Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

Computational study on the existence of organic peroxy radical-water complexes (RO2.H2O)

The existence of a series of organic peroxy radical-water complexes [CH3O2.H2O (methyl peroxy); CH3CH2O2.H2O (ethyl peroxy); CH3C(O)O2.H2O (acetyl peroxy); CH3C(O)CH2O2.H2O (acetonyl peroxy); CH2(OH)O2.H2O (hydroxyl methyl peroxy); CH2(OH)CH2O2.H2O (2-hydroxy ethyl peroxy); CH2(F)O2.H2O (fluoro methyl peroxy); CH2(F)CH2O2.H2O (2-fluoro ethyl peroxy)] is evaluated using high level ab initio calculations. A wide range of binding energies is predicted for these complexes, in which the difference in binding energies can be explained by examination of the composition of the R group attached to the peroxy moiety. The general trend in binding energies has been determined to be as follows: fluorine approximately alkyl < carbonyl < alcohol. The weakest bound complex, CH3O2.H2O, is calculated to be bound by 2.3 kcal mol-1, and the strongest, the CH2(OH)O2.H2O complex, is bound by 5.1 kcal mol-1. The binding energy of the peroxy radical-water complexes which contain carbonyl and alcohol groups indicates that these complexes may perturb the kinetics and product branching ratios of reactions involving these complexes.     

CH3CH2+O(3P)反应机理的理论研究

The reaction for CH3CH2+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the QCISD(T)/6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major products are the CH2O＋CH3, CH3CHO+H and CH2CH2+OH in the reaction. For the products CH2O＋CH3 and CH3CHO+H, the major production channels are A1: (R)→IM1→TS3→(A) and B1: (R)→IM1→TS4→(B), respectively. The majority of the products CH2CH2+OH are formed via the direct abstraction channels C1 and C2: (R)→TS1(TS2)→(C). In addition, the results suggest that the barrier heights to form the CO reaction channels are very high, so the CO is not a major product in the reaction.     

Low-energy paths for the unimolecular decomposition of CH3OH: a G2M/statistical theory study

The potential energy surface (PES) of the CH3OH system has been characterized by ab initio molecular orbital theory calculations at the G2M level of theory. The mechanisms for the decomposition of CH3OH and the related bimolecular reactions, CH3 + OH and 1CH2 + H2O, have been elucidated. The rate constants for these processes have been calculated using variational RRKM theory and compared with available experimental data. The total decomposition rate constants of CH3OH at the high- and low-pressure limits can be represented by k infinity = 1.56 x 10(16) exp(-44,310/T) s-1 and kAr0 = 1.60 x 10(36) T-12.2 exp(-48,140/T) cm3 molecule-1 s-1, respectively, covering the temperature range 1000-3000 K, in reasonable agreement with the experimental values. Our results indicate that the product branching ratios are strongly pressure dependent, with the production of CH3 + OH and 1CH2 + H2O dominant under high (P > 10(3) Torr) and low (P < 1 atm) pressures, respectively. For the bimolecular reaction of CH3 and OH, the total rate constant and the yields of 1CH2 + H2O and H2 + HCOH at lower pressures (P < 5 Torr) could be reasonably accounted for by the theory. For the reaction of 1CH2 with H2O, both the yield of CH3 + OH and the total rate constant could also be satisfactorily predicted theoretically. The production of 3CH2 + H2O by the singlet to triplet surface crossing, predicted to occur at 4.3 kcal mol-1 above the H2C...OH2 van der Waals complex (which lies 82.7 kcal mol-1 above CH3OH), was neglected in our calculations.     

Mechanism for the gas‐phase reaction between OH and 3‐methylfuran: A theoretical study

The mechanism for the OH + 3‐methylfuran reaction has been studied via ab initio calculations to investigate various reaction pathways on the doublet potential energy surface. Optimizations of the reactants, products, intermediates, and transition structures are conducted using the MP2 level of theory with the 6‐311G(d,p) basis set. The single‐point electronic energy of each optimized geometry is refined with G3MP2 and G3MP2B3 calculations. The theoretical study suggests that the OH + 3‐methylfuran reaction is dominated by the formation of HC(O)CH?C(CH₃)CHOH (P7) and CH(OH)CH?C(CH₃)C(O)H (P9), formed from two low‐lying adducts, IM1 and IM2. The direct hydrogen abstraction pathways and the S_N2 reaction may play a minor or negligible role in the overall reaction of OH with 3‐methylfuran. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

锥形硼烷B5H10X的结构和成键性质

采用从头算分子轨道法对锥型硼烷Ｂ５Ｈ１０Ｘ（Ｘ＝Ｂｅ＾－,Ｂ,Ｃ＾＋,ＢｅＨ,ＣＨ＾２＋,Ｂ＾２－,Ｃ＾－,Ｎ,Ｏ＾＋,ＢＨ＾－,ＣＨ,ＮＨ＾＋和ＯＨ＾２＋）进行了研究,结果表明,端氢和桥氢原子与帽基原子相对位置的变化是由帽基原子和环原子轨道的弥散程度及环的尺寸效应共同决定的,端氢原子对桥氢原子的空间位置有着制约作用。     

Determination of the CH + O2 product channels

The multichannel CH + O2 reaction was studied at room temperature, in a low-pressure fast-flow reactor. CH radical was obtained from the reaction of CHBr3 with potassium atoms. The overall rate constant was determined from the decay of CH with distance, O2 being introduced in excess. The result, after corrections for axial and radial diffusion, is k = (3.6 +/- 0.5) x 10(-11) cm3 molecule-1 s-1. The OH(A2 sigma +) chemiluminescence was observed, confirming the existence of the OH + CO channel. The vibrational population distribution of OH(A2 sigma +) is 32% in the v' = 1 level and 68% in the v' = 0 level (+/- 5%). The relative atomic concentrations were determined by resonance fluorescence in the vacuum ultraviolet. A ratio of 1.4 +/- 0.2 was found between the H atom density (H atoms being produced from the H + CO2 channel and from the HCO dissociation) and the O atom density (O + HCO). Ab initio calculations of the transition structures have been performed, associated with statistical estimations. The estimated branching ratios are: O + HCO, 20%; O + H + CO, 30%; H + CO2, 30%; and CO + OH, 20%.     

An ab initio study on thermal rearrangement reactions of 1-silylprop-2-en-1-ol H3SiCH(OH)CH=CH2

The thermal rearrangement reactions of 1-silylprop-2-en-1-ol H3SiCH(OH)CH=CH2 were studied by ab initio calculations at the G2(MP2) and G3 levels. The reaction mechanisms were revealed through ab initio molecular orbital theory. On the basis of the MP2(full)/6-31G(d) optimized geometries, harmonic vibrational frequencies of various stationary points were calculated. The reaction paths were investigated and confirmed by intrinsic reaction coordinate (IRC) calculations. The results show that the thermal rearrangements of H3SiCH(OH)CH=CH2 happen in two ways. One is via the Brook rearrangement reactions (reaction A), and the silyl group migrates from carbon atom to oxygen atom passing through a double three-membered ring transition state, forming allyloxysilane CH2=CHCH2OSiH3. In the other, the reactant undergoes a dyotropic rearrangement; the hydroxyl group migrates from carbon atom to silicon atom coupled with a simultaneous migration of a hydrogen atom from silicon atom to carbon atom, forming allylsilanol CH2=CHCH2SiH2OH (reaction B). The barriers for reactions A and B were computed to be 343.5 and 203.7 kJ/mol, respectively, at the G3 level. The changes of the thermodynamic functions, entropy (DeltaS), entropy (DeltaS(doubledagger)) for the transition state, enthalpy (DeltaH), and free energy (DeltaG) were calculated by using the MP2(full)/6-31G(d) optimized geometries, and harmonic vibrational frequencies of reactants, transition states, and products with statistical mechanical methods, and equilibrium constant K(T) and reaction rate constant k(T) in canonical variational transition-state theory (CVT) with centrifugal-dominant small-curvature tunneling approximation (SCT) were calculated over a temperature range 400-1300 K. The conventional transition-state theory (TST) rate constants were also calculated for the purposes of comparison. The influences of the vinyl group attached to the center carbon of the alpha-silyl alcohols on reactions were discussed.     

Modeling of protonation processes in acetohydroxamic acid

This work presents a theoretical study of acetohydroxamic acid and its protonation processes using ab initio methodology at the MP2(FC)/cc-pdVZ level. We find the amide form more stable than the imidic tautomer by less than 1.0 kcal mol(-)(1). For comparison with the experimental data, a three-dimensional conformational study is performed on the most stable tautomer (amide). From this study, the different barriers to rotation and inversion are determined and the intramolecular hydrogen bond between the OH group and the carbonyl oxygen is characterized. The electrostatic potential distribution shows three possible sites for electrophilic attack, but it is shown that only two of them, the carbonyl oxygen and the nitrogen atoms, are actual protonation sites. The protonation energy (proton affinity) is obtained from the results of the neutral and charged species. Proton affinities for the species charged on the carbonyl oxygen and the nitrogen atoms are estimated to be 203.4 and 194.5 kcal mol(-)(1), respectively. The development of a statistical model permits the quantification of DeltaG (gas-phase basicity) for the two protonation processes. In this way, the carbonyl oxygen protonated form is found to be more stable than that of the nitrogen atoms by 8.3 kcal mol(-)(1) at 1 atm and 298.15 K, due to the enthalpic contribution. As temperature increases, the proportion of the nitrogen protonated form increases slightly.     

Conformational stability of CH3CH2PH2BH3 from temperature dependent FT-IR spectra of xenon solutions and r0 structural parameters

Variable temperature (-55--100 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylphosphine-borane, CH3CH2PH2BH3, and ethylphosphine-borane-d5 dissolved in liquid xenon have been recorded. From these data, the enthalpy difference has been determined to be 86 +/- 8 cm(-1) (1.03 +/- 0.10 kJ/mol), with the trans conformer the more stable rotamer. Complete vibrational assignments are presented for both conformers, which are consistent with the predicted frequencies obtained from the ab initio MP2/6-31G(d) calculations. The optimized geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, and depolarization ratios have been obtained from RHF/6-31G(d) and/or MP2/6-31G(d) ab initio calculations. These quantities are compared to the corresponding experimental quantities when appropriate as well as with some corresponding results for some similar molecules. The r0 structural parameters have been obtained from a combination of the previously reported microwave rotational constants and ab initio predicted parameters.     

Kinetics and mechanism of the gas phase reaction of chlorine atoms with i-propanol

FTIR smog chamber techniques and ab initio calculations have been used to investigate the kinetics and mechanism of the reaction of Cl atoms with i-propanol in 700 Torr of N(2) at 296 K. The reaction is observed to proceed with a rate constant of k(1) = (8.28 +/- 0.97) x 10(-11) cm(3) molecule(-1) s(-1) and gives CH(3)C(OH)CH(3) and CH(3)CH(OH)CH(2) radicals in yields of 85 +/- 7 and 15 +/- 7%, respectively. Calculations indicate that abstraction of the secondary H can proceed through a lower energy pathway than the primary. Rapid decomposition of the chlorination product CH(3)CCl(OH)CH(3) complicates its direct detection, likely due to heterogeneous chemistry. IR spectra for the chlorides CH(3)CCl(OH)CH(3) and CH(3)CH(OH)CH(2)Cl were inferred experimentally and assignments confirmed via comparison with ab initio computed spectra.     

Vibrational frequencies and infrared intensities of the hydrogen-bonded complexes of nitrous acid with ethers: ab initio and DFT studies

The vibrational spectra of the binary complexes formed by HONO-trans and HONO-cis with dimethyl and diethyl ethers have been investigated using ab initio calculations at the SCF and MP2 levels with 6-311++G(d,p) basis set and B3LYP calculations with 6-31G(d,p) and 6-31+G(d,p) basis sets. Full geometry optimisation was made for the complexes studied. The accuracy of the ab initio calculations have been estimated by comparison between the predicted values of the vibrational characteristics (vibrational frequencies and infrared intensities) and the available experimental data. It was established, that the methods, used in this study are well adapted to the problem under examination. The predicted values with the B3LYP calculations are very near to the results, obtained with 6-311++G(d,p)/MP2. The ab initio and DFT calculations show that the changes in the vibrational characteristics (vibrational frequencies and infrared intensities) upon hydrogen bonding for the hydrogen-bonded complex (CH3)2O...HONO-trans are larger than for the complex (CH3)2O...HONO-cis.     

Addition of water, methanol, and ammonia to Al3O3- clusters: reaction products, transition states, and electron detachment energies

Products of reactions between the book and kite isomers of Al3O3- and three important molecules are studied with electronic structure calculations. Dissociative adsorption of H2O or CH3OH is highly exothermic and proton-transfer barriers between anion-molecule complexes and the products of these reactions are low. For NH3, the reaction energies are less exothermic and the corresponding barriers are higher. Depending on experimental conditions, Al3O3- (NH3) coordination complexes or products of dissociative adsorption may be prepared. Vertical electron detachment energies of stable anions are predicted with ab initio electron propagator calculations and are in close agreement with experiments on Al3O3- and its products with H2O and CH3OH. Changes in the localization properties of two Al-centered Dyson orbitals account for the differences between the photoelectron spectra of Al3O3- and those of the product anions.     

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.     

The effects of water vapor on the CH3O2 self-reaction and reaction with HO2

The gas phase reactions of CH3O2 + CH3O2, HO2 + HO2, and CH3O2 + HO2 in the presence of water vapor have been studied at temperatures between 263 and 303 K using laser flash photolysis coupled with UV time-resolved absorption detection at 220 and 260 nm. Water vapor concentrations were quantified using tunable diode laser spectroscopy operating in the mid-IR. The HO2 self-reaction rate constant is significantly enhanced by water vapor, consistent with what others have reported, whereas the CH3O2 self-reaction and the cross-reaction (CH3O2 + HO2) rate constants are nearly unaffected. The enhancement in the HO2 self-reaction rate coefficient occurs because of the formation of a strongly bound (6.9 kcal mol(-1)) HO2 x H2O complex during the reaction mechanism where the H2O acts as an energy chaperone. The nominal impact of water vapor on the CH3O2 self-reaction rate coefficient is consistent with recent high level ab initio calculations that predict a weakly bound CH3O2 x H2O complex (2.3 kcal mol(-1)). The smaller binding energy of the CH3O2 x H2O complex does not favor its formation and consequent participation in the methyl peroxy self-reaction mechanism.     

Structure, stability and vibrational spectrum of the hydrogen-bonded complex between HNO3 and H2O. Ab initio and DFT studies

The structure, stability and vibrational spectrum of the binary complex between HONO2 and H2O have been investigated using ab initio calculations at SCF and MP2 levels with different basis sets and B3LYP/6-31G(d,p) calculations. Full geometry optimization was made for the complex studied. It was established that the hydrogen-bonded H2O...HONO2 complex has a planar structure. The corrected values of the dissociation energy at the SCF and MP2 levels and B3LYP calculations are indicative of relatively strong OH...O hydrogen-bonded interaction. The changes in the vibrational characteristics (vibrational frequencies and infrared intensities) arising from the hydrogen bonding between HONO2 and H2O have been estimated by using the ab initio calculations at SCF and MP2 levels and B3LYP/6-31G(d,p) calculations. It was established that the most sensitive to the complexation is the stretching O-H vibration from HONO2. In agreement with the experiment, its vibrational frequency in the complex is shifted to lower wavenumbers. The predicted frequency shift with the B3LYP/6-31G(d,p) calculations (-439 cm(-1)) is in the best agreement with the experimentally measured (-498 cm(-1)). The intensity of this vibration increases dramatically upon hydrogen bonding. The ab initio calculations at the SCF level predict an increase up to five times; at the MP2 level up to 10 times and the B3LYP/6-31G(d,p) predicted increase is up to 17 times. The good agreement between the predicted values of the frequency shifts and those experimentally observed show that the structure of the hydrogen-bonded complex H2O...HONO2 is reliable.     

Influence of H2 on the gas-phase decomposition of formic acid: a theoretical study

Gas-phase decomposition of formic acid results in final products CO + H2O and CO2 + H2. Experimentally, the CO/CO2 ratio tends to be large, in contradiction with mechanism studies, which show almost equal activation energies for dehydration and decarboxylation. In this work, the influence of H2 on the decomposition mechanism of HCOOH was explored using ab initio calculations at the CCSD(T)/6-311++G**//MP2/6-311++G** level. It was found that, in the presence of H2, the reaction channels leading to CO + H2O are more than those leading to CO2 + H2. With competitive energy, H2 addition to HCOOH can reduce the latter into HCHO, which then dissociates into CO + H2 catalyzed by H2O. Compared to trans-HCOOH, cis-HCOOH and cis-C(OH)2, conformers required for decarboxylation, are less populated due to interactions with H2.     

β-羟基丙醛基态与激发态氢迁移反应的从头算研究

本文用从头算RHF和UHF方法在3-21G基组上研究了β-羟基丙醛基态和激发态分解为甲醛和乙烯醇的反应机理。优化得到了各反应途径的过渡态和中间体, 其结果为: 基态β-羟基丙醛经过一个六元环过渡态和一个氢键中间体形成产物, 反应属于氢迁移和断键的协同过程; 激发三态β-羟基丙醛的分解途径首先经过一个氢迁移六元环过渡态形成双自由基中间体, 然后该中间体的分解包括两条相互竞争的途径, 它们各自经过一个断碳碳键的过渡态和一个氢键激-基态配合物中间体而形成两类产物, 一类为甲醛的基态和乙烯醇的激发态, 另一类为甲醛的激发态和乙烯醇的基态。激发态反应的两条通道均属于先氢迁移后断键分解的分步过程, 且反应的第二步为速控步骤。计算结果表明, 激发态反应活化位垒都比基态的低。     

Theoretical study of the structures, stability and vibrational spectra of the nitrous acid complexes with CH4

The structures, stability and vibrational spectra of the binary complexes CH4...HONO-trans and CH4...HONO-cis have been investigated using ab initio calculations at the SCF and MP2 levels with 6-311++G(d,p) basis set and B3LYP calculations with 6-31G(d,p) and 6-31+G(d,p) basis sets. Full geometry optimization was made for the complexes studied. It was established that the complex CH4...HONO-trans is more stable by 0.41 kcal mol(-1) than the complex CH4...HONO-cis. The accuracy of the ab initio calculations have been estimated by comparison between the predicted values of the vibrational characteristics (vibrational frequencies and infrared intensities) and the available experimental data. It was established, that the methods, used in this study are well adapted to the problem under examination. The predicted values with the B3LYP calculations are very near to the results, obtained with 6-311++G(d,p)/MP2. The changes in the vibrational characteristics of methane and trans-, cis-nitrous acid upon formation of the hydrogen bond show that the complexes CH4...HONO-trans and CH4...HONO-cis have geometry in which the OH group interacts with a methane molecule forming a single hydrogen bond. This fact is confirmed by relatively strong perturbation of the OH stretching vibration to lower frequencies and an increase of the infrared intensity of this vibration up to three times upon hydrogen bonding.     

Hydroxyl-radical-initiated oxidation mechanism of bromopropane

Bromopropane has been considered as a replacement for chlorofluorocarbons used as the active component of industrial cleaning solvents, more specifically for HCFC-141b. The proposed mechanism for the atmospheric oxidation of bromopropane is studied via ab initio methodology. Ab initio molecular orbital methods at the CCSD(T)/6-311++G(2df,2p)//MP2/6-31G(d) level of theory have been used to determine the structure and energetics of the 58 species and transition states involved in the atmospheric oxidation of bromopropane. The calculations show that the major oxidation species is bromoacetone. Other brominated species that result from the oxidation are BrCH 2CH 2C(O)H, BrC(O)CH 2CH 3, and BrC(O)H, potential new bromine reservoir species that result from bromopropane in the atmosphere.