Enzymatic catalysis of urea decomposition: elimination or hydrolysis?

We present a high-level quantum chemical study of possible reaction mechanisms associated with the catalytic decomposition of urea by a bioinorganic mimetic of the dinickel active site of urease. We chose the phthalazine-dinickel complexes of Lippard and co-workers, because these mimetics have been shown to hydrolytically degrade urea. High-level quantum chemical methodologies were utilized to identify stable intermediates and transition-state structures along several possible reaction pathways. The computed results were then used to further analyze what may occur in the active site of urease. Valuable information on the latter has been extracted from experimental data, computational approaches, and unpublished molecular dynamics simulations. On the basis of these comparative studies, we propose that both the elimination and hydrolytic pathways may compete for urea decomposition in the active site of urease.     

The hydrolysis of urea and the proficiency of urease

We present the results of a computational study of the solution phase decomposition of urea, which provides insight into probable reaction pathways for the urease-catalyzed reaction. Calculations, which were used to derive thermodynamic parameters that were further used for a kinetic analysis, have been done at the solvent-corrected MP2/6-311++G** level. Both elimination and hydrolytic pathways have been considered. Elimination is favored for the solution phase reaction, which proceeds by H-bond coordination of a water molecule to the amine nitrogen atoms. The coordination of one water molecule greatly facilitates the reaction by allowing it to proceed through a cyclic six-member transition state. Aspects of the water-urea H-bond interactions have also provided insights into critical aspects of the hydrogen bond pattern in the urease active site. On the basis of a kinetic analysis, we have estimated the proficiency of urease and have predicted that it is the most proficient enzyme identified to date.     

Molecular modeling studies on the urease active site and the enzyme-catalyzed urea hydrolysis

Summary These studies are an attempt to gain better insight into the pharmacophore requirements of urease. On the basis of published information on this enzyme (EXAFS, amino acid sequence, essential groups at the active site) a hypothetical nickel-tripeptide complex, as preliminary substitute for the urease active site was modeled using computer-aided molecular modeling techniques. The results suggest two alternative docking modes of urea and reaction intermediates, corresponding to two different reaction mechanisms. Both binding modes are compatible with the docking of known potent inhibitors such as selected hydroxamic acids and phosphorodiamides. The results can be used to help in the design of new potential inhibitors of urease.     

Pyrolysis of methyl tert-butyl ether (MTBE). 2. Theoretical study of decomposition pathways

The thermal decomposition pathways of MTBE have been investigated using the G3B3 method. On the basis of the experimental observation and theoretical calculation, the pyrolysis channels are provided, especially for primary pyrolysis reactions. The primary decomposition pathways include formation of methanol and isobutene, CH4 elimination, H2 elimination and C-H, C-C, C-O bond cleavage reactions. Among them, the formation channel of methanol and isobutene is the lowest energy pathway, which is in accordance with experimental observation. Furthermore, the secondary pyrolysis pathways have been calculated as well, including decomposition of tert-butyl radical, isobutene, methanol and acetone. The radicals play an important role in the formation of pyrolysis products, for example, tert-butyl radical and allyl radical are major precursors for the formation of allene and propyne. Although some isomers (isobutene and 1-butene, allene and propyne, acetone and propanal) are identified in our experiment, these isomerization reaction pathways occur merely at the high temperature due to their high activation energies. The theoretical calculation can explain the experimental results reported in part 1 and shed further light on the thermal decomposition pathways.     

The burden borne by urease

At the active site of urease, urea undergoes nucleophilic attack by water, whereas urea decomposes in solution by elimination of ammonia so that its rate of spontaneous hydrolysis is unknown. Quantum mechanical simulations have been interpreted as indicating that urea hydrolysis is extremely slow, compared with other biological reactions proceeding spontaneously, and that urease surpasses all other enzymes in its power to enhance the rate of a reaction. We tested that possibility experimentally by examining the hydrolysis of 1,1,3,3-tetramethylurea, from which elimination cannot occur. In neutral solution at 25 degrees C, the rate constant for the uncatalyzed hydrolysis of tetramethylurea is 4.2 x 10-12 s-1, which does not differ greatly from the rate constants observed for the uncatalyzed hydrolysis of acetamide (5.1 x 10-11 s-1) or N,N-dimethylacetamide (1.8 x 10-11 s-1) under the same conditions. We estimate that the proficiency of urease as a catalyst, (kcat/Km)/knon, is 8 x 1017 M-1, slightly higher than the values for other metalloenzymes (carboxypeptidase b and cytidine deaminase) that catalyze the hydrolysis of similar bonds.     

Energy dependence of the roaming atom pathway in formaldehyde decomposition

Recently, a new mechanism of formaldehyde decomposition leading to molecular products CO and H(2) has been discovered, termed the "roaming atom" mechanism. Formaldehyde decomposition from the ground state via the roaming atom mechanism leads to rotationally cold CO and vibrationally hot H(2), whereas formaldehyde decomposition through the conventional molecular channel leads to rotationally hot CO and vibrationally cold H(2). This discovery has shown that it is possible to have multiple pathways for a reaction leading to the same products with dramatically different product state distributions. Detailed investigations of the dynamics of these two pathways have been reported recently. This paper focuses on an investigation of the energy dependence of the roaming atom mechanism up to 1500 cm(-1) above the threshold of the radical channel, H(2)CO-->H+HCO. The influence of excitation energy on the roaming atom and molecular elimination pathways is reported, and the branching fraction between the roaming atom channel and molecular channel is obtained using high-resolution dc slice imaging and photofragment excitation spectroscopy. From the branching fractions and the reaction rates of the radical channel, the overall competition between all three dissociation channels is estimated. These results are compared with recent quasiclassical trajectory calculations on a global H(2)CO potential energy surface.     

Why urea eliminates ammonia rather than hydrolyzes in aqueous solution

A joint QM/MM and ab initio study on the decomposition of urea in the gas phase and in aqueous solution is reported. Numerous possible mechanisms of intramolecular decomposition and hydrolysis have been explored; intramolecular NH3 elimination assisted by a water molecule is found to have the lowest activation energy. The solvent effects were elucidated using the TIP4P explicit water model with free energy perturbation calculations in conjunction with QM/MM Monte Carlo simulations. The explicit representation of the solvent was found to be essential for detailed resolution of the mechanism, identification of the rate-determining step, and evaluation of the barrier. The assisting water molecule acts as a hydrogen shuttle for the first step of the elimination reaction. The forming zwitterionic intermediate, H3NCONH, participates in 8-9 hydrogen bonds with water molecules. Its decomposition is found to be the rate-limiting step, and the overall free energy of activation for the decomposition of urea in water is computed to be approximately 37 kcal/mol; the barrier for hydrolysis by an addition/elimination mechanism is found to be approximately 40 kcal/mol. The differences in the electronic structure of the transition states of the NH3 elimination and hydrolysis were examined via natural bond order analysis. Destruction of urea's resonance stabilization during hydrolysis via an addition/elimination mechanism and its preservation in the rearrangement to the H3NCONH intermediate were identified as important factors in determining the preferred reaction route.     

A kinetic-catalytic method with repeated addition of one reactant — the determination of manganese, iodide, urease and cadmium

The use of a new kinetic-catalytic method with repeated addition of one reactant in the same system is described. The determination of manganese (periodate—malachite green; photometric observation), iodide (cerium(IV)—arsenic(III); potentiometric observation) and urease (hydrolytic splitting of urea; potentiometric observation) serves to illustrate the procedure.     

Colorimetric detection of urea,urease, and urease inhibitor based on the peroxidase-like activity of gold nanoparticles

Herein, we reported for the first time that gold nanoparticles-catalyzed 3,3′,5,5′-tetramethylbenzidine-H₂O₂ system can serve as an ultrasensitive colorimetric pH indicator. Gold nanoparticles acted as a catalyst and imitated the function of horseradish peroxidase. The absorbance at 450 nm of the yellow-color product in the catalytic reaction exhibited a linear fashion over the pH range of 6.40–6.60. On the basis of this property, we constructed a novel sensing platform for the determination of urea, urease, and urease inhibitor. The limit of detection for urea and urease was 5 μM and 1.8 U/L, respectively. The half-maximal inhibition value IC₅₀ of acetohydroxamic acid was found to be 0.05 mM. Urea in human urine and urease in soil were detected with satisfied results.     

The mechanism of unimolecular decomposition of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane. A computational DFT study

By using the B3LYP level of density functional theory, possible decomposition reaction pathways of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) in the gas phase have been investigated. We have found several types of reactions for this process: homolytic cleavage of an N-N bond to form the NO2* group; HONO elimination; C-C and C-N bonds breaking leading to ring opening; and H-migration. On the basis of the results of computation scanning of the potential energy surface, the most favorite pathway of CL-20 unimolecular decomposition that results in the formation of the stable aromatic compound 1,5-dihydrodiimidazo[4,5-b:4',5'-e]pyrazine has been proposed.     

The Structure of the Elusive Urease–Urea Complex Unveils the Mechanism of a Paradigmatic Nickel‐Dependent Enzyme

Urease, the most efficient enzyme known, contains an essential dinuclear Ni^II cluster in the active site. It catalyzes the hydrolysis of urea, inducing a rapid pH increase that has negative effects on human health and agriculture. Thus, the control of urease activity is of utmost importance in medical, pharmaceutical, and agro‐environmental applications. All known urease inhibitors are either toxic or inefficient. The development of new and efficient chemicals able to inhibit urease relies on the knowledge of all steps of the catalytic mechanism. The short (microseconds) lifetime of the urease–urea complex has hampered the determination of its structure. The present study uses fluoride to substitute the hydroxide acting as the co‐substrate in the reaction, preventing the occurrence of the catalytic steps that follow substrate binding. The 1.42 Å crystal structure of the urease–urea complex, reported here, resolves the enduring debate on the mechanism of this metalloenzyme.     

一些抑制剂对脲酶反应速率的影响

利用氨气敏电极研究硝酸镍，磷酸盐及ＥＤＴＡ等酶抑制剂对脲酶分解尿素反应速率的影响以及抑制作用机理。     

Metal-catalyzed hydroxylaminolysis of unactivated amide and peptide bonds

Kinetics of the hydroxylaminolysis of acetamide, glycinamide, glycylglycine and triglycine have been studied in the range of temperatures 37-60 degrees C as a function of pH and hydroxylamine concentration. Rate constants for specific acid, general-acid and general-base catalyzed pathways have been determined for all substrates (for glycine derivatives rate constants for different protonation forms were obtained). Testing different metal ions as possible reaction catalysts revealed a significant catalytic effect of Zn(II) on the hydroxylaminolysis of glycine substrates, but not acetamide. On the basis of the kinetic results, a mechanism of Zn(II) catalysis is proposed, which involves the coordination of the metal ion to the alpha-amino group of the substrate and the base-assisted nucleophilic attack of hydroxylamine on the bound substrate. The product analysis by proton NMR shows that the primary reaction product in the catalytic reaction is glycine hydroxamic acid, which undergoes further Zn(II)-catalyzed hydrolysis to glycine. Thus the final result of the Zn(II)-catalyzed treatment of peptides by hydroxylamine is hydrolytic cleavage.     

单脉冲激波管中1,2-二氯乙烷的热裂解

在单脉冲激波管上,研究了1,2-二氯乙烷的热裂解.实验的激波条件为:温度区间1020 K＜T＜1190 K, 压力: P=0.12 MPa,实验时间τ=0.5 ms;实验气体为1,2-二氯乙烷稀释于Ar气中(3.95 mmol/L).以4-甲基-1-环己烯作为对比速率法实验的内标物,用4-甲基-1-环己烯开环反应的速率常数k=1015.3exp(-33400/T) s-1,以及从其产物的浓度推定出实验温度.经激波加热后的实验气体的终产物用气相色谱分析出主要成分为C2H3Cl,指示出主要反应通道为β消去反应.如把所有产物C2H3Cl都归于β消去反应,则可推定出表观之反应速率常数k1a=5.0×1013exp(-30000/T) s-1.对于由C-Cl键断键反应引发的链反应的可能影响做了分析研究.用了一种简便分析可推知在实验的温度范围内的低端(1020 K)链反应的影响可以忽略,而在其高端(1190 K)链反应将给出10%的终产物C2H3Cl的附加浓度,获得真实的β消去反应速率常数则必须把这部分予以扣除.经过这样的校正之后,最后得到CH2ClCH2Clβ消去反应速率常数为k1c=2.3×1013exp(-29200/T) s-1.     

Photodissociation of azulene at 193 nm: ab initio and RRKM study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of azulene at 6.4 eV (the laser wavelength of 193 nm) upon absorption of one UV photon followed by internal conversion into the ground electronic state. Reaction pathways leading to various decomposition products have been mapped out at the G3(MP2,CC)//B3LYP level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for the dissociation products have been calculated using the steady-state approach. The results show that photoexcited azulene can readily isomerize to naphthalene and the major dissociation channel is elimination of an H-atom from naphthalene. The branching ratio of this channel decreases with an increase of the photon energy. Acetylene elimination is the second probable reaction channel and its branching ratio rises as the photon energy increases. The main C8H6 fragments at 193 nm are phenylacetylene and pentalene and the yield of the latter grows fast with the increasing excitation energy.     

Role of the metal ion in formyl-peptide bond hydrolysis by a peptide deformylase active site model

The catalytic mechanism of peptide deformylase enzymes containing zinc, iron, cobalt, and nickel dications was explored in the gas phase and in the protein environment. The study was performed at the density functional level using three model systems to simulate the active site. The work had the aim to evaluate the effect of metal substitution on the hydrolytic properties and the possible different performances of the various catalysts. Results indicated that all of the metallic forms are active to hydrolyze the formyl-peptide bond and that the reaction pathways do not show significant peculiarities on going from a particular metal ion to another. No significant modification of the reaction paths occurs in solvent.     

DIPOLAR APROTIC SOLVENT EFFECTS IN THE HYDROLYSIS OF PHENYLMETHANESULFONATES AND PHENYLSULFONYLACETATES

Abstract

The hydrolytic behaviour under alkaline conditions of a group of sulfur compounds containing an active methylene group, in aqueous solvent mixtures with dimethylsulfoxide as the co-solvent has been investigated. The substrates studied are substituted phenyl phenylmethanesulfonates (A), substituted phenyl p-nitrophenylmethanesulfonates (B) and substituted phenylsulfonylacetates (C). It is known that methylenes adjacent to the sulfonyl group are acidic and evidences are available for the formation of the corresponding anions in alkaline solutions. Structure-reactivity correlations strongly suggest that these react not by the conventional addition–elimination mechanism (B_AC ²), but by an elimination-addition mechanism (ElcB) involving a slow decomposition of the corresponding anions. The rate of hydrolysis of (A) increases with increasing percentage of dimethylsulfoxide in the solvent mixtures, whereas, the reverse is the case with (B) and (C). The results are analysed on the basis of a spectrum of pathways in the ElcB mechanism, and on the basis of the relative solvation of ground and transition states of the reaction.     

Amperometric Urea Biosensor Using Aminated Glassy Carbon Electrode Covered with Urease Immobilized Carbon Sheet,Based on the Electrode Oxidation of Carbamic Acid

A large oxidation current can be observed when ammonium carbamate aqueous solution is electrolyzed using a glassy carbon electrode (GCE) at a potential exceeding 1.0 V vs. Ag/AgCl and amino groups are introduced at the surface of the GCE. Aminated GCE exhibits the electrocatalytic activity of the oxidation of ammonium carbamate that is produced from urea as an intermediate product of urease reaction, and a distinct oxidation current is observed when the aminated GCE is used to oxidize the urea in the urease solution. A novel amperometric determination method to detect urea has been developed. This method is based on the electrooxidation of carbamic acid produced during urease reactions. Urease is immobilized to polymaleimidostyrene (PMS) coated on the insulated amorphous carbon sheet set on the aminated GCE surface. A good linear relationship is observed between urea concentration and the electrolytic current of the urease‐immobilized electrode in the concentration range from 0.5 mM to 21.0 mM. The proposed urea biosensor has an effective merit in that the interference resulting from ammonia and pH change caused by the urease reaction can be eliminated, differing from conventional urea biosensors.     

Ab initio study of the unimolecular decomposition of 2‐butenenitrile: Molecular elimination channels

Ab initio molecular orbital calculations have been performed for the unimolecular decomposition of 2‐butenenitrile (CH₃CH?CHCN), especially for HCN and H₂ molecular elimination channels. Structures and energies of the reactants, products, and relevant species in the individual reaction pathways were determined by MP2 gradient optimization and MP4 CCSD(T) single‐point energy calculations. Direct 1,1 and 1,2 molecular eliminations and H or CN migration followed by elimination channels were identified. Dissociation rates for the individual reaction pathways were calculated from vibrational frequencies at the ab initio transition state geometries by employing Rice–Ramsperger–Kassel–Marcus theory, from which channel branching ratios were determined. It was concluded that the most important reaction channel should be the direct 1,1 three‐center molecular elimination of HCN. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical study of the formation of naphthalene from the radical/π-bond addition between single-ring aromatic hydrocarbons

The experimental investigations performed in the 1960s on the o-benzyne + benzene reaction as well as the more recent studies on reactions involving π-electrons highlight the importance of π-bonding for different combustion processes related to PAH's and soot formation. In the present investigation radical/π-bond addition reactions between single-ring aromatic compounds have been proposed and computationally investigated as possible pathways for the formation of two-ring fused compounds, such as naphthalene, which serve as precursors to soot formation. The computationally generated optimized structures for the stationary points were obtained with uB3LYP/6-311+G(d,p) calculations, while the energies of the optimized complexes were refined using the uCCSD(T) method and the cc-pVDZ basis set. The computations have addressed the relevance of a number of radical/π-bond addition reactions including the singlet benzene + o-benzyne reaction, which leads to formation of naphthalene and acetylene through fragmentation of the benzobicyclo[2,2,2]octatriene intermediate. For this reaction, the high-pressure limit rate constants for the individual elementary reactions involved in the overall process were evaluated using transition state theory analysis. Other radical/π-bond addition reactions studied were between benzene and triplet o-benzyne, between benzene and phenyl radical, and between phenyl radicals, for all of which potential energy surfaces were produced. On the basis of the results of these reaction studies, it was found necessary to propose and subsequently confirm additional, alternative pathways for the formation of the types of PAH compounds found in combustion systems. The potential energy surface for one reaction in particular, the phenyl + phenyl addition, is shown to contain a low-energy channel leading to formation of naphthalene that is energetically comparable to the other examined conventional pathways leading to formation of biphenyl compounds. This channel is the first evidence of a reaction which involves an aromatic radical adding to the nonradical π-bond site of another aromatic radical which leads directly to a fused ring structure.