) is the main cause of cancer-associated deaths in both men and women globally with a very high mortality rate. The microRNAs (miRNAs) are a class of noncoding RNAs consisting of 18–25 nucleotides. They inhibit translation of protein through binding to complementary target mRNAs. The non-coding miRNAs are recognized as potent biomarkers for detection, development and treatment of malignancy. In this study, we screened a set of 12 genes over expressed in small cell lung cancer, non small cell lung cancer and the genes involved in both categories and their binding sites for human miRNAs as no work was reported yet. Screening of human miRNAs revealed that a few genes showed numerous miRNA binding sites. Free energy values of mRNA sequences revealed that they might acquire compact folded structure causing complexity for miRNAs to interact. GC content in the target site was relatively higher than that of their flanks. It was observed through analysis of cosine similarity metric and compAI parameters that the genes related to lung cancer were encoded with non optimal codons and thus might be translationally less efficient for producing polypeptides. Gene ontology analysis was carried out to understand the diverse functions of these 12 genes.     

On the hydrolysis mechanisms of amides and peptides

Here the possibility is raised that peptide hydrolysis, in the absence of catalysis by proteases or buffers, may still have a self‐catalyzing mechanism that differs from ordinary amide hydrolysis. Second, an attempt is made to clarify the ongoing confusion in the computational chemistry literature regarding the rate‐limiting step in ordinary amide hydrolysis. Third, Gibbs activation energies (free‐energy barriers) for formamide hydrolysis are derived from rate constants and presented under different concentration conventions, for ease of comparison to values from computational chemistry predictions past and future.     

Y-Hydroxyphosphonate inducing single-chain antibodies capable of catalyzing soman hydrolysis

A γ-hydroxyphosphonate P6 (O1-methyl-O2-(1, 2, 2-trimethylpropyl)-2-hydroxy-5-nitro-phenyl methylphosphonic acid) which is proposed to be an analog of the transition state in hydrolysis of soman was synthesized. Artificial antigens were obtained by conjugating P6 to the carrier proteins BSA (bovine serum albumin) and LPH (Limulus polyphenus hemocyanin). Mice were immunized with P6-LPH and recombinant single-chain antibody phage display library was constructed. After 4 rounds of panning against P6-BSA and competitive inhibition enzyme immunoassay, more than 70 strains of phage antibodies capable of binding soman were obtained and 11 of them can accelerate the hydrolysis reaction of soman. One of them (EP6) was studied further. Soluble single-chain antibody was prepared and purification was performed by gel filtration and ion exchange chromatography. The kinetic experiment was carried out showing that the turnover number kcatt= 198 min-1 and the rate enhancement kcatkuncat = 122 419. When 0.16 mg · mL-1     

Comparison of antibody and albumin catalyzed hydrolysis of steroidalp-nitrophenylcarbonates

A monoclonal antibody (MAb) was produced against thep-nitrophenylphosphate derivative of 3α,5β-lithocholic acid, a transition-state analog for hydrolysis of a steroidalp-nitrophenylcarbonate. The indicated reaction was catalyzed by this Ab with kinetic constants k_cat = 4.0 × 10^-2min and K_m = 3.3 μM at pH 9.0 and 35°C. The Ab also hydrolyzed the isomericp-nitrophenylcarbonate of 3β,5β-lithocholic acid with k_cat = 8.4 × 10^-2/min and K_m = 1.0 μM. Bovine serum albumin (BSA) was found to catalyze the same reactions with similar turnover rates and Michaelis constants of 15 and 14 μM, respectively. Although the BSA-catalyzed reaction was only weakly inhibited by the phosphate ester TSA (IC₅₀ ca. 40 μM), the Ab-catalyzed reaction was completely inhibited at less than 1 μM of the TSA. The relative rates and efficiencies of the MAbcatalyzed and BSA-catalyzed reactions are discussed in the context of the hydrophobic sites and intrinsic reactivity of the protein surfaces, and the induction of groups on the Ab to enhance the enzymatic function.     

胶束催化对硝基苯酚乙酸酯碱性水解的动力学研究

碱性溶液中羧酸酯的催化水解反应有些报道[1~4],OH-对乙酸酯的亲核进攻,形成了一个阴离子四面体中间物,该四面体中间物的C为sp3杂化,反应裂解成为CH3COO-和对硝基苯酚。然而,目前对胶束溶液中对硝基苯酚乙酸酯的碱性水解方面的系统研究还未见报到,因此,本文在30℃、1·62×10-3     

The mechanism of formamide hydrolysis in water from ab initio calculations and simulations

The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule. Its interaction with the bulk has been treated with the aid of a dielectric continuum model. Molecular dynamics simulations at the combined density functional/molecular mechanics level have been carried out in parallel to better understand the structure of the reaction intermediates in aqueous solution. Overall, the most favored mechanism predicted by our study involves two reaction steps. In the first step, the carbonyl group of the formamide molecule is hydrated to form a diol intermediate. The corresponding transition structure involves two water molecules. From this intermediate, a water-assisted proton transfer occurs from one of the hydroxy groups to the amino group. This reaction step may lead either to the formation of a new reaction intermediate with a marked zwitterionic character or to dissociation of the system into ammonia and formic acid. The zwitterionic intermediate dissociates quite easily but its lifetime is not negligible and it could play a role in the hydrolysis of substituted amides or peptides. The predicted pseudo-first-order kinetic constant for the rate-limiting step (the first step) of the hydrolysis reaction at 25 degrees C (3.9x10(-10) s(-1)) is in excellent agreement with experimental data (1.1x10(-10) s(-1)).     

催化2-(对甲氧苯氧基)-四氢吡喃缩醛键水解的抗体研究

以2-[对-(3-羧基)-丙基氧苯]-亚氨基哌啶(2)为半抗原, 联接载体蛋白后免疫动物, 并经杂交瘤技术获得十株单克隆抗体, 其中一株单抗1D1在pH=5.6, 37℃条件下能催化2-(对-甲氧苯氧基)-四氢吡喃(1)缩醛键水解, 加速37倍。     

Direct preparation of primary amides from carboxylic acids and urea using imidazole under microwave irradiation

A very simple and efficient solvent-free procedure for the preparation of primary amides is described from carboxylic acids and urea using imidazole under microwave irradiation. Various aliphatic and aromatic primary amides were prepared in good yields by this direct amidation method.     

Simultaneous catalytic hydrolysis of carbonyl sulfide and carbon disulfide over Al2O3-K/CAC catalyst at low temperature

In this work, a series of coal-based active carbon(CAC) catalysts loaded by Al2O3were prepared by sol-gel method and used for the simultaneous catalytic hydrolysis of carbonyl sulfide(COS) and carbon disulfide(CS2) at relatively low temperatures of 30-70 ℃. The influences of calcinations temperatures and operation conditions such as: reaction temperature, O2concentration, gas hourly space velocity(GHSV) and relative humidity(RH) were also discussed respectively. The results showed that catalysts with 5.0 wt% Al2O3calcined at 300 ℃ had superior activity for the simultaneous catalytic hydrolysis of COS and CS2. When the reaction temperature was above 50 ℃, catalytic hydrolysis activity of COS could be enhanced but that of CS2was inhibited. Too high RH could make the catalytic hydrolysis activities of COS and CS2decrease. A small amount of O2introduction could enhance the simultaneous catalytic hydrolysis activities of COS and CS2.     

Facile synthesis of small crystal ZSM-5 zeolite by acid-catalyzed hydrolysis of tetraethylorthosilicate

Small crystal zeolites ZSM-5 with sizes of 150–300 nm were synthesized using the colloidal silicate precursors as the silica source created by the acid-catalyzed hydrolysis of tetraethylorthosilicate with tetrapropylammonium bromide as the structure-directing agent within a short crystallization time of 20–35 h. The precursors and final products were detected by XRD, SEM, ICP and DLS. Supported by the National Natural Science Foundation of China (Grant No. 20776069), Key Natural Science Foundation for Universities of Jiangsu Province (Grant No. 06KJA53012), and Program for Changjiang Scholars and Innovative Research Team in University (Grant No. PCSIRT 0732)     

Reaction of p‐toluenesulfonyl isocyanate with polymers having amide moieties and hydrolysis of the obtained polymers

The chemical modification of polymers having amide moieties was carried out with p‐toluenesulfonyl isocyanate. The resulting polymers revealed high hydrolytic character. For example, poly(acrylamide) was refluxed with an excess amount of p‐toluenesulfonyl isocyanate in THF for 50 h to obtain a structurally modified polymer in 76% yield, whose sulfonylurea functionality was 100%. The resulting polymer was subjected to hydrolysis in a 1 M NaOH solution at 50 °C to convert 90% of the sulfonylurea in the side chain to the carboxylic acid moieties. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 3440–3449, 2000     

X-Ray structures of two families of hydrolytic antibodies

The catalytic mechanisms of two esterase-like catalytic antibodies (Abs) have been determined, based on kinetic data and on structures of the complexes with transition-state analogs and with a stable substrate analog of the reactions they catalyze. Both Abs stabilize the oxyanion intermediate close to the transition state in ester hydrolysis. The different geometries of the hydrogen bonds that participate in this stabilization account for most of the difference between the efficiencies of these two Abs.     

Influence of surface characteristics on carbon disulfide catalytic hydrolysis over modified lake sediment biochar and research on deactivated mechanism

A series of lake sediment biochar (LSB) catalysts modified by metal oxides and basic functional groups were utilized for removal of carbon disulfide (CS₂) in yellow phosphorus tail gas. The influences of preparation and modification conditions for surface characteristics of Fe-KOH/LSB on removal of CS₂ were investigated. Surface area and pore structure analyses indicated that preparation processes were aimed to increase the micropore structure of LSB. Diffuse reflection using transform of Fourier infrared radiation results showed that Fe had high hydrolysis activity for CS₂ and low oxidation activity for H₂S. Thermogravimetric/differential thermal analysis results indicated that low calcination temperature was not conducive to the generation of Fe₂O₃ and high calcination temperature led to the oxidation of LSB. CO₂ temperature programmed desorption results stated that high alkalinity site strength could improve the catalytic hydrolysis performance. High KOH content could enhance alkalinity site strength but led to the block of pore. These modification factors mainly controlled the catalytic hydrolysis ability of Fe-KOH/LSB. X-ray photoelectron spectroscopy results claimed that the deactivation of Fe-KOH/LSB was attributed to the generation of S and sulfate, and the consumption of active component. In the deactivation process, S and sulfate generated and covered the activity sites, and Fe₂O₃ was converted into FeSO₄ or Fe₂(SO₄)₃, which led to the deactivation.     

Synthesis of dimeric estradiol enzyme model containing imidazolyl and study on its catalytic efficiency in hydrolysis of carboxylates and phosphates

Dimeric estradiol enzyme model (2) was synthesized by etherification of 2,4-bis(N-imidazolylmethyl)-17β-estradiol (1) with 1,3-dibromopropane in the presence of anhydrous K2CO3. Hydrolysis of carboxylates and phosphates catalyzed by the model showed Michaelis-Menten kinetic behavior. Hydrophobic interaction between the model and ester accelerates the hydrolysis markedly, rate enhancement of up to 65 and 285 fold, relative to imidazole, is observed.     

On the hydrolysis mechanism of the second-generation anticancer drug carboplatin

The hydrolysis reaction mechanisms of carboplatin, a second-generation anticancer drug, have been explored by combining density functional theory (DFT) with the conductor-like dielectric continuum model (CPCM) approach. The decomposition of carboplatin in water is expected to take place through a biphasic mechanism with a ring-opening process followed by the loss of the malonato ligand. We have investigated this reaction in water and acid conditions and established that the number of protons present in the malonato ligand has a direct effect on the energetics of this system. Close observation of the optimised structures revealed a necessary systematic water molecule in the vicinity of the amino groups of carboplatin. For this reason we have also investigated this reaction with an explicit water molecule. From the computed potential-energy surfaces it is established that the water hydrolysis takes place with an activation barrier of 30 kcal mol(-1), confirming the very slow reaction observed experimentally. The decomposition of carboplatin upon acidification was also investigated and we have computed a 21 kcal mol(-1) barrier to be overcome (experimental value 23 kcal mol(-1)). We have also established that the rate-limiting process is the first hydration, and ascertained the importance of a water molecule close to the two amine groups in lowering the activation barriers for the ring-opening reaction.     

N-(6-Methyl-2-pyridyl)acrylamide: a case of amide hydrolysis without the assistance of acid or base in the synthesis of water-driven H-bonded polymeric chains

Amide hydrolysis of N-(6-methyl-2-pyridyl)acrylamide without the assistance of either acid or base produces the aminopyridinium carboxylate salt at low or room temperature. The carboxylate ion and the free amine functionalities are cooperatively involved in hydrogen bonding with lattice water to form a new hydrogen-bonded polymeric chain.