Molecular Dynamics and Combined QM/MM Studies on the Deactivation of anti-Tubercular Drug Isoniazid by Arylamine N-Acetyltransferases

Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics(QM/MM) study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases(NATs) and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as 'general base' rather than 'general acid'.If all the residues(including H2O molecules) were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement.     

Structure of a C26H28 alkene formed via titanium-promoted reductive dimerization of 4-(spirocyclopropyl)-pentacyclo[5.4.0.02,6.03,10.05,9]undecan-8-one

A spiro-fused C₂₆H₂₈ cage≓ dimer hydrocarbon contains two three-membered rings, two four-membered rings, eight five-membered rings, and two six-membered rings. The molecule is calculated by molecular mechanics to have 902 kJ/mol of strain energy distributed primarily between angle strain (457 kJ/mol) and torsional interactions (368 kJ/mol). Molecular mechanics calculations and a geometry-optimized ab initio calculation are used to analyze the bond lengths and bond angles in the molecule. There is one major discrepancy between observed and calculated distances.     

Ab initio study on the mechanism of reaction HNCO+NH2

Ab initio UMP2 and UQCISD(T) calculations, with 6-311G** basis sets, were performed for the titled reactions. The results show that the reactions have two product channels: NH₂+ HNCO?NH₃+NCO (1) and NH₂+HNCO?N₂H₃+CO (2), where reaction (1) is a hydrogen abstraction reaction via an H-bonded complex (HBC), lowering the energy by 32.48 kJ/mol relative to reactants. The calculated QCISD(T)//MP2(full) energy barrier is 29.04 kJ/mol, which is in excellent accordance with the experimental value of 29.09 kJ/mol. In the range of reaction temperature 2300–2700 K, transition theory rate constant for reaction (1) is 1.68×10¹¹–3.29×10¹¹ mL·mol^-1·s^-1, which is close to the experimental one of 5.0×10¹¹mL·mol^-1·s^-1or less. However, reaction (2) is a stepwise reaction proceeding via two orientation modes,cis andtrans, and the energy barriers for the rate-control step at our best calculations are 92.79 kJ/mol (forcis-mode) and 147.43 kJ/mol (fortrans-mode), respectively, which is much higher than reaction (1). So reaction (1) is the main channel for the titled reaction.     

(H_2O)_n(n=0～2)催化HS和HOCl反应机理的理论研究

在CCSD(T)/6-311+G(3df,2p)//M06-2X/6-311+G(3df,2p)水平上研究了(H_2O)n(n=0~2)催化HS和HOCl的反应机理.结果表明,HS与HOCl反应中HS夺取HOCl上的H原子形成产物H_2S和ClO.在无水催化时,该反应存在2种不同的路径(分别经过过渡态TS1和TS2,二者互为顺反结构),对应的能垒分别为100.28和100.91kJ/mol,到达产物(H_2S+ClO)需吸收18.99kJ/mol能量,反应不易发生;在单个水分子参与时,水分子可通过形成弱相互作用或者作为H原子转移桥梁影响反应机理,获得了4种水催化路径,能垒(间于53.97~92.39kJ/mol之间)均低于无水催化过程.同时发现,在反应到达产物前,水分子可以与产物形成中间体IM,IM相对能仅为0.46kJ/mol,有利于产物形成;有2个水分子参与反应时,找到了3条催化路径,最优反应路径过渡态TS7的能垒为45.05kJ/mol,低于无水催化过程,相比单个水分子最优路径能垒(53.97kJ/mol)并无显著降低.     

Kinetics of low temperature CO oxidation over Pt/SnO2 catalyst

In a CO−O₂ stoichiometric mixture, the kinetic parameters, reaction order, rate constant and activation energy of CO oxidation over a Pt/SnO₂ catalyst have been measured using a fixed bed flow reactor near 0°C. The results show that it is a first-order reaction. The activation energy of CO oxidation over Pt/SnO₂ prepared with SnO₂ calcined at 300°C was approximately 21 kJ/mol. The activation energy of CO oxidation over Pt/SnO₂ changed slowly with SnO₂ calcination temperature above 400°C, and reached approximately 45 kJ/mol.     

Quantitative studies on furfural and organic acid formation during hydrothermal,acidic and alkaline degradation ofD-xylose

Summary Chromatographic analysis of the degradation ofD-xylose either in plain water or aqueous sulfuric acid at temperatures ranging from 180 – 220°C gave up to 50 mol% of furfural. Activation energies did not differ significantly between reactions in plain water (E _a =119.4 kJ/mol), 0.001M H₂SO₄ (E _a =120.6 kJ/mol), 0.01M H₂SO₄ (E _a =130.8 kJ/mol), and 0.1M H₂SO₄ (E _a =120.7 kJ/mol). However, under alkaline conditions the activation energy was only 63.7 kJ/mol, indicating a different reaction mechanism. Isotachophoretic analyses revealed the formation of pyruvic, formic, glycolic, lactic, and acetic acid. While the relative yields of these acids ranged from 0.8 to 7% under hydrothermal and acidic conditions, 10 – 23% were obtained in alkaline degradation.

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Quantitative Studien zur Bildung von Furfural und organischen Säuren während des hydrothermalen, sauren und alkalischen Abbaues vonD-Xylose

Zusammenfassung Die chromatographische Analyse des Abbaues vonD-Xylose in reinem Wasser und Schwefelsäure bei Temperaturen von 180 – 220°C ergab die Bildung von bis zu 50 mol% Furfural. In bezug auf die Aktivierungsenergie zeigten sich keine signifikanten Unterschiede zwischen dem Abbau vonD-Xylose in reinem Wasser (E _a =119.4 kJ/mol), 0.001M H₂SO₄ (E _a =120.6 kJ/mol), 0.01M H₂SO₄ (E _a =130.8 kJ/mol), and 0.1M H₂SO₄ (E _a =120.7 kJ/mol). Unter alkalischen Bedingungen hingegen betrug die Aktivierungsenergie nur 63.7 kJ/mol. Dies weist auf einen unterschiedlichen Reaktionsmechanismus hin. Ferner konnte mittels Isotachophorese die Bildung von Brenztraubensäure, Ameisensäure, Glycolsäure, Milchsäure und Essigsäure nachgewiesen werden. Während sich die relativen Ausbeuten in Wasser und Schwefelsäure zwischen 0.8 und 7% bewegten, betrugen sie unter alkalischen Bedingungen 10 bis 23%.

     

钐(II)类卡宾CH3SmCH2I与乙烯环丙烷化反应及溶剂化效应的理论研究

用密度泛函B3LYP方法研究了过渡金属钐类卡宾与乙烯的环丙烷化反应的机理. 对钐类卡宾试剂CH₃SmCH₂I和CH₂CH₂反应的反应物、中间体、过渡态和产物构型的全部结构几何参数进行了优化, 并计算了THF溶液的溶剂化效应, 用内禀反应坐标(IRC)计算和频率分析方法, 对过渡态进行了验证. 结果表明: CH₃SmCH₂I与CH₂CH₂环丙烷化反应按亚甲基转移机理(通道A)和卡宾金属化机理(通道B)都可以进行, 与锂类卡宾的反应机理相同, 通道A比通道B反应的势垒降低了14.65 kJ/mol. 溶剂化效应使通道B比通道A的反应势垒大幅度提高, 更有利于反应沿通道A进行, 而不利于通道B.     

Mechanism for the addition of carbenoid CH2ClLi to formaldehyde

Ab initio HF/6-31G calculations have been performed for the addition mechanism of carbenoid CH₂ClLi with formaldehyde in tetrahydrofuran. An early complex of formaldehyde with CH₂ClLi is first formed with quite exothermic effect. Only a little activation energy of 14.6 kJ/mol is needed for the complex developing into the product through a transition state with coplanar bicyclic structure. In this process, the eletrophilic attack of carbonyl carbon of formaldehyde is more active than the nucleophilic attack of carbon of carbenoid. The exothermal effect of this addition process isupto 216.5kJ/mol.     

Ab initio study of gas phase and water-assisted tautomerization of maleimide and formamide

Maleimide serves as an important starting material in the synthesis of drugs and enzyme inhibitors. In the present paper, knowing the importance of tautomerization in maleimide for its drug action, potential energy surface of maleimide is studied and its tautomerization has been discussed and compared with tautomerization of formamide. Gas phase tautomerization of maleimide requires large amount of energy (23·21 kcal/mol) in comparison to formamide (15·05 kcal/mol) at HF/6-31+G* level. Thus making the proton transfer reaction a difficult process in gas phase. Water molecule lowers the energy barrier of tautomerization thus facilitating the tautomerization of maleimide to 5-hydroxy-pyrrol-2-one. Water assisted tautomerization of maleimide requires 19·60 kcal/mol energy at HF/6-31+G* and 17·63 kcal/mol energy at B3LYP/6-31+G* level, a decrease of 3·61 and 5·96 kcal/mol over gas phase tautomerization. Whereas, tautomerization of formamide requires 14·16 and 12·84 kcal/mol energy, a decrease of 0·89 and 2·01 kcal/mol energy over gas phase tautomerization at HF/6-31+G* and B3LYP/6-31+G* level, respectively. Water-assisted tautomerization in maleimide and formamide showed that difference in energy barrier reduces to 2·83 kcal/mol from 10·41 kcal/mol (in gas phase) at B3LYP level, which resulted that maleimide readily undergoes tautomerization in water molecule.     

Vapor phase hydrogenation of o -chloronitrobenzene ( o -CNB) over alumina supported palladium catalyst — a kinetic study

Kinetics of the vapor phase hydrogenation of o-chloronitrobenzene (o-CNB) over Pd/Al₂O₃ catalyst has been studied in a downflow microreactor under atmospheric pressure. Reaction rates have been measured at three different temperatures with respect to the partial pressures of o-CNB and hydrogen. The order of the reaction with respect to o-CNB was 0.53 at 280°C and increased with increasing temperature. However, with respect to hydrogen, a negative order was observed at 280°C, which decreased further with increasing in temperature. The apparent activation energy (Ea), from the Arrhenius plot was found to be 41 kJ/mol. On the basis of kinetic results a surface mechanism is suggested.     

Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid

The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311 G(3df,2p)//UMP2(full)/6-311 G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.     

组氨酸残基在芳基胺类N-乙酰基转移酶（NATs）乙酰化过程中有何作用？——量子化学研究

Arylamine N-acetyltransferases(NATs,EC 2.3.1.5)catalyze an acetyl group transfer from acetyl coenzyme A(AcCoA)to primary arylamines and play a very important role in the metabolism and bioactivation of drugs andcarcinogens.Experiments revealed that His-107 was likely the residues responsible for mediating acetyl transfer.The full catalytic mechanism of acetylation process has been examined by density functional theory.The results in-dicate that,if the acetyl group is directly transferred from the donor,p-nitrophenyl acetate,to the acceptor,cysteine,the high activation energy will be a great hindrance.These energies have dropped in a little range of 20—25 kJ/molwhen His-107 assisted the transfer process.However,when protonated His-107 mediated the reaction,the activa-tion energies have been dropped about 73—85 kJ/mol.Our calculations strongly supported an enzyme acetylationmechanism that experiences a thiolate-imidazolium pair,and verified the presumption from experiments.     

Theoretical studies on the structures and isomerization of the LiSiF3 system

Various possible isomers of LiSiF₃ system and isomerization between them have been studied at G2(MP2) level usingab initio calculations. The relative energies of four minimum points on the potential energy surface are-128.6,-194.3,-12.7 and-122.8 kJ/mol (taking the sum of the energies of LiF and SiF₂ as zero). The structural energy of the four-membered ring that contains three F-Si-F-Li four-membered rings with C_3v symmetry is the lowest. The highest potential barrier for the isomerization of the remaining three- or four-membered structure is 12.5 kJ/ mol. Project supported by the National Natural Science Foundation of China (Grant No. 29673026).     

DFT Study of Methylene Blue Adsorption on ZnTiO3 and TiO2 Surfaces (101)

The search for alternative materials with high dye adsorption capacity, such as methylene blue (MB), remains the focus of current studies. This computational study focuses on oxides ZnTiO₃ and TiO₂ (anatase phase) and on their adsorptive properties. Computational calculations based on DFT methods were performed using the Viena Ab initio Simulation Package (VASP) code to study the electronic properties of these oxides. The bandgap energy values calculated by the Hubbard U (GGA + U) method for ZnTiO₃ and TiO₂ were 3.17 and 3.21 eV, respectively, which are consistent with the experimental data. The most favorable orientation of the MB adsorbed on the surface (101) of both oxides is semi-perpendicular. Stronger adsorption was observed on the ZnTiO₃ surface (−282.05 kJ/mol) than on TiO₂ (–10.95 kJ/mol). Anchoring of the MB molecule on both surfaces was carried out by means of two protons in a bidentate chelating (BC) adsorption model. The high adsorption energy of the MB dye on the ZnTiO₃ surface shows the potential value of using this mixed oxide as a dye adsorbent for several technological and environmental applications.     

Adsorption and Decomposition Mechanism of 1,1‐Diamino‐2,2‐dinitroethylene on Al(111) Surface by Periodic DFT Calculations

The adsorption of 1,1‐diamino‐2,2‐dinitroethylene (FOX‐7) molecule on the Al(111) surface was investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4×4×2) slab model and three‐dimensional periodic boundary conditions. The strong attractive forces between oxygen and aluminum atoms induce the N? O bond breaking of the FOX‐7. Subsequently, the dissociated oxygen atoms and radical fragment of FOX‐7 oxidize the Al surface. The largest adsorption energy is ?940.5 kJ/mol. Most of charge transfer is 3.31e from the Al surface to the fragment of FOX‐7 molecule. We also investigated the adsorption and decomposition mechanism of FOX‐7 molecule on the Al(111) surface. The activation energy for the dissociation steps of P2 con?guration is as large as 428.8 kJ/mol, while activation energies of other con?gurations are much smaller, in range of 2.4 to 147.7 kJ/mol.     

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second‐order Møller–Plesset (MP2)/6‐31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero‐point energy (ZPE) and CCSD(T)/6‐31G* single‐point calculations. From the PES obtained with the CCSD(T)//MP2/6‐31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four‐membered ring intermediate, INT2, which is a barrier‐free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four‐membered product P_2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier‐free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier‐free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P₃ via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

An investigation on the reaction mechanism of the F2+Cl2→2ClF using the B3LYP method

The reaction mechanism of F₂+Cl₂→2ClF has been investigated with the density functional theory at the B3LYP/6‐311G* level. Six transition states have been found for the three possible reaction paths and verified by the normal mode vibrational and IRC analyses. Ab initio MP2/6‐311G* geometry optimizations and CCSD(T)/6‐311G(2df)//MP2/6‐311G* single‐point energy calculations have been performed for comparison. It is found that when the F₂ (or Cl₂) molecule decomposes into atoms first and then the F (or Cl) atom reacts with the molecule Cl₂ (or F₂) nearly along the molecular axis, the energy barrier is very low. The calculated energy barrier of F attacking Cl₂ is zero and that of Cl attacking F₂ is only 15.57 kJ?mol^?1 at the B3LYP level. However, the calculated dissociation energies of F₂ and Cl₂ are as high as 145.40 and 192.48 kJ?mol^?1, respectively. When the reaction proceeds through a bimolecular reaction mechanism, two four‐center transition states are obtained and the lower energy barrier is 218.69 kJ?mol^?1. Therefore, the title reaction F₂+Cl₂→2ClF is most probably initiated from the atomization of the F₂ molecule and terminated by the reaction of F attacking Cl₂ nearly along the Cl? Cl bond. MP2 calculations lead to the same conclusion, but the geometry of TS and the energy barrier are somewhat different. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002     

A fully ab initio potential energy surface for ClH2 reactive system

Anab initio analytical potential energy surface called BW3 for the ClH₂ reactive system is presented. The fit of this surface is based on about 1 200ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H₂ and HCl, and the endothermicity of the Cl + H₂ abstraction reaction. For the Cl + H₂ abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + ClH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.     

Oxidation of methanol by FeO2+ in water: DFT calculations in the gas phase and ab initio MD simulations in water solution

We investigate the mechanism of methanol oxidation to formaldehyde by ironoxido ([Fe(IV)O]2+), the alleged active intermediate in the Fenton reaction. The most likely reaction mechanisms are explored with density functional theory (DFT) calculations on microsolvated clusters in the gas phase and, for a selected set of mechanisms, with constrained Car-Parrinello molecular dynamics (CPMD) simulations in water solution. Helmholtz free energy differences are calculated using thermodynamic integration in a simulation box with 31 water molecules at 300 K. The mechanism of the reaction is investigated with an emphasis on whether FeO2+ attacks methanol at a C-H bond or at the O-H bond. We conclude that the most likely mechanism is attack by the oxido oxygen at the C-H bond ("direct CH mechanism"). We calculate an upper bound for the reaction Helmholtz free energy barrier in solution of 50 kJ/mol for the C-H hydrogen transfer, after which transfer of the O-H hydrogen proceeds spontaneously. An alternative mechanism, starting with coordination of methanol directly to Fe ("coordination OH mechanism"), cannot be ruled out, as it involves a reaction Helmholtz free energy barrier in solution of 44 +/- 10 kJ/mol. However, this coordination mechanism has the disadvantage of requiring a prior ligand substitution reaction, to replace a water ligand by methanol. Because of the strong acidity of [FeO(H2O)5]2+, we also investigate the effect of deprotonation of a first-shell water molecule. However, this is found to increase the barriers for all mechanisms.     

Pd/Cu(111)双金属表面催化糠醛脱碳及加氢的反应机理

采用密度泛函理论(DFT)研究糠醛在最稳定Pd/Cu(111)双金属表面上的吸附构型和糠醛脱碳及加氢的反应机理。结果表明,当糠醛初始吸附于O_3-Pd-top、O_7-Cu-hcp位时,吸附构型最稳定,其吸附能为73.4 kJ/mol。糠醛在Pd/Cu(111)双金属表面上更易发生脱碳反应。对于糠醛脱碳反应,所需活化能较低,各个基元反应均为放热反应,糠醛更易先失去支链上的H形成(C_4H_3O)CO,然后中间体脱碳加氢得到呋喃,其中,C_4H_3O加氢生成呋喃所需活化能(72.6 kJ/mol)最高,是反应的控速步骤。对于加氢反应,糠醛与首个氢原子的反应需要最大的活化能(290.4 kJ/mol),是反应的限速步骤。