DFT analysis of the active site in catalytic metabolic redox reactions of mononuclear molybdenum enzymes

Abstract

Model complexes [Mo^VIO₂(S₂C₂Me₂)SMe]^? (A, derived from the X-ray crystal structure of native sulfite oxidase (SO)) and [Mo^VIO₂(mnt)₂]^2? (B, coordination mode similar to the active site of selenate reductase (SeR)) were computed at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of Density Functional Theory in order to study their behavior in oxidation of selenite (Se^IV) and sulfite (S^IV) to selenate (Se^VI) and sulfate (S^VI), respectively. For the oxidation of sulfite, computational model A, which resembles the SO active site, is clearly the best choice (lowest barrier, minor exothermicity). For the reduction of selenate, a smaller activation is computed for model A; however, the reaction is less exothermic with model B, which resembles the SeR active site.     

Siroheme‐containing sulfite reductase: A density functional investigation of the mechanism

Siroheme‐containing sulfite reductases (SiR) catalyze the six‐electron reduction of sulfite to sulfide via a mechanism involving sulfite binding at the heme iron. The exact sequence in which the required electrons and protons are delivered to the heme‐bound sulfite has received little attention to date. Here, a detailed account is given of these steps, based on density functional theory, thus providing data for the first attempt to draw a detailed picture of sulfite reduction in SiR by theoretical methods. Parallels are shown with reduction of other small molecules at heme centers: dioxygen (including generation of sulfide high‐valent iron centers akin to hemoproteins Compounds I and II), nitrite (including linkage isomerism akin to the nitro/nitrito known for nitrite reducing proteins), or nitric oxide. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study on the mechanism of the DNA repair protein Fpg

In this article, theoretical and calculational study at the DFT and ONIOM level are carried out on the Fpg glycosylase catalytic mechanism, to answer some mechanistic questions unclear yet. Representative S_N2 mechanism has been confirmed for all the models. The value 21.35 kcal/mol of the intrinsic activation barrier computed by the ONIOM (BP86/6‐311G**:AM1) approach agrees quite well with the experimental result of 20.66 kcal/mol. It has been found out that the electrostatic interaction between the positively charged Arg222 residue and the electronegative oxoG base is the most important influence on the excision process. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Class I ribonucleotide reductase revisited: the effect of removing a proton on Glu441

The substrate mechanism of class I ribonucleotide reductase has been revisited using the hybrid density functional B3LYP method. The molecular model used is based on the X-ray structure and includes all the residues of the R1 subunit commonly considered in the RNR substrate conversion scheme: Cys439 initiating the reaction as a thiyl radical, the redox-active cysteines Cys225 and Cys462, and the catalytically important Glu441 and Asn437. In contrast to previous theoretical studies of the overall mechanism, Glu441 is added as an anion. All relevant transition states have been optimized, including one where an electron is transferred 8 A from the disulfide to the substrate simultaneously with a proton transfer from Glu441. The calculated barrier for this step is 19.1 kcal/mol, which can be compared to the rate-limiting barrier indicated by experiments of about 17 kcal/mol. Even though the calculated barrier is somewhat higher than the experimental limit, the discrepancy is within the normal error bounds of B3LYP. The suggestion from the present modeling study is thus that a protonated Glu441 does not need to be present at the active site from the beginning of the catalytic cycle. However, the previously suggested mechanism with an initial protonation of Glu441 cannot be ruled out, because even with the cost added for protonation of Glu441 with a typical pK(a) of 4, the barrier for that mechanism is lower than the one obtained for the present mechanism. The results are compared to experimental results and suggestions.     

Flavin-mediated photoinactivation of spinach leaf nitrate reductase involving superoxide radical and activating effect of hydrogen peroxide

Irradiation with white light of spinach leaf nitrate reductase (NR) in the presence of flavin mononucleotide (FMN) and ethylenediaminetetraacetic acid (EDTA) resulted in a gradual loss of the enzyme activity, measured with reduced methyl viologen as electron donor. Inactivation of NR was dependent on oxygen and was prevented by superoxide dismutase. On the contrary, the presence of catalase markedly enhanced the rate of inactivation. Nitrate showed a protective effect. NR previously inactivated by irradiation in the presence of FMN and EDTA was greatly reactivated by a short preincubation of the inactive enzyme with either ferricyanide or H₂O₂. These results suggest that spinach leaf NR is reversibly inactivated by photogenerated O₂ , while H₂O₂ has an activating effect.     

燃煤固硫及催化燃烧一体化添加剂的催化作用机理研究

用热重法研究了燃煤固硫及催化燃烧一体化添加剂对峰峰烟煤的催化燃烧和催化固硫作用，采用非等温燃烧反应模型和粒子模型，计算了加入一体化添加剂前后煤的燃烧反应动力学和固硫反应动力学参数，对一体化添加剂的催化作用机理进行了分析。结果表明，一体化添加剂中金属催化组分Fe2O3对煤的燃烧和固硫组分CaO的固硫均起到了较好的催化促进作用。一体化添加剂的加入可提高煤的燃烧反应速率，外加金属离子通过电荷迁移使碳表面的棱、角、缺陷等活性部位增加，加快了氧气的吸附速度，使反应活化能和频率因子降低。在燃烧固硫反应，一体化添加剂中金属助剂Fe2O3催化了SO2转变为SO3的过程，使固硫组分CaO的硫酸盐化反应表面化学反应速度常数k和有效扩散系数D增大，在固硫反应的产物层扩散控制阶段，Fe2O3的存在使得CaO晶粒团之间相互接触黏连的几率减小，减轻了固硫产物CaSO4的团聚，弱化了扩散作用的影响，减轻了CaO固硫反应的孔窒息效应。     

六甲基二硅烷催化裂解的理论计算

采用密度泛函(DFT)及二级微扰理论(MP2)对六甲基二硅烷的催化裂解过程进行了计算.结果显示,该反应分三步进行,各步的能垒分别为144.9、77.4及214.9 kJ·mol-1,决定反应速度的是第三步.总反应是放热的,其中各步的焓变分别为22.4、-237.6、-127.6 kJ·Mol-1,反应的标准吉布斯自由能变为-348.7 kJ·mol-1,平衡常数为1.221×1061,在常温及常压下有较大的裂解倾向,理论产率比较高,计算结果与实验结果一致.     

Kinetics and mechanism of thermal decomposition of hydroxylammonium nitrate

The kinetics of thermal decomposition of melted hydroxylammonium nitrate have been investigated by the rate of heat production in the temperature range 84.8–120.9°C. The decomposition proceeds with autocatalysis and up to 60 % of conversion the rate of the process increases proportionally to the square of the degree of decomposition. The initial rate is proportional to the square of the concentration of HNO₃ formed due to dissociation of the salt. The activation energy of this process is 15.3±1.8 kcal/mol. It is suggested that the initial stage the process proceeds via interaction between N₂O₃ and NH₃OH⁺, whereas the subsequent acceleration is due to oxidation of NH₃OH⁺ by nitrogen oxides formed as well as by nitrous acid.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1897–1901, November, 1993.     

New computational evidence for the catalytic mechanism of carbonic anhydrase

Some aspects of the catalytic mechanism of HCA have been investigated. Either a zinc-bound water or a zinc-bound hydroxide has been considered as a nucleophile attacking CO ₂. No reaction path exists in the former case, while a transition state for the nucleophilic attack has been located in the latter (barrier of 7.6 kcal mol⁻¹). This activation energy is determined by the breaking of the hydrogen-bond network that shields the zinc-bound hydroxide when the CO ₂ molecule approaches the reaction center. No ambiguity exists about the mechanism for the internal rearrangement of the zinc–bicarbonate complex. The rotation pathway (Lindskog mechanism) proposed by many authors is too energy demanding since it causes the breaking of the hydrogen-bond network around the bicarbonate. The only possible rearrangement mechanism is a proton transfer (Lipscomb) that occurs in two steps (each step corresponding to a double proton transfer) and involves the Thr199 residue as a proton shuttle. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.     

Study of the effect of the ligand structure on the catalytic activity of Pd@ ligand decorated halloysite: Combination of experimental and computational studies

Taking advantage of computational chemistry, the best diamine for the synthesis of a multi‐dentate ligand from the reaction with 3‐(trimethoxysilyl) propylisocyanate (TEPI) was selected. Actually, predictive Density Functional Theory (DFT) calculations provided the right diamino chain, i.e. ethylenediamine, capable to sequester a palladium atom, together with the relatively polar solvent toluene, and then undergo the experiments as a selective catalytic agent. The ligand was then prepared and applied for the decoration of the halloysite (Hal) outer surface to furnish an efficient support for the immobilization of Pd nanoparticles. The resulting catalyst exhibited high catalytic activity for hydrogenation of nitroarenes. Moreover, it showed high selectivity towards nitro functional group. The study of the catalyst recyclability confirmed that the catalyst could be recycled for several reaction runs with only slight loss of the catalytic activity and Pd leaching. Hot filtration test also proved the heterogeneous nature of the catalysis.     

A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase

The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two‐layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn‐bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate‐determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn‐bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate‐determining step is the proton transfer from Zn‐OH to 6‐NH₂ of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

DFT investigation of the interaction between gold(I) complexes and the active site of thioredoxin reductase

The binding of the [Au(PMe₃)]⁺ fragment to cysteine, selenocysteine and the tetrapeptides H₂NGlyCysAGlyCOOH (A = Cys, Sec) has been investigated by DFT methods as a model for the binding of gold(I) to the selenium-containing active site of thioredoxin reductase. The calculations demonstrate both a higher acidity of Se-H compared to S-H and a stronger binding of gold at the selenium site compared to sulphur. Se-H dissociation at the selenium site increases the reducing power of the tetrapeptide H₂NGlyCysSecGlyCOOH whilst gold coordination at selenium has the opposite effect.     

Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2'-azido-2'-deoxyribonucleoside 5'-diphosphates

2'-azido-2'-deoxyribonucleoside 5'-diphosphates are mechanism-based inhibitors of Ribonucleotide Reductase. Considerable effort has been made to elucidate their mechanism of inhibition, which is still controversial and not fully understood. Previous studies have detected the formation of a radical intermediate when the inhibitors interact with the enzyme, and several authors have proposed possible structures for this radical. We have conducted a theoretical study of the possible reactions involved, which allowed us to identify the structure of the new radical among the several proposals. A new reactional path is also proposed that is the most kinetically favored to yield this radical and ultimately inactivate the enzyme. The energetic involved in this mechanism, both for radical formation and radical decay, as well as the calculated Hyperfine Coupling Constants for the radical intermediate, are in agreement with the correspondent experimental values. This mechanistic alternative is fully coherent with remaining experimental data.     

DFT Study on the Os+-catalytic Reduction Reaction of N2O with He in the Gas Phase

The Os+-catalytic reduction of N<,2>O by H<,2> in gas phase has been theoretically investigated with B3LYP method.The reaction mechanisms on the sextet and quartet surfaces were found to be similar.The calculated sextet potential energy profiles show that the two reactions involved in the catalytic cycle, Os<'+>+ N<,2>O→OsO<'+>+N<,2> and OsO<'+>+H2→Os<'+>+H<,2>O, have barriers of 28.3 and 123.3 kJ/mol, respectively.In contrast, the reactions on the quartet surfaces are energetically much more favorable.These results rationalize the experimentally observed low catalytic reactivity of sextet (ground-state) Os<'+>.Further, the crossing between the sextet and quartet Surfaces are also suggested and qualitatively discussed.     

DFT Study on the Os^＋-catalytic Reduction Reaction of N2O with H2 in the Gas Phase

The Os+-catalytic reduction of N2O by H2 in gas phase has been theoretically investigated with B3LYP method.The reaction mechanisms on the sextet and quartet surfaces were found to be similar.The calculated sextet potential energy profiles show that the two reactions involved in the catalytic cycle,Os+ + N2O → OsO+ + N2 and OsO+ + H2 → Os+ + H2O,have barriers of 28.3 and 123.3 kJ/mol,respectively.In contrast,the reactions on the quartet surfaces are energetically much more favorable.These results rationalize the experimentally observed low catalytic reactivity of sextet(ground-state) Os+.Further,the crossing between the sextet and quartet surfaces are also suggested and qualitatively discussed.     

硝酸氯氧分子（O2C1ONO2）结构的理论研究

实验获得的光谱数据预言大气中能够稳定存在的含氯储仓分子应包含硝酸氯氧。通过理论计算给出硝酸氯氧分子存在的分子结构、结合方式，在此构型基础上计算出的分子振动频率与实验测定值较为一致，并给出了硝酸氯氧分子稳定存在的理论依据     

Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase

The catalytic mechanism of molybdenum containing CO dehydrogenase has been studied using hybrid DFT methods with quite large chemical models. The recent high-resolution X-ray structure, showing the surprising presence of copper linked to molybdenum, was used as a starting point. A pathway was initially found with a low barrier for C-O bond formation and CO2 release. However, this pathway did not include the formation of any S-CO2 species, which had been suggested by experiments with an n-butylisocyanide inhibitor. When these SCO2 structures were studied they were found to lead to deep minima, making CO2 release much more difficult. A large effort was spent, including investigations of other spin states, varying the number of protons and electrons, adding water, etc., until a plausible pathway for S-C bond cleavage was found. In this pathway a water molecule is inserted in between molybdenum and the SCO2 group. Full catalytic cycles, including electron and proton transfers, are constructed both with and without S-C bond formation. When these pathways are extended to two full catalytic cycles it can be understood why the formation of the S-C bond actually makes catalysis faster, even though the individual step of CO2 release becomes much more difficult. These results agree well with experimental findings.     

催化裂化催化剂有机硫氮转化机理量子化学分析

国家环保法规的日益严格使得对催化裂化（FCC）再生烟气提出了更高的管控要求,再生烟气中污染物组成复杂且转化机制尚不清楚,迫切需要深入理解FCC待生催化剂中污染物的转化机理。对待生催化剂中有机硫和有机氮进行合理简化,选取合适的模型化合物,采用Gassian09软件,在B3LYP/def2-TZVP级别下,对模型化合物进行几何优化得到最稳定构型,并进行振动分析。利用Multiwfn多功能波函数分析仪对优化后模型化合物进行Laplacian键级分析（LBO）,通过LBO键级计算结果,得到自由基在再生过程中的详细转化机理。结果表明,含氮化合物中C—N键和含硫化合物中C—S键与C—C键相比均较弱,在催化剂再生过程中会优先发生断裂,生成不同的含氮（NH3、HCN）、含硫（H2S、COS）中间体,随后进一步与氧气反应生成相应的NOx、SOx。     

Experimental and theoretical studying the thermolysis of nitrate

This paper presents calorimeter measurement for the thermal decomposition of n-propyl nitrate (NPN), isopropyl nitrate (IPN) and 2-ethylhexyl nitrate (EHN). Similar experimental results of triethylene glycol dinitrate (tri-EGDN) and tetraethylene glycol dinitrate (tetra-EGDN) are included for comparison. The potential energy surfaces (PESs) along O-NO₂ bond stretch are investigated using the DFT (B3P86, B3PW91 and B3LYP), ab initio Hartree-Fock and PM3 methods. The good coincidence of experimental with theoretical results indicates that initial stage in the thermal decomposition of five nitrates is only unimolecular homolytical dissociation of the O-NO₂ bonds and the activation energies of thermolysis by DSC correspond to the energies of O-NO₂ bond scission of nitrates.