A quantum chemical study of the catalysis for cytidine deaminase: contribution of the extra water molecule

Cytidine deaminase is known as an important enzyme responsible for the hydrolytic deamination of cytidine, which is applied as a key step to the conversion of the precursor of the cancer drug to an active form in the living body. Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. In this work, the catalysis of cytidine deaminase for the hydrolytic deamination was examined using cytosine as a model of cytidine and the model molecules for the active site of cytidine deaminase by means of the quantum chemical method. We especially investigated the contribution of the water molecule from the solvent to the catalysis, because the X-ray diffraction analysis of a crystal structure has revealed the existence of the water molecule in the vicinity of the substrate bound to the active site inside the cleft. Our computations showed that the extra water molecule from the solvent has a possibility to support the catalysis of cytidine deaminase.     

Role of Asp102 in the catalytic relay system of serine proteases: a theoretical study

The role of Asp102 in the catalytic relay system of serine proteases is studied theoretically by calculating the free energy profiles of the single proton-transfer reaction by the Asn102 mutant trypsin and the concerted double proton-transfer reaction (so-called the charge-relay mechanism) of the wild-type trypsin. For each reaction, the reaction free energy profile of the rate-determining step (the tetrahedral intermediate formation step) is calculated by using ab initio QM/MM electronic structure calculations combined with molecular dynamics-free energy perturbation method. In the mutant reaction, the free energy monotonically increases along the reaction path. The rate-determining step of the mutant reaction is the formation of tetrahedral intermediate complex, not the base (His57) abstraction of the proton from Ser195. In contrast to the single proton-transfer reaction of the wild-type, MD simulations of the enzyme-substrate complex show that the catalytically favorable alignment of the relay system (the hydrogen bonding network between the mutant triad, His57, Asn102, and Ser195) is rarely observed even in the presence of a substrate at the active site. In the double proton-transfer reaction, the energy barrier is observed at the proton abstraction step, which corresponds to the rate-determining step of the single proton-transfer reaction of the wild-type. Although both reaction profiles show an increase of the activation barrier by several kcals/mol, these increases have different energetic origins: a large energetic loss of the electrostatic stabilization between His57 and Asn102 in the mutant reaction, while the lack of stabilization by the protein environment in the double proton-transfer reaction. Comparing the present results with the single proton transfer of the wild-type, Asp102 is proven to play two important roles in the catalytic process. One is to stabilize the protonated His57, or ionic intermediate, formed during the acylation, and the other is to fix the configuration around the active site, which is favorable to promote the catalytic process. These two factors are closely related to each other and are indispensable for the efficient catalysis. Also the present calculations suggest the importance of the remote site interaction between His57 and Val213-Ser214 at the catalytic transition state.     

Determination of plasma cytidine deaminase activity by HPLC

Cytidine deaminase is an enzyme of nucleic acid metabolism, the measurement of which has been proposed as a useful test for the early detection of pre-eclamptic toxaemia in pregnancy. The enzyme converts the nucleoside cytidine to uridine, with the release of ammonia, and it is the measurement of this latter compound that forms the basis of the conventional methods for the assay of cytidine deaminase. The low activity of the enzyme requires long incubation times, which in turn increase the possibility of contamination by exogenous ammonia. We have developed a new method for determining cytidine deaminase activity, utilising high performance liquid chromatography to measure the production of uridine. This method uses much shorter incubation times and is unaffected by ammonia contamination. This paper describes the development of the method and its comparison with the established assay. The relative merits of each are discussed. Finally, the adaptation of incubation and chromatographic conditions, in order to measure other enzymes of nucleic acid metabolism which are of clinical interest, is briefly mentioned.     

CuI/BtH催化苯硫酚与对甲氧基溴苯C–S偶联合成(4-甲氧基)(苯基)硫醚反应机理理论研究

采用密度泛函理论(DFT)中的B3LYP方法对CuI/BtH催化苯硫酚与对甲氧基溴苯C–S偶联合成(4-甲氧基)(苯基)硫醚反应机理进行了理论研究.在6-31+G(d)基组水平上,全参数优化了气相条件和N,N-二甲基甲酰胺(DMF)溶剂化条件下反应机理中所有反应物、过渡态、中间体和产物构型,对优化后各化合物的构型在B3LYP/6-311++G(d,p)基组下进行了单点能计算和零点能矫正,通过能量和振动频率分析以及内禀反应坐标(IRC)计算证实了中间体和过渡态的合理性.并且在优化计算相同基组水平上,应用自然键轨道(NBO)理论和分子中的原子(AIM)理论分析了复合物的成键特征和轨道间相互作用.在CuI单独催化此反应的机理中,计算得到一条反应路径,控制步骤所需活化能是180.49 kJ/mol(sol).而当CuI/BtH共同催化反应时,计算得到两条反应通道IA和IB,其中IA为最优反应通道,控制步骤所需活化能为101.77kJ/mol(sol);IB反应通道控制步骤活化能为143.78 kJ/mol(sol).配体苯并三唑(BtH)加入反应有效地降低了反应控制步骤所需活化能,同时有利于产物和催化剂的分离,这与实验所得结论一致.     

Theoretical modeling study for the phosphonylation mechanisms of the catalytic triad of acetylcholinesterase by sarin

Potential energy surfaces for the process of phosphonylation of the catalytic triad of acetylcholinesterase by sarin have been explored at the B3LYP/6-311G(d,p) level of theory through a computational study. It is concluded that the phosphonylation process involves a critical addition-elimination mechanism. The first nucleophilic addition process is the rate-determining step. The following elimination process of the fluoride ion comprises a composite reaction that includes several steps, and it occurs rapidly by comparison with the rate-determining step. The mobility characteristics of histidine play an important role in the reaction. A double proton-transfer mechanism is proposed for the catalytic triad during the phosphonylation process of sarin on AChE. The effect of aqueous solvation has been considered via the polarizable continuum model (PCM). One concludes that the energy barriers are generally lowered in solvent, compared to the gas-phase reactions.     

The role of the halogen bond in iodothyronine deiodinase: Dependence on chalcogen substitution in naphthyl-based mimetics

The effects on the activity of thyroxine (T4) due to the chalcogen replacement in a series of peri-substituted naphthalenes mimicking the catalytic function of deiodinase enzymes are computationally examined using density functional theory. In particular, T4 inner-ring deiodination pathways assisted by naphthyl-based models bearing two tellurols and a tellurol-thiol pair in peri-position are explored and compared with the analogous energy profiles for the naphthalene mimic having two selenols. The presence of a halogen bond (XB) in the intermediate formed in the first step and involved in the rate-determining step of the reaction is assumed to facilitate the process increasing the rate of the reaction. The rate-determining step calculated energy barrier heights allow rationalizing the experimentally observed superior catalytic activity of tellurium containing mimics. Charge displacement analysis is used to ascertain the presence and the role of the electron density charge transfer occurring in the rate-determining step of the reaction, suggesting the incipient formation or presence of a XB interaction. © 2019 Wiley Periodicals, Inc.     

Using correlations to compare additions to alkenes: homogeneous hydrogenation by using Wilkinson's catalyst

Plots of the logarithms of relative rates of homogeneous catalytic hydrogenation of alkenes (log k(rel) values) by using Wilkinson's catalyst versus their ionization potentials (IPs) and versus their lowest unoccupied molecular orbital energy levels (LUMOs) display good-to-excellent correlations. The correlations indicate that the rate-determining step of this reaction is a nucleophilic addition to the alkene double bond, which is dependent upon both electronic effects and steric effects. This conclusion is in agreement with only two of three previously proposed mechanisms for the reaction, effectively ruling out one in which the rate-determining step involves electrophilic addition to the alkene. Characteristics of the analysis using these correlations are compared and contrasted with other additions to alkenes, such as the Wacker oxidation, to probe patterns in transition state characteristics.     

A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase

A QM/MM method that combines ONIOM quantum chemistry and molecular dynamics is developed and applied to a step in the deamination of cytosine to uracil in yeast cytosine deaminase (yCD). A two-layer ONIOM calculation is used for the reaction complex, with an inner part treated at a high level for the chemical reaction (bond breaking) and a middle part treated at a lower level for relevant protein residues that are frozen in the quantum optimization. An outer layer (protein and solvent) is treated using MD. Configurations for the entire system are generated using MD and optimized with ONIOM. The method permits the use of high-level quantum calculations along with sufficient configurational sampling to approximate the potential of mean force for certain bond-breaking reactions. A previously proposed reaction mechanism for deamination (Sklenak, S.; Yao, L. S.; Cukier, R. I.; Yan, H. G. J. Am. Chem. Soc. 2004, 126, 14879) requires breaking the bond between a catalytic zinc and the O4 of uracil in order to permit product release. Using an ONIOM approach, direct bond cleavage was found to be energetically unfavorable. In the work presented here, the combined ONIOM MD method is used to show that the barrier for bond cleavage is small, approximately 3 kcal/mol, and, consequently, should not be the rate-limiting step in the reaction.     

A mild, palladium-catalyzed method for the dehydrohalogenation of alkyl bromides: synthetic and mechanistic studies

We have exploited a typically undesired elementary step in cross-coupling reactions, β-hydride elimination, to accomplish palladium-catalyzed dehydrohalogenations of alkyl bromides to form terminal olefins. We have applied this method, which proceeds in excellent yield at room temperature in the presence of a variety of functional groups, to a formal total synthesis of (R)-mevalonolactone. Our mechanistic studies have established that the rate-determining step can vary with the structure of the alkyl bromide and, most significantly, that L(2)PdHBr (L = phosphine), an intermediate that is often invoked in palladium-catalyzed processes such as the Heck reaction, is not an intermediate in the active catalytic cycle.     

Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process

The reaction mechanism of serine proteases (trypsin), which catalyze peptide hydrolysis, is studied theoretically by ab initio QM/MM electronic structure calculations combined with Molecular Dynamics-Free Energy Perturbation calculations. We have calculated the entire reaction free energy profiles of the first reaction step of this enzyme (acylation process). The present calculations show that the rate-determining step of the acylation is the formation of the tetrahedral intermediate, and the breakdown of this intermediate has a small energy barrier. The calculated activation free energy for the acylation is approximately 17.8 kcal/mol at QM/MM MP2/(aug)-cc-pVDZ//HF/6-31(+)G/AMBER level, and this reaction is an exothermic process. MD simulations of the enzyme-substrate (ES) complex and the free enzyme in aqueous phase show that the substrate binding induces slight conformational changes around the active site, which favor the alignment of the reactive fragments (His57, Asp102, and Ser195) together in a reactive orientation. It is also shown that the proton transfer from Ser195 to His57 and the nucleophilic attack of Ser195 to the carbonyl carbon of the scissile bond of the substrate occur in a concerted manner. In this reaction, protein environment plays a crucial role to lowering the activation free energy by stabilizing the tetrahedral intermediate compared to the ES complex. The polarization energy calculations show that the enzyme active site is in a very polar environment because of the polar main chain contributions of protein. Also, the ground-state destabilization effect (steric strain) is not a major catalytic factor. The most important catalytic factor of stabilizing the tetrahedral intermediate is the electrostatic interaction between the active site and particular regions of protein: the main chain NH groups in Gly193 and Ser195 (so-called oxyanion hole region) stabilize negative charge generated on the carbonyl oxygen of the scissile bond, and the main chain carbonyl groups in Ile212 approximately Ser214 stabilize a positive charge generated on the imidazole ring of His57.     

Fundamental reaction mechanism for cocaine hydrolysis in human butyrylcholinesterase

Butyrylcholinesterase (BChE)-cocaine binding and the fundamental pathway for BChE-catalyzed hydrolysis of cocaine have been studied by molecular modeling, molecular dynamics (MD) simulations, and ab initio calculations. Modeling and simulations indicate that the structures of the prereactive BChE/substrate complexes for (-)-cocaine and (+)-cocaine are all similar to that of the corresponding prereactive BChE/butyrylcholine (BCh) complex. The overall binding of BChE with (-)-cocaine and (+)-cocaine is also similar to that proposed with butyrylthiocholine and succinyldithiocholine, i.e., (-)- or (+)-cocaine first slides down the substrate-binding gorge to bind to Trp-82 and stands vertically in the gorge between Asp-70 and Trp-82 (nonprereactive complex) and then rotates to a position in the catalytic site within a favorable distance for nucleophilic attack and hydrolysis by Ser-198 (prereactive complex). In the prereactive complex, cocaine lies horizontally at the bottom of the gorge. The fundamental catalytic hydrolysis pathway, consisting of acylation and deacylation stages similar to those for ester hydrolysis by other serine hydrolases, was proposed on the basis of the simulated prereactive complex and confirmed theoretically by ab initio reaction coordinate calculations. Both the acylation and deacylation follow a double-proton-transfer mechanism. The calculated energetic results show that within the chemical reaction process the highest energy barrier and Gibbs free energy barrier are all associated with the first step of deacylation. The calculated ratio of the rate constant (k(cat)) for the catalytic hydrolysis to that (k(0)) for the spontaneous hydrolysis is approximately 9.0 x 10(7). The estimated k(cat)/k(0) value of approximately 9.0 x 10(7) is in excellent agreement with the experimentally derived k(cat)/k(0) value of approximately 7.2 x 10(7) for (+)-cocaine, whereas it is approximately 2000 times larger than the experimentally derived k(cat)/k(0) value of approximately 4.4 x 10(4) for (-)-cocaine. All of the results suggest that the rate-determining step of the BChE-catalyzed hydrolysis of (+)-cocaine is the first step of deacylation, whereas for (-)-cocaine the change from the nonprereactive complex to the prereactive complex is rate-determining and has a Gibbs free energy barrier higher than that for the first step of deacylation by approximately 4 kcal/mol. A further analysis of the structural changes from the nonprereactive complex to the prereactive complex reveals specific amino acid residues hindering the structural changes, providing initial clues for the rational design of BChE mutants with improved catalytic activity for (-)-cocaine.     

CO在Pd平板与Pd38团簇表面上的催化氧化机理研究

采用密度泛函理论(DFT)计算模拟Pd平板和Pd_(38)团簇上的CO催化氧化过程,分析了CO在Pd催化剂表面上的氧化反应机理。结果表明,在Pd_(38)团簇模型上CO催化氧化的决速步骤是O_2的解离,反应能垒为0.65 eV,而在Pd平板模型上的决速步骤是CO的氧化,其反应能垒为0.87 eV。对比决速步骤的活化能发现,CO在Pd_(38)团簇上的氧化反应更易进行,说明CO氧化更易在小颗粒催化剂表面上进行,即Pd催化剂的活性与活性组分颗粒大小相关,活性组分颗粒越小,暴露的活性位点越多,其催化活性也越高。     

An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase

We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.     

Application of ab initio molecular dynamics for a priori elucidation of the mechanism in unimolecular decomposition: the case of 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO).

We have tested a new and general approach for the theoretical study of unimolecular decomposition. By combining the power of the ab initio molecular dynamics (MD) and ab initio molecular orbital (MO) methods, our approach requires no prior experimental knowledge or intuitive assumptions about the decomposition. Instead, the reaction channels are first sampled theoretically by simulating a molecule at high temperature in a number of trajectories, using the density functional theory (DFT) based ab initio MD method with a planewave basis set and pseudopotentials. Each type of these channels is then further examined by well-established ab initio MO method to locate the energy barrier and transition structure and to verify the ab initio MD results. The power of such an approach is demonstrated in a case study for the complicated unimolecular thermal decomposition of NTO (5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one), with several interesting new features uncovered. The C-NO2 homolysis is indeed the dominant channel at high temperature, while the departing NO2 could capture a H atom from the NTO ring to form HONO, by either a concerted bond breaking mechanism or by a bimolecular reaction between the NO2 group and the triazol ring. At lower temperature, the dissociation channels initiated by hydrogen migrations should be activated first. The channel with hydrogen migration followed by ring opening and then by HONO loss has an energy barrier of 38.0 kcal/mol at the rate-determining step, being the lowest among all the investigated dissociation paths and much lower than previously thought. The energy barrier for nitro-nitrite rearrangement is lower than that for the C-NO2 homolysis but makes only a minor contribution due to the entropy factor. And the NTO ring could rupture in the two C-N bonds connected to the carbonyl carbon, and the energy barriers for such processes are only 2-4 kcal/mol higher than that for the C-NO2 homolysis.     

Concerted or stepwise hydrogen transfer in the transfer hydrogenation of acetophenone catalyzed by ruthenium-acetamido complex: a theoretical mechanistic investigation

In this paper, the mechanism of transfer hydrogenation of acetophenone catalyzed by ruthenium-acetamido complex was studied using density function theory (DFT) method. The catalytic cycle of transfer hydrogenation consists of hydrogen transfer (HT) step and dehydrogenation (DH) step of isopropanol (IPA). Inner sphere mechanism (paths 1 and 7) and outer sphere mechanism (paths 2-6) in HT step are fully investigated. Calculated results indicate that DH step of IPA (from (i)1 to (i)2) is the rate-determining step in the whole catalytic cycle, which has a potential energy barrier of 16.2 kcal/mol. On the other hand, the maximum potential energy barriers of paths 1-7 in the HT step are 5.9, 12.7, 24.4, 16.8, 23.7, 7.2, and 6.1 kcal/mol, respectively. The inner sphere pathways (paths 1 and 7) are favorable hydrogen transfer modes compared with outer sphere pathways, and the proton transferred to the oxygen atom of acetophenone comes from the hydroxyl group but not from amino group of acetamido ligand. Those theoretical results are in agreement with experimental report. However, in view of this DFT study in the inner sphere mechanism of HT step, hydride transfer and proton transfer are concerted and asynchronous hydrogen transfer but not a stepwise one, and hydride transfer precedes proton transfer in this case.     

The measurement of nucleoside deaminases by high performance liquid chromatography and their use in clinical chemistry.

The measurement of the nucleoside deaminases--cytidine deaminase, guanosine deaminase and adenosine deaminase--by reversed phase high performance liquid chromatography is reviewed. The clinical value of assaying the enzyme activity is discussed for each of these enzymes. Both cytidine deaminase and adenosine deaminase measurements have proven clinical value, although the use of the assay of cytidine deaminase in the diagnosis of pre-eclampsia is probably not helpful.     

Mechanistic Insights into the Selectivity of Norcarane Oxidation by Oxo-Manganese(V) Porphyrin Complexes

Oxo-Mn(V) porphyrin complexes perform competitive hydroxylation, desaturation, and radical rearrangement reactions using diagnostic substrate norcarane. Initial C−H cleavage proceeds through the two hydrogen abstraction steps from the two adjacent carbon on the norcarane and then through selective reactions various products are generated. Using density functional theory calculations, we show that the hydroxylation and desaturation reactions are triggered by a rate-determining H-abstraction step, whereas the rate-determining step for the radical rearrangement is located at the rebound step ( TS2 ). We find that the endo- 2 reaction is favorable over other reactions, which is consistent with the experimental result. Furthermore, the competitive pathways for norcarane oxidation depend on the non-covalent interaction between norcarane and the porphyrin-ring, and orbital energy gaps between donor and acceptor orbitals because of stable or unstable acceptor orbital. The stereo- and regio-selectivities of norcarane oxidation are hardly sensitive to the zero-point energy and thermal free energy corrections.     

Heck reactions of alkenes with aryl iodides and aryl bromides: Rate-determining steps deduced from a comparative kinetic study of competing and noncompeting reactions

Joint kinetic analysis of competition and noncompetition experiments can provide important information and sometimes a direct answer concerning the rate-determining step of a catalytic reaction. Applying this approach to the Heck reaction has demonstrated that alkenes; reactive aryl iodides; and, contrary to the conventional opinion, unactivated aryl bromides participate in rapid steps of the Heck reaction. For aryl iodides, the rate-determining step includes the dissociation of a C-H bond. At the same time, kinetic data for the dissolution of palladium reacting with aryl bromides suggest that the rate of the catalytic reaction is determined by the slow dissolution of palladium aggregates.     

纳米Pd上H2O2的电催化还原反应

利用纳米Pd颗粒修饰的Au旋转圆盘电极, 通过强制对流条件下的线性电势扫描伏安法, 研究了酸性介质中H2O2在纳米Pd催化剂上的电还原反应. 动力学研究结果表明, H2O2在纳米Pd上电还原反应的表观活化能为27.6 kJ·mol-1, 反应为2电子转移过程, 电解质的阴离子类型显著影响纳米Pd对H2O2电化学还原反应的催化性能. 根据动力学电流与H2O2浓度及与H+浓度的关系, 提出了Pd催化H2O2电还原反应可能的速率控制步骤, 并讨论了其可能的反应机理.     

An efficient methyltrioxorhenium(VII)-catalyzed transformation of hydrotrioxides (ROOOH) into dihydrogen trioxide (HOOOH)

Dihydrogen trioxide (HOOOH) is formed nearly quantitatively in the low-temperature (-70 degrees C) methyltrioxorhenium(VII) (MTO)-catalyzed transformation of silyl hydrotrioxides (R3SiOOOH), and some acetal hydrotrioxides, in various solvents, as confirmed by 1H, and 17O NMR spectroscopy. The calculated energetics (B3LYP) for the catalytic cycle, using H3SiOOOH as a model system, is consistent with the experimentally observed activation energy (9.5 +/- 2.0 kcal/mol) and a small kinetic solvent isotope effect (kH2O/kD2O = 1.1 +/- 0.1), indicating an initial concerted reaction between the silyl hydrotrioxide and MTO in the rate-determining step. With the addition of water in the next step, the intermediate undergoes a sigma-bond metathesis reaction to break the Re-OOOH bond and form HOOOH, together with the second dihydroxy intermediate. The final step in the catalytic cycle involves a second, catalytic water that lowers the barrier to form H3SiOH and MTO.