Mechanism of product release in NO detoxification from Mycobacterium tuberculosis truncated hemoglobin N

The capability of Mycobacterium tuberculosis to rest in latency in the infected organism appears to be related to the disposal of detoxification mechanisms, which converts the nitric oxide (NO) produced by macrophages during the initial growth infection stage into a nitrate anion. Such a reaction appears to be associated with the truncated hemoglobin N (trHbN). Even though previous experimental and theoretical studies have examined the pathways used by NO and O2 to access the heme cavity, the eggression pathway of the nitrate anion is still a challenging question. In this work we present results obtained by means of classical and quantum chemistry simulations that show that trHbN is able to release rapidly the nitrate anion using an eggression pathway other than those used for the entry of both O2 and NO and that its release is promoted by hydration of the heme cavity. These results provide a detailed understanding of the molecular basis of the NO detoxification mechanism used by trHbN to guarantee an efficient NO detoxification and thus warrant survival of the microorganism under stress conditions.     

Theoretical study of the mechanism of NO2 production from NO + ClO

The reaction of NO with ClO has been studied theoretically using density-functional and wave function methods (B3LYP and CCSD(T)). Although a barrier for cis and trans additions could be located at the RCCSD(T) and UCCSD(T) levels, no barrier exists at the B3LYP/6-311+G(d) level. Variational transition state theory on a CASPT2(12,12)/ANO-L//B3LYP/6-311+G(d) surface was used to calculate the rate constants for addition. The rate constant for cis addition was faster than that for trans addition (cis:trans 1:0.76 at 298 K). The rate constant data summed for cis and trans addition in the range 200-1000 K were fit to a temperature-dependent rate in the form kdi) = 3.30 x 10(-13)T(0.558) exp(305/T) cm3.molecule(-1).s(-1), which is in good agreement with experiment. When the data are fit to an Arrhenius plot in the range 200-400 K, an activation barrier of -0.35 kcal/mol is obtained. The formation of ClNO2 from ONOCl has a much higher activation enthalpy from the trans isomer compared to the cis isomer. In fact, the preferred decomposition pathway from trans-ONOCl to NO2 + Cl is predicted to go through the cis-ONOCl intermediate. The trans --> cis isomerization rate constant is kiso = 1.92 x 10(13) exp(-4730/T) s(-1) using transition state theory.     

Theoretical study on the mechanism of the 1CHCl + NO reaction

The complex doublet potential energy surface of the CHClNO system, including 31 minimum isomers and 84 transition states, is investigated at the QCISD(T)/6-311G(d, p)//B3LYP/6-31G(d, p) level in order to explore the possible reaction mechanism of the singlet CHCl with NO. Various possible isomerization and dissociation channels are probed. The initial association between 1CHCl and NO at the terminal N-site can almost barrierlessly lead to the chainlike adducts HClCNO a (a1, a2) followed by the direct Cl-extrusion to product P9 Cl + HCNO, which is the most feasible channel. Much less competitively, a (a1, a2) undergoes a ring-closure leading to the cyclic isomer c-C(HCl)NO d followed by a concerted Cl-shift and N-O cleavage of d to form the branched isomers ClNC(H)O f (f1, f2). Eventually, f (f1, f2) may take a direct H-extrusion to produce P7 H + ClNCO or a concerted 1,2-H-shift and Cl-extrusion to form P1 Cl + HNCO. The low-lying products P2 HCl + NCO, P3 Cl + HOCN, P14 HCO + 3NCl, P6 ClO + HCN, and P13 ClNC + OH may have the lowest yields observed. Our calculations show that the product distributions of the title reaction are quite different from those of the analogous 1CHF + NO reaction, yet are similar to those of another analogous 3CH2 + NO reaction. The similarities and discrepancies among the three reactions are discussed in terms of the substitution effect. The present article may assist in future experimental identification of the product distributions for the title reaction and may be helpful for understanding the halogenated carbene chemistry.     

Theoretical study on the mechanism of the 1CHCl + NO2 reactions

The radical-molecule reaction mechanism of (1)CHCl with NO(2) has been explored theoretically at the B3LYP/6-311G(d, p) and CCSD(T)/6-311G(d, p) (single-point) levels of theory. Thirteen minimum isomers and 29 transition states are located. The initial association between (1)CHCl and NO(2) proceeds most likely through the carbon-to-middle-nitrogen attack leading to an energy-rich adduct a (HClCNO(2)), which is found to be a barrierless process. Staring from a, the most feasible channel is to undergo a concerted O-shift and C--N bond rupture leading to product P(2) (NO + HClCO). The minor product pathways are the direct O-extrusion of a to P(3) (O + HClCNO-cis) as well as the 1,3-H-shift of a to isomer b (ClCNOOH) followed by a concerted OH-shift leading to d (HOClCNO), which will dissociate to product P(8) (NO + ClCOH) via C--N cleavage. Because the transition states and isomers involved in the most feasible channel all lie below the reactants, the title reaction is expected to be rapid, as is consistent with the measured rate constant at 296 K. The comparison with the analogous reactions (3)CH(2) + NO(2) are discussed. The present study may be useful for further experimental investigation of the title reaction.     

Theoretical study on the kinetics and mechanism for the reaction of FCO with NO

The radical reaction mechanism of FCO + NO on the ground electronic state energy surface has been studied at the G2M level of theory based on the geometric parameters optimized at the B3LYP/6-311+G(d) level of theory. The two kinds of reaction pathways include the direct fluorine abstraction channel producing CO + FNO and the association channel forming the FC(O)NO complex. The former has a distinct barrier of 8.9 kcal mol(-1), while the latter is a barrierless association process. The rate constant of this reaction system in the temperature range 200-3000 K has been calculated by the microcanonical VTST/RRKM theory. The theoretical result shows that the predicted total rate constants exhibit a negative-temperature dependence and positive-pressure effect at lower temperatures. Under the experimental conditions, the predicted values are in good agreement with the experimental results. In addition, the predicted branching ratios clearly indicate that the dominant product channel is the formation of FC(O)NO at low temperatures and FNO + CO at high temperatures (>500 K).     

Theoretical study on the mechanism of the CH2F + NO2 reaction

Despite the importance of the Fluoromethyl radicals in combustion chemistry, very little experimental information on their reactions toward stable molecules is available in the literature. Motivated by recent laboratory characterization about the reaction kinetics of Chloromethyl radicals with NO2, we carried out a detailed potential energy survey on the CH2F + NO2 reaction at the B3LYP/6-311G(d,p) and MC-QCISD (single-point) levels as an attempt toward understanding the CH2F + NO2 reaction mechanism. It is shown that the CH2F radical can react with NO2 to barrierlessly generate adduct a (H2FCNO2), followed by isomerization to b1 (H2FCONO-trans) which can easily interconvert to b2 (H2FCONO-cis). Subsequently, Starting from b (b1, b2), the most feasible pathway is the C--F and N--O1 bonds cleavage along with N--F bond formation of b (b1, b2) leading to P1 (CH2O + FNO), or the direct N--O1 weak-bond fission of b (b1, b2) to give P2 (CH2FO + NO), or the 1,3-H-shift associated with N--O1 bond rupture of b1 to form P3 (CHFO + HNO), all of which may have comparable contribution to the reaction CH2F + NO2. Much less competitively, b2 either take the 1,4-H-shift and O1--N bond cleavage to form product P4 (CHFO + HON) or undergo a concerted H-shift to isomer c2 (HFCONOH), followed by dissociation to P4. Because the rate-determining transition state (TSab1) in the most competitive channels is only 0.3 kcal/mol higher than the reactants in energy, the CH2F + NO2 reaction is expected to be rapid, and may thus be expected to significantly contribute to elimination of nitrogen dioxide pollutants. The similarities and discrepancies among the CH2X + NO2 (X = H, F, and Cl) reactions are discussed in terms of the electronegativity of halogen atom. The present article may assist in future experimental identification of the product distributions for the title reaction, and may be helpful for understanding the halogenated methyl chemistry.     

Theoretical study on the reaction mechanism of NO and CO catalyzed by Rh atom

The gas-phase reaction mechanism of NO and CO catalyzed by Rh atom has been systematically investigated on the ground and first excited states at CCSD(T)//B3LYP/6-311+G(2d), SDD level. This reaction is mainly divided into two reaction stages, NO deoxygenation to generate N₂O and then the deoxygenation of N₂O with CO to form N₂ and CO₂. The crucial reaction step deals with the NO deoxygenation to generate N₂O catalyzed by Rh atom, in which the self-deoxygenation of NO reaction pathway is kinetically more preferable than that in the presence of CO. The minimal energy reaction pathway includes the rate-determining step about N–N bond formation. Once the NO deoxygenation with CO catalyzed by rhodium atom takes place, the reaction results in the intermediate RhN. Then, the reaction of RhN with CO is kinetically more favorable than that with NO, while both of them are thermodynamically preferable. These results can qualitatively explain the experimental finding of N₂O, NCO, and CN species in the NO + CO reaction. For the N₂O deoxygenation with CO catalyzed by rhodium atom, the reaction goes facilely forward, which involves the rate-determining step concerning CO₂ formation. CO plays a dominating role in the RhO reduction to regenerate Rh atom. The complexes, OCRhNO, RhON₂, RhNNO, ORhN₂, RhCO₂, RhNCO, and ORhCN, are thermodynamically preferred. Rh atom possesses stronger capability for the N₂O deoxygenation than Rh⁺ cation.     

CH3+HNCO反应机理的理论研究

异氰酸(HNCO)分解引发的一系列自由基反应是氮氧化物快速消除机理[1,2](RAPRENOX)所研究的领域,该反应涉及到燃烧化学中氮氧化物NOX的消除,所以获得这些反应准确的位垒就成为实验化学和理论化学所要解决的问题。本文中我们重点研究CH3+HNCO反应机理,探讨CH3自由基是否也能象氮氢自由基一样,在异氰酸(HNCO)分解反应中起作用。1　计算方法用量子化学MP2方法,在6 311++G 水平上计算了CH3自由基与HNCO反应的反应物、产物、中间体和过渡态的几何构型,用QCISD(T)方法在6 311++G 水平上计算了它们的能量。通过振动分析确定…     

Theoretical study of the mechanism for the ClOO + NO reaction on the singlet potential energy surface

A detailed quantum chemical study is performed on the mechanism of ClOO + NO reaction at the B3LYP/6-311+G (2d) level of theory combined with CCSD (T) single point energy calculation. The possible product channels for the reaction are obtained and discussed on the basis of the singlet [ClNO₃] potential energy surface. The calculation indicates that the dominant product for the title reaction is ClO + NO₂ by the direct dissociation of the initial adduct, and the formation of the other products is much less likely since they are unfavorable kinetically. A comparison is also made between the title reaction and the analogous reaction of FO₂ + NO to gain a deeper insight into the mechanism of the XO₂ + NO reactions.     

Theoretical study on the reaction mechanism of (CH3)3CO(.) radical with NO

The reaction mechanism of (CH3)3CO(.) radical with NO is theoretically investigated at the B3LYP/6-31G* level. The results show that the reaction is multi-channel in the single state and triplet state. The potential energy surfaces of reaction paths in the single state are lower than that in the triple state. The balance reaction: (CH3)3CONO←→ (CH3)3CO(.)+NO, whose potential energy surface is the lowest in all the reaction paths, makes the probability of measuring (CH3)3CO(.) radical increase. So NO may be considered as a stabilizing reagent for the (CH3)3CO(.)radical.     

Theoretical study of the phosphotriesterase reaction mechanism

Phosphotriesterase (PTE) is a binuclear zinc enzyme that catalyzes the hydrolysis of extremely toxic organophosphate triesters. In the present work, we have investigated the reaction mechanism of PTE using the hybrid density functional theory method B3LYP. We present a potential energy surface for the reaction and provide characterization of the transition states and intermediates. We used the high resolution crystal structure to construct a model of the active site of PTE, containing the two zinc ions and their first shell ligands. The calculations provide strong support to an associative mechanism for the hydrolysis of phosphotriesters by PTE. No protonation of the leaving group was found to be necessary. In particular, the calculations demonstrate that the nucleophilicity of the bridging hydroxide is sufficient to be utilized in the hydrolysis reaction, a feature that is of importance for a number of other di-zinc enzymes.     

Theoretical study of NO adsorption on gold surfaces

The activities of neutral,anionic,and cationic Au(111),Au(100),and Au(310) surfaces,as well as an Au adatom on Au(111) surface towards NO adsorption have been studied by performing density functional theory calculations.It was found that the activity of gold increases as the coordination number of the gold atoms decreases,and that the cationic surfaces are generally more active than the neutral and anionic surfaces.The activity of Au surfaces towards NO adsorption is attributable to the presence of low coor...     

Theoretical study of volume changes accompanying xenon-lysozyme binding: implications for the molecular mechanism of pressure reversal of anesthesia

The change in partial molar volume (PMV) accompanying the xenon-lysozyme binding was investigated for elucidating the molecular mechanism of the pressure reversal of general anesthesia, using the three-dimensional reference interaction site model theory of molecular solvation. An increase of the PMV from xenon binding to the substrate binding site of lysozyme was found, and the binding is suppressed by pressure, while the internal site binding did not change the PMV. The PMV change was analyzed by decomposing it into several contributions from geometry and hydration. We also analyzed the hydration change due to the binding. From the results, we draw a molecular picture of the PMV change accompanying xenon-lysozyme binding, which gives a possible mechanism of pressure reversal of anesthesia.     

The reaction mechanism of Cytochrome P450 NO reductase: a detailed quantum mechanics/molecular mechanics study

A detailed QM/MM study on the reaction mechanism of Cytochrome P450 NO reductase is reported. Two reaction pathways connecting the two well-characterized intermediates as well as two putative intermediates that represent the unknown third intermediate are explored, with emphasis on the unusual direct reduction of the enzymatic active site by the cofactor NADH. Activation barriers and kinetic isotope effect are calculated and reveal that reduction of the NO-bound species occurs in form of a hydride ion transfer. Furthermore, the impact of different hydrogen bonds in the active site to binding and reactivity of NADH is explored. The calculated kinetic and thermodynamic properties for both modelled pathways are used for the kinetic simulation of the entire reaction course. It is thus shown that the unknown key intermediate is the singlet diradical Fe(III)-NHOH(?). It is also found that the mechanism of the N-N bond formation is spin-recoupling, which is only possible due to the diradical character of the key intermediate.     

Theoretical study of the Si2NO potential energy surface

The structures, spectroscopies, and stabilities of the doublet Si₂NO radical are explored at the density functional theory (DFT) and ab initio levels. Seventeen isomers are located, connected by 26 interconversion transition states. At the CCSD(T)/6‐311+G(2df)//QCISD/6‐311G(d)+ZPVE level, three low‐lying isomers are predicted, that is, one bent species SiNSiO 3 (5.1 kcal/mol) containing the important Si?N triple bonding and two four‐membered ring isomers including cyclic cSiNSiO 1 (0.0) with Si? Si cross‐bonding with C_2v symmetry and puckered cSiNSiO 1′ (11.9) with divalent carbene character. Three low‐lying isomers 1, 1′, and 3 have reasonable kinetic stabilities and might be observable either experimentally or astrophysically. The possible formation strategies of 1, 1′, and 3 in laboratory and in space are discussed in detail. The calculated vibrational frequencies and possible formation processes of 3 are consistent with recent experimental observations. In light of the fact that no cyclic nitrogen‐containing species have been detected in space, two cyclic isomers 1 and 1′ could be promising candidates. Furthermore, the bonding nature of three isomers 1, 1′, and 3 is analyzed. The calculated results are also compared with those of the analogue C₂NO radical. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Autoxidation of giant extracellular hemoglobin of Glossoscolex paulistus: molecular mechanism and oligomeric implications

Giant extracellular hemoglobins present high redox stability due to their supramolecular architecture, high number of polypeptide chains and great compaction of protein subunits. The oligomeric assembly and the changes in the polypeptidic structure can influence the autoxidation rate of the heme proteins, being that different nucleophiles can act in this process due to pH alterations. In the present work, we have studied the autoxidation rate of whole Glossoscolex paulistus (HbGp) giant extracellular hemoglobin, as well as the autoxidation rate of the isolated d monomer of HbGp studied regarding pH variations. The kinetic decay behavior is dependent on pH, presenting mono-exponential or bi-exponential character, depending on the oligomeric state of the protein. Thus, the oligomeric dissociation in specific pH values demonstrated a bi-exponential kinetic decay. A mono-exponential kinetic behavior was verified in the pH range of 5.9–7.3, which is assigned to the native whole protein. In alkaline medium, the presence of hydroxide ions leads the autoxidation of whole hemoglobin to a complex behavior, which is described by the combination of two first-order kinetics. The slow process occurs due to the d monomer autoxidation. At pH 7.0, the kinetic is mono-exponential, indicating a highly conserved oligomeric structure. In acid medium, the proton-catalyzed autoxidation occurs both on the whole hemoglobin and in the d monomer. It has been found that proximal and distal histidines develop determinant roles regarding the autoxidation rate, being that the distal histidine controls the contact of ligands with the ferrous center through a very interesting “swinging door” mechanism. Despite the significant sensitivity of the distal histidine to the presence of protons, water molecules and anions, the influence of chemical changes around the heme, such as pH changes, is much more effective in hemoproteins without this amino acid as distal residue. This fact denotes the ability of HbGp to adapt to environmental disturbances caused by the presence of the distal histidine, which is responsible for the great redox and oligomeric stabilities encountered in HbGp.     

Theoretical studies of molecular complexes: a probe into basis set and correlation effects

We investigate the effect of basis set size, correlation effects and interplanar separation on the theoretical electronic structure of stacking complexes of para- and meta-hydroxyaruline with formamidinium cation, constructed as analogs for the complexes of 5- and 6-hydroxytryptamine with imidazolium cation.     

苯并噻二唑醇解反应机理的理论研究

苯并噻二唑（BTH）是新型植保制剂。预防对象包括白粉病、锈病、霜霉病等阻引。 为更好地了解BTH的环境行为，本文研究了BTH醇解反应机理及反应的动力学。     

Theoretical study on the mechanism of the (3)CH(2) + NO(2) reaction

The complex doublet potential energy surface of the CH(2)NO(2) system is investigated at the B3LYP/6-31G(d,p) and QCISD(T)/6-311G(d,p) (single-point) levels to explore the possible reaction mechanism of the triplet CH(2) radical with NO(2). Forty minimum isomers and 92 transition states are located. For the most relevant reaction pathways, the high-level QCISD(T)/6-311 + G(2df,2p) calculations are performed at the B3LYP/6-31G(d,p) geometries to accurately determine the energetics. It is found that the top attack of the (3)CH(2) radical at the N-atom of NO(2) first forms the branched open-chain H(2)CNO(2) a with no barrier followed by ring closure to give the three-membered ring isomer cC(H(2))ON-O b that will almost barrierlessly dissociate to product P(1) H(2)CO + NO. The lesser followed competitive channel is the 1,3-H-shift of a to isomer HCN(O)OH c, which will take subsequent cis-trans conversion and dissociation to P(2) OH + HCNO. The direct O-extrusion of a to product P(3) (3)O + H(2)CNO is even much less feasible. Because the intermediates and transition states involved in the above three channels are all lower than the reactants in energy, the title reaction is expected to be rapid, as is consistent with the measured large rate constant at room temperature. Formation of the other very low-lying dissociation products such as NH(2) + CO(2), OH + HNCO and H(2)O + NCO seems unlikely due to kinetic hindrance. Moreover, the (3)CH(2) attack at the end-O of NO(2) is a barrier-consumed process, and thus may only be of significance at very high temperatures. The reaction of the singlet CH(2) with NO(2) is also briefly discussed. Our calculated results may assist in future laboratory identification of the products of the title reaction.     

Theoretical study of the ozonolysis of allyl acetate: mechanism and kinetics

The potential energy surface (PES) and mechanism of the reaction of allyl acetate (AAC) with O₃ are investigated by using density functional theory (DFT) and ab initio (MP2 and CCSD(T)) methods. The kinetics and main product branching ratios over the temperature range of (200–2,000 K) and at various pressures are obtained by employing multichannel Rice–Ramsperger–Kassel–Marcus (RRKM) theory. The results show that the main products are 2-oxoethyl acetate and formaldehyde. Two channels are found for the decomposition of primary ozonides: one path is corresponding to the 2-oxoethyl acetate + CH₂OO formation (R1); the other channel products formaldehyde + CH₃C(O)OCH₂CHOO (R2). In the whole temperature range, R1 is calculated to be preferable and its product yield accounts for 60–77% of the total while R2 is found to contribute 20–40% to the total product yield. The overall rate constants show pressure independence and strong positive temperature dependence.