Theoretical study on the hydrolytic deamination mechanism of adenosine

The hydrolytic deamination mechanism of adenosine to produce inosine was studied using density functional method on two models. One is adenine and the other is adenosine. Optimized geometries of reactants, intermediates, transition states, and products were determined at B3LYP/6-311G(d,p) level. IRC calculations were performed on the transition states to verify whether it is the real transition state that connects the corresponding intermediates. Single point calculations were carried out on the previous optimized geometries obtained during IRC calculations. Four pathways have been determined for the hydrolytic deamination of adenosine. Pathway d is the most favorable pathway. In this pathway a tetra-coordinated intermediate is formed through hydrolysis reaction, then the deamination reaction takes place, which causes the cleavage of C6–N10 bond and the creation of C=O bond. Unlike the deamination of adenine, the attacking side of water molecule has effect on the deamination of adenosine. The energy barriers of adenosine deamination are a little higher than those of adenine deamination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

The water-assisted hydrolytic deamination mechanism of adenine was studied using density functional method at B3LYP/6-311G(d,p) level. Intrinsic reaction coordinate (IRC) calculations were performed on the transition states to verify whether it is the real transition states that connect the corresponding intermediates. Single-point calculations were carried out on the previous optimized geometries obtained during IRC calculations. The activation energies have also been calculated using G3MP2//B3LYP/6-311G(d,p) method. The water molecules attack the adenine and a tetrahedral intermediate forms. Then, two different intermediates have been obtained through different bond rotations. In pathway a, the second water molecule takes part in the formation of transition state and acts as a bridge to transfer hydrogen atom, while in pathway b, the second water molecule does not involve in the creation of transition state and only acts as a medium. The energy barriers are 23.40 and 37.17 kcal/mol for pathways a and b, respectively. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

水催化HBrO与OH自由基反应的微观机理

采用密度泛函理论,分别在B3LYP/6-311++g(d,p)和B3LYP/aug-cc-PVTZ理论水平下,系统研究了无水和水催化的OH自由基与HBrO反应,即HBrO+OH和HBrO+OH+H_2O 2个反应的微观反应机理,给出了所有可能发生的反应路径,并指出能量最低的反应通道.对于没有水参与的反应,由于OH自由基进攻HBrO方式不同,存在顺式方向和反式方向2种进攻方式的反应路径;当有一分子水参与反应时,考虑HBrO H_2O复合物与OH自由基的反应和HBrO与H_2O OH复合物2种反应情况,共发现4条不同的反应路径.这2种反应的所有路径均是在OH自由基提取氢之前以氢键复合物形式存在,反应过程均为无势垒加合过程,总反应为放热反应.水对目标反应起催化作用,有效地降低了反应的势垒,可以加快OH自由基和HBrO的消耗速度.     

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.     

Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

Theoretical study of [Li(H2O)n]+ and [K(H2O)n]+ (n = 1−4) complexes

The geometries, successive binding energies, vibrational frequencies, and infrared intensities are calculated for the [Li(H₂O)_n]⁺ and [K(H₂O)_n]⁺ (n = 1?4) complexes. The basis sets used are 6-31G* and LANL 1DZ (Los Alamos ECP +DZ ) at the SCF and MP 2 levels. There is an agreement for calculated structures and frequencies between the MP 2/6-31G* and MP 2/LANL 1DZ basis sets, which indicates that the latter can be used for calculations of water complexes with heavier ions. Our results are in a reasonable agreement with available experimental data and facilitate experimental study of these complexes. © 1995 John Wiley & Sons, Inc.     

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

CH2与HNCO反应机理的量子化学研究

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所研究的领域,由于该反应在燃烧化学中讨论氮氧化物NOx的消除过程十分重要,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,本文采用量子化学方法,研究了CH2与HNCO体系的反应机理,力求从理论角度给出合理的解释。     

Theoretical studies of UO2(H2O)n(2+), NpO2(H2O)n(+), and PuO2(H2O)n(2+) complexes (n=4-6) in aqueous solution and gas phase

Extensive ab initio calculations both in gas phase and solution have been carried out to study the equilibrium structure, vibrational frequencies, and bonding characteristics of various actinyl (UO2(2+), NpO2(+), and PuO2(2+)) and their hydrated forms, AnO2(H2O)n(z+) (n=4, 5, and 6). Bulk solvent effects were studied using a continuum method. The geometries were fully optimized at the coupled-cluster singles + doubles (CCSD), density-functional theory (DFT), and M?ller-Plesset (MP2) level of theories. In addition vibrational frequencies have been obtained at the CCSD as well as MP2/DFT levels. The results show that both the short-range and long-range solvent effects are important. The combined discrete-continuum model, in which the ionic solute and the solvent molecules in the first and second solvation shells are treated quantum mechanically while the solvent is simulated by a continuum model, can predict accurately the bonding characteristics. Moreover, our values of solvation free energies suggest that five- and six-coordinations are equally preferred for UO2(2+), and five-coordinated species are preferred for NpO2(+) and PuO2(2+). On the basis of combined quantum-chemical and continuum treatments of the hydrated complexes, we are able to determine the optimal cavity radii for the solvation models. The coupled-cluster computations with large basis sets were employed for the vibrational spectra and equilibrium geometries both of which compare quite favorably with experiment. Our most accurate computations reveal that both five- and six-coordination complexes are important for these species.     

A theoretical ab initio study on the H(2)NO + O(3) reaction

The deviation of the NH(2) pseudo-first-order decay Arrhenius plots of the NH(2) + O(3) reaction at high ozone pressures measured by experimentalists, has been attributed to the regeneration of NH(2) radicals due to the subsequent reactions of the products of this reaction with ozone. Although these products have not yet been characterized experimentally, the radical H(2)NO has been postulated, because it can regenerate NH(2) radicals through the reactions: H(2)NO + O(3) --> NH(2) + O(2) and H(2)NO + O(3) --> HNO + OH + O(2). With the purpose of providing a reasonable explanation from a theoretical point of view to the kinetic observed behaviour of the NH(2) + O(3) system, we have carried ab initio electronic structure calculations on both H(2)NO + O(3) possible reactions. The results obtained in this article, however, predict that of both reactions proposed, only the H(2)NO + O(3) --> NH(2) + O(2) reaction would regenerate indeed NH(2) radicals, explaining thus the deviation of the NH(2) pseudo-first-order decay observed experimentally.     

Theoretical study on (Al2O3)n (n = 1-10 and 30) fullerenes and H2 adsorption properties

The structures and stabilities of (Al2O3)n (n = 1-10 and 30) clusters were studied by means of first principles calculations. The calculated results reveal that the global minima of small (Al2O3)n (n = 1-5) clusters are cage structures with high symmetries, in which Al and O atoms are three- and two-coordinated, respectively, and are linked to neighbors via single bonds. Beyond (Al2O3)5, we calculated both cage and cage-dimer structures for (Al2O3)n (n = 6-10), and the results show that, at this size range, cage-dimer structures are more stable than cage structures. Furthermore, an onion-like motif for (Al2O3)10 was studied, and it is interesting to find that, at this size, the onion structure is more favorable than cage and cage-dimer structures. For large clusters, a shell structure of Al60O90 is suggested. Electronic properties and calculations on hydrogen adsorption of these aluminum oxide structures are reported, and we discuss their possible use as hydrogen storage materials.     

N_2O与氧负离子微观反应机理的理论研究

采用G3B3//B3LYP理论水平对反应O-+N2O的双重电子态势能面反应机理进行了详细的理论研究.该反应涉及的各个稳定点的构型、振动频率是在B3LYP/6-311++G(d,p)理论水平下计算的.计算结果表明,得到的反应焓变与已有实验值相吻合,该反应主反应通道是O-+N2O→NO+NO-,而生成O2-+N2的反应通道是次反应通道.     

Theoretical study of the dehydrogenate reaction of H2S by Sc+(1D)

The reaction Sc⁺(¹D)+H₂S→Sc⁺S+H₂ is theoretically investigated by ab initio MO methods. Two possible reaction channels on the singlet potential surface (PES) and the reaction mechanism are examined and discussed. Three regions of the potential surface were studied, the molecular complex, the S‐H insertion products and the transition states for the reaction. In addition the singlet and triplet PESs of this reaction system are compared in an investigation the chemistry of excited electronic state. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 60–64, 2001     

Theoretical studies of O2−:(H2O)n clusters

The interaction of superoxide ion O₂^? with up to four water molecules [O₂^?: (H₂O)_n, n = 1, 2, 4] has been investigated using ab initio molecular orbital theory. The binding energy of O₂^?: H₂O is calculated to be ?20.6 kcal/mol in good agreement with gas phase experimental data. At the MP3/6-31G^* level the O₂^?:H₂O complex has a C_2v structure with a double (cyclic) hydrogen bond between O₂^? and H₂O. A C_s structure with a single hydrogen bond is only 0.7 kcal/mol less stable. Interaction of H₂O with the doubly occupied π^* orbital of O₂^? is preferred slightly over interaction with the singly occupied π^* orbital. Natural bond orbital analysis suggests that both electrostatic and charge transfer interactions are important in anionic complexes. The charge transfer occurs predominantly in the O₂^? → H₂O direction and is important in determining the relative stabilities of the different structures and states. Singly and doubly hydrogen-bonded structures for the O₂^?: (H₂O)₂ and O₂^?: (H₂O)₄ clusters were found to be similar in stability and the increase in binding of the cluster becomes smaller as each additional water molecule is added to the cluster.     

草酰胺桥联双核铜配合物金属胶束催化BNPP水解的动力学和机理研究

合成了草酰胺桥联双核铜配合物(RCu2(H2O)2(ClO4)2)(A)和(R′Cu2(H2O)2(ClO4)2)(B)。研究了A、B与表面活性剂LSS和CTAB形成的金属胶束催化二(对硝基苯酚)磷酸二酯(BNPP)水解机理,建立了动力学模型。结果表明在25℃、pH=7的条件下,该类金属胶束对BNPP水解有催化作用,BNPP催化水解速率比其自水解速率提高1×106倍,这是由于双核铜配合物中两个铜离子的协同作用、表面活性剂胶束的浓聚效应和pH效应所致。因此含双水的草酰胺桥联双核铜配合物金属胶束是一较好的磷酸二酯水解酶的模拟模型。     

Theoretical study of Al(n) and Al(n)O (n = 2-10) clusters

The stable structures, energies, and electronic properties of neutral, cationic, and anionic clusters of Al(n) (n = 2-10) are studied systematically at the B3LYP/6-311G(2d) level. We find that our optimized structures of Al5(+), Al9(+), Al9(-), Al10, Al10(+), and Al10(-) clusters are more stable than the corresponding ones proposed in previous literature reports. For the studied neutral aluminum clusters, our results show that the stability has an odd/even alternation phenomenon. We also find that the Al3, Al7, Al7(+), and Al7(-) structures are more stable than their neighbors according to their binding energies. For Al7(+) with a special stability, the nucleus-independent chemical shifts and resonance energies are calculated to evaluate its aromaticity. In addition, we present results on hardness, ionization potential, and electron detachment energy. On the basis of the stable structures of the neutral Al(n) (n = 2-10) clusters, the Al(n)O (n = 2-10) clusters are further investigated at the B3LYP/6-311G(2d), and the lowest-energy structures are searched. The structures show that oxygen tends to either be absorbed at the surface of the aluminum clusters or be inserted between Al atoms to form an Al(n-1)OAl motif, of which the Al(n-1) part retains the stable structure of pure aluminum clusters.     

H2CO和NO2反应机理的密度泛函理论计算研究

用密度泛函理论方法在UB3LYP/ 6-311++G(d,p)并包含零点能水平上计算得到了H2CO和NO2反应的势能面.在势能面上找到了由H2CO和NO2反应生成HCO和trans-HONO的两条反应通道.直接H迁移反应通道的势垒只有90.54 kJ*mol-1,是主要的反应通道,其TST速率是7.9 cm3*mol-1*s-1,与文献值相符;另一条通道是H2CO异构化为trans-HCOH,然后C位H迁移,最后生成的HOC分子异构化为HCO,这条通道反应势垒高达348.03 kJ*mol-1,是一条次要反应通道.     

Theoretical study of reaction mechanism for CH2CHX(XH,F, Cl) with ozone

In this work, we study the reaction mechanism of the CH₂CHX(X?H, F, Cl) with ozone reactions, using ab initio MP2 method at 6‐311++g** basis set level. The geometric configurations of reactants, intermediates, transition states, and products were optimized, and the energies were obtained at the QCISD(T)/6‐311++G** level. The transition states and intermediates of the reactions were verified by the vibrational analysis. The results show that the ozonolysis of ethylene and its derivatives is reasonable and believable along the Criegee mechanism. The results also show that the activation energies of the controlling steps along the fluoroethylene and chloroethylene with ozone reaction pathways were lower than that along the ethylene with ozone reaction pathway. That is to say, the derivatives of ethylene have the higher activity to react with ozone and deplete the ozone layer. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

s-四嗪-水簇复合物的理论研究

用量子化学B3LYP方法和6-31＋＋G**基函数研究了s-四嗪-水簇复合物基态分子间相互作用, 并进行了构型优化和频率计算, 分别得到无虚频稳定的s-四嗪-(水)₂复合物、s-四嗪-(水)₃复合物和s-四嗪-(水)₄复合物6个、9个和12个. 复合物存在较强的氢键作用, 复合物结构中形成一个N…H—O氢键并终止于O…H—C氢键的氢键水链构型最稳定. 经基组重叠误差和零点振动能校正后, 最稳定的1∶2, 1∶3和1∶4(摩尔比)复合物的结合能分别是41.35, 70.9和 94.61 kJ/mol. 振动分析显示氢键的形成使复合物中水分子H—O键对称伸缩振动频率减小(红移). 研究表明N…H键越短, N…H—O键角越接近直线, 稳定化能越大, 氢键作用越强. 同时, 用含时密度泛函理论方法在TD-B3LYP/6-31＋＋G**水平计算了s-四嗪单体及其氢键复合物的第一¹(n, p*)激发态的垂直激发能.