Theoretical study on the mechanism and kinetics of atmospheric reactions NH2OH + OOH and NH2CH3 + OOH

Mechanism and kinetics of NH₂OH + OOH and NH₂CH₃ + OOH reactions were studied at the B3LYP and M062X levels of theory using the 6-311++G(3df, 3pd) basis set. The NH₂OH + OOH and NH₂CH₃ + OOH reactions proceed through different paths which lead to different products. Transition state structure and activation energy of each path were calculated. The calculated activation energies of hydrogen abstraction reactions were smaller than 25 kcal/mol and of substitution reactions are in the range of 50–70 kcal/mol. The rate constants were calculated using transition state theory (TST) modified for tunneling effect at 273–2000 K.     

DFT study on the mechanism of trimolecular radical reactions: isomerisation in small clusters

ABSTRACT

Structural and thermodynamic properties of 48 trimolecular clusters containing one radicl and two protic molecules (H₂O, NH₃, H₂O₂, CH₃OH, HOCl) were studied at B3LYP/6-311++G(3df,3pd) level of theory. These radical-clusters have non-cyclic structures and are stabilised via two inter-molecular hydrogen bonding interactions. The calculated enthalpies of formation of the radical-clusters were generally in the range of ?30 to ?50 kJ/mol. The calculated activation energies (E_a) of the intra-cluster hydrogen transfers were smaller than 70 kJ/mol. Also, structures and thermodynamics of 15 cyclic molecular clusters as well as multi-hydrogen transfers in them were investigated. The results showed that the stability of the cyclic clusters and activation energies of the multi-hydrogen transfers depend on the cluster size.     

Can tetra‐tert‐butylethylene be formed by ion–ion recombination or ion–molecule reaction of two di‐tert‐butylcarbene units?—a DFT study

The reaction channels of di‐tert‐butylcarbene ( 2 ), its radical anion, ( 3 ) and its radical cation ( 4 ) were investigated theoretically by using DFT/B3LYP with 6‐31+G(d) basis set and 6‐311+G(2d,p) for single point energy calculations. Conversion of the neutral carbene 2 to the charged species 3 and 4 results in significant geometric changes. In cation 4 two different types of C? (CH₃)₃ bonds are observed: one elongated sigma bond called “axial” with 1.61 Å and two normal sigma bonds with a bond length of 1.55 Å. Species 2 and 4 have an electron deficient carbon center; therefore, migration of CH₃ and H is observed from adjacent tert‐butyl groups with low activation energies in the range of 6–9 kcal/mol like similar Wagner–Meerwein rearrangements in the neopentyl‐cation system. Neutral carbene 2 shows C? H insertion to give a cyclopropane derivative with an activation energy of 6.1 kcal/mol in agreement with former calculations. Contrary to species 2 and 4 , the radical anion 3 has an electron rich carbon center which results in much higher calculated activation energies of 26.3 and 42.1 kcal/mol for H and CH₃ migrations, respectively. NBO charge distribution indicates that the hydrogen migrates as a proton. The central issue of this work is the question: how can tetra‐tert‐butylethylene ( 1 ) be prepared from reaction of either species 2 , 3 , or 4 as precursors? The ion–ion reaction between 3 and 4 to give alkene 1 with a calculated reaction enthalpy of 203.5 kcal/mol is extremely exothermic. This high energy decomposes alkene 1 after its formation into two molecules of carbene 2 spontaneously. Ion–molecule reaction of radical anion 3 with the neutral carbene 2 is a much better choice: via a proper oriented charge–transfer complex the radical anion of tetra‐tert‐butylethylene (11) is formed. The electron affinity of 1 was calculated to be negligible. Copyright © 2010 John Wiley & Sons, Ltd.     

Understanding halogen‐substituent assistance in H‐atom abstraction‐based reactions of CHCl•− with CH4 − nXn (X = H,F, Cl; n = 0–3)

The effect of halogen‐substituent on hydrogen abstraction mechanisms was studied by applying density functional theory functional calculations to the gas‐phase reactions between CHCl^?? and CH_{4 ? n}X_n (X = H, F, Cl; n = 0–3), and it is found that a heavier X substituent in the substrate results in a greater stabilization of corresponding complex, a lower activation energy, a faster H‐abstraction reaction, and greater exothermicity. However, CH₄– reaction is more reactive than CH₃F– reaction under the same condition because of dominant π‐donation from the electronegative F atom. We also explored the reactivity difference for the seven reactions in terms of factors derived from bond order, second‐order perturbative energy, and activation strain model analysis. The rate constants are evaluated over a wide temperature range of 298–1000 K by the conventional transition state theory. Copyright © 2014 John Wiley & Sons, Ltd.     

Theoretical study on the reactions of CH3NHNH2 with ground state O(3P) atom and excited state O(1D) atom

The reaction mechanisms of methylhydrazine (CH₃NHNH₂) with O(³P) and O(¹D) atoms have been explored theoretically at the MPW1K/6-311+G(d,p), MP2/6-311+G(d,p), MCG3-MPWPW91 (single-point), and CCSD(T)/cc-pVTZ (single-point) levels. The triplet potential energy surface for the reaction of CH₃NHNH₂ with O(³P) includes seven stable isomers and eight transition states. When the O(³P) atom approaches CH₃NHNH₂, the heavy atoms, namely N and C atoms, are the favourable combining points. O(³P) atom attacking the middle-N atom in CH₃NHNH₂ results in the formation of an energy-rich isomer (CH₃NHONH₂) followed by migration of O(³P) atom from middle-N atom to middle-H atom leading to the product P6 (CH₃NNH₂+OH), which is one of the most favourable routes. The estimated major product CH₃NNH₂ is consistent with the experimental measurements. Reaction of O(¹D) + CH₃NHNH₂ presents different features as compared with O(³P) + CH₃NHNH₂. O(¹D) atom will first insert into C–H2, N1–H4, and N2–H5 bonds barrierlessly to form the three adducts, respectively. There are two most favourable paths for O(¹D) + CH₃NHNH₂. One is that the C–N bond cleavage accompanied by a concerted H shift from O atom to N atom (mid-N) leads to the product P_I (CH₂O + NH₂NH₂), and the other is that the N–N bond rupture along with a concerted H shift from O to N (end-N) forms P_IV (CH₃NH₂ + HNO). The similarities and discrepancies between two reactions are discussed.     

From electronic structure to model application of key reactions for gasoline/alcohol combustion: Hydrogen-atom abstraction by CH3OȮ radicals

Hydrogen atom abstraction by methyl peroxy (CH₃OȮ) radicals can play an important role in gasoline/ethanol interacting chemistry for fuels that produce high concentrations of methyl radicals. Detailed kinetic reactions for hydrogen atom abstraction by CH₃OȮ radicals from the components of FGF-LLNL (a gasoline surrogate) including cyclopentane, toluene, 1-hexene, n-heptane, and isooctane have been systematically studied in this work. The M06–2X/6–311++G(d,p) level of theory was used to obtain the optimized structure and vibrational frequency for all stationary points and the low-frequency torsional modes. The 1-D hindered rotor treatment for low-frequency torsional modes was treated at M06–2X/6–31G level of theory. The UCCSD(T)-F12a/cc-pVDZ-F12 and QCISD(T)/CBS level of theory were used to calculate single point energies for all species. High pressure limiting rate constants for all hydrogen atom abstraction channels were performed using conventional transition state theory with unsymmetric tunneling corrections. Individual rate constants are reported in the temperature range from 298.15 to 2000 K. Our computed results show that the abstraction of allylic hydrogen atoms from 1-hexene is the fastest at low temperatures. When the temperature increases, the hydrogen atom abstraction reaction channel at the primary alkyl site gradually becomes dominant. Thermodynamics properties for all stable species and high-pressure limiting rate constants for each reaction pathway obtained in this work were incorporated into the latest gasoline surrogate/ethanol model to investigate the influence of the rate constants calculated here on model predicted ignition delay times.     

Rate coefficients and kinetic isotope effects of the abstraction reaction of H atoms from methylsilane

ABSTRACT

Thermal rate constants for chemical reactions using improved canonical variational transition state theory (ICVT) with small-curvature tunnelling (SCT) contributions in a temperature range 180–2000 K are reported. The general procedure is used with high-quality ab initio computations and semi-classical reaction probabilities along the minimum energy path (MEP). The approach is based on a vibrational adiabatic reaction path and is applied to the multiple-channel hydrogen abstraction reaction H + SiH₃CH₃ → products and its isotopically substituted variants. All the degrees of freedom are optimised and harmonic vibrational frequencies and zero-point energies are calculated at the MP2 level with the cc-pVTZ basis set. Single-point energies are calculated at a higher level of theory; CCSD(T)-F12a/VTZ-F12. ICVT/SCT rate constants show that the quantum tunnelling contributions at low temperatures are relatively important and the H-abstraction channel from SiH₃ group of SiH₃CH₃ is the major pathway. The total rate constants are given by the following expression: k_tot(ICVT/SCT) = 2.29 10^?18 T^2.42 exp(?350.9/T) cm³ molec^?1 s^?1. These calculated rates are in agreement with the available experiments. The ICVT/SCT method is further exploited to predict primary and secondary kinetic isotope effects, respectively).     

Theoretical study on the molecular tautomerism of the 3-hydroxy-pyridin-4-one system

3-hydroxy-pyridin-4-one is a parent molecule for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. In this work, relative stabilities of some possible tautomers were investigated using several quantum chemical methods: CBS (complete basis set methods), Gn, DFT (density functional theory), Hartree–Fock and MP2. Performed calculations show that the system under consideration exists as a mixture of two tautomers with comparable energies. Among them, the hydroxypyridinone structure of the studied molecular system seems to be a bit more stable than the o-dihydroxypyridine one, by a few kJ/mol only. Aromaticity and intra-molecular hydrogen bonding are the main effects influencing the stability of the studied tautomeric structures. Consequently, aromatic effects were calculated using several indices of aromaticity: HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shift), H, PDI (para delocalisation index), MCI (multi-centre index) and ASE (aromatic stabilisation energy). The strength of possible intra-molecular hydrogen bonds (H-bonds) was determined by means of the AIM (atoms-in-molecules) method and by calculating enthalpies for theoretical reactions that do or do not involve H-bonds. The AIM method was employed to understand how variations in atomic energies influence the stability of different tautomeric structures.     

Natural bond orbital (NBO) analysis of the angular group induced bond alternation (AGIBA) substituent effect

The geometries, natural charges, and resonance structures of 11 monosubstituted benzene derivatives were analyzed at the B3LYP/6‐311++G(d,p) and HF/6‐311++G(d, p) levels of theory. The following angular substituents were chosen: OCH₃, CH₂CH₃, OH, SH, NHCH₃, NHNH₂, N?O, CH?CH₂, N?CH₂, N?NH, and CHO. The analysis of resonance structures was performed by using two different methodologies: harmonic oscillator stabilization energies (HOSE) and natural resonance theory (NRT). Also, the natural bond orbital (NBO) donor–acceptor stabilization energies for different resonance structures were calculated. We found that for all the substituents, the purely geometric resonance stabilization parameter (HOSE) is linearly correlated with quantum chemically derived resonance structure weight (NRT) of a given structure. Also, the calculations provide qualitative support for the earlier assumption of a through space angular group induced bond alternation (AGIBA) effect. Copyright © 2010 John Wiley & Sons, Ltd.     

Mechanistic study of the reaction of methyl peroxy radical (CH3O2) with formaldehyde (CH2O)

ABSTRACT

A direct dynamic study on the reactions of CH₃O₂?+?CH₂O was carried out over the temperature range of 300–1500?K. All stationary points were calculated with the M06-2X/6-311++G(d,p) level of theory and identified for local minimum. The energetic parameters were refined at QCISD (T)/cc-pVTZ and CCSD (T)/cc-pVTZ levels of theory. Three channels were explored and a reaction of hydrogen abstraction from CH₂O by CH₃O₂ was identified as dominant channel which involves the formation of a prereactive complex in the entrance channel. The rate coefficient of the dominant channel was calculated with TST and TST/Eck and the Eckart tunnelling effect is only important over the lower temperature region. The calculated rate coefficient of the dominant channel has positive temperature dependence and agrees reasonably with the available literature data.     

NMR Line Shape for a Rectangular Configuration of Nuclei

We present an approach to describe nuclear magnetic resonance absorption of dipolar-coupled rectangular configuration of nuclear spins associated with reorientation of ethylene bridge (–CH₂–CH₂–) in the crystal. The approach was applied to investigate reorientational mobility of dabco-linkers (1,4-diazobycyclo[2,2,2]octane) in metal–organic framework [Zn₂(bdc)₂(dabco)] (bdc—benzenedicarboxylate). Dabco rotation around the N–N axis is shown to remain down to 80 K and the activation energy of the molecule reorientation does not exceed 12 kJ/mol.     

Computational study on structures,thermochemical properties,and bond energies of disulfide oxygen (S–S–O)‐bridged CH3SSOH and CH3SS(=O)H and radicals

Cleavage of disulfide bonds is a common method used in linking peptides to proteins in biochemical reactions. The structures, internal rotor potentials, bond energies, and thermochemical properties (Δ_fH°, S°, and Cp(T)) of the S–S bridge molecules CH₃SSOH and CH₃SS(=O)H and the radicals CH₃SS?=O and C?H₂SSOH that correspond to H‐atom loss are determined by computational chemistry. Structure and thermochemical parameters (S° and Cp(T)) are determined using density functional Becke, three‐parameter, Lee–Yang–Parr (B3LYP)/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p). The enthalpies of formation for stable species are calculated using the total energies at B3LYP/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p), and the higher level composite CBS–QB3 levels with work reactions that are close to isodesmic in most cases. The enthalpies of formation for CH₃SSOH, CH₃SS(=O)H are ?38.3 and ?16.6 kcal mol^?1, respectively, where the difference is in enthalpy RSO–H versus RS(=O)–H bonding. The C–H bond energy of CH₃SSOH is 99.2 kcal mol^?1, and the O–H bond energy is weaker at 76.9 kcal mol^?1. Cleavage of the weak O–H bond in CH₃SSOH results in an electron rearrangement upon loss of the CH₃SSO–H hydrogen atom; the radical rearranges to form the more stable CH₃SS· = O radical structure. Cleavage of the C–H bond in CH₃SS(=O)H results in an unstable [CH₂SS(=O)H]* intermediate, which decomposes exothermically to lower energy CH₂ = S + HSO. The CH₃SS(=O)–H bond energy is quite weak at 54.8 kcal mol^?1 with the H–C bond estimated at between 91 and 98 kcal mol^?1. Disulfide bond energies for CH₃S–SOH and CH3S–S(=O)H are low: 67.1 and 39.2 kcal mol^?1. Copyright © 2011 John Wiley & Sons, Ltd.     

Hydrogen abstraction reactions of hydroxyl radicals with 1,1,2,2-tetrachloroethane, 1,1,1,2-tetrachloroethane and pentachloroethane studied by using semi-classical transition state theory

The hydrogen abstraction reactions by OH radicals from CHCl₂CHCl₂ (R1), CH₂ClCCl₃ (R2) and C₂HCl₅ (R3) are investigated theoretically by semi-classical transition state theory. Many high-level density functional, ab initio and combinatory electronic structure calculation methods are used to evaluate the energies and ro-vibrational properties of the stationary points for the title reactions. x_ij vibrational anharmonicity coefficients, needed for semi-classical transition state theory, are calculated at the KMLYP/cc-pVTZ level of theory. Thermal rate coefficients are computed over the temperature range from 200 to 2000 K and compared with available experimental data. The computed rate constants for the reactions R1, R2 and R3 are fitted to the equation k(T) = ATⁿexp?[ ? E(T + T₀)/(T² + T²₀)].     

The adsorption of hydrogen on iron; A surface orbital modified occupancy — bond energy bond order calculation

A Surface Orbital Modified Occupancy — Bond Energy Bond Order (SOMO-BEBO) model calculation of hydrogen adsorption on iron is presented. This calculation represents a novel approach to the CFSO-BEBO method in that the calculation is correlated in a consistent way with the thermal desorption spectra of the hydrogen-iron system. Heats of molecular adsorption calculated are ?32.88, ?35.68 and ?49.57 kJ/mol for the iron (110), (100), and (111) surfaces, respectively. Heats of dissociative adsorption calculated are ?54.40, ?75.30 and ?87.90 kJ/mol for the three states on the iron (111) surface; ?51.21 and ? 73.62 kJ/mol for the two states on the iron (100) surface; and ?63.78 kJ/mol for the one state on the iron (110) surface. Activation energies for dissociative adsorption were found to be small or zero for the iron (111) surface while non-zero activation energies of 49.27 and 45.05 kJ/mol were calculated for the iron (100) and (110) surfaces, respectively. The FeH single-order bond energy has been calculated to be 298.2 kJ/mol. The radius of the hydrogen surface atom has been estimated to be 1.52 × 10^?10 m consistent with the expected size of an H^? ion. The elimination of certain surface sites for molecular adsorption as a result of the ferromagnetism of iron is suggested by the calculation. The reason for the absence of well defined LEED patterns for hydrogen adsorption on the iron (111) and (100) surfaces [Bozso et al., Appl. Surface Sci. 1 (1977) 103] is explained on the basis of the size of the H^? surface ion. The adsorption of hydrogen on the iron (110) surface is consistent with a relatively stable, small-sized H⁺₂ surface ion giving, therefore, a regular LEED pattern and a positive surface potential upon adsorption of hydrogen on this surface.     

Kinetics of chemical vapor deposition of SiC from methyltrichlorosilane and hydrogen

In this study, the dependence of the deposition rate on processing parameters, such as temperature, and partial pressure is studied by chemical vapor deposition from mixture of methyltrichlorosilane (CH₃SiCl₃, MTS) and hydrogen. The kinetics investigation is carried out in a tubular, hot-wall reactor coupled to a sensitive magnetic suspension microbalance. The results show that the active energy limited by surface reactions is 188 kJ/mol. In the case, the deposition rate is linear to the partial pressure of MTS and the square of partial pressure of hydrogen. SiCl₂ and CH₃ are proposed as the effective precursor for SiC. A reaction model was proposed concluding gas phase reactions and surface reactions. The theoretical relation between deposition rate and partial pressures of MTS and H₂ was in a good accordance with experimental results.     

Evaluation of Activation Energies for Pairwise and Non-Pairwise Hydrogen Addition to Propyne Over Pd/Aluminosilicate Fiberglass Catalyst by Parahydrogen-Induced Polarization (PHIP)

Hydrogenation of propyne to propene over Pd/aluminosilicate fiberglass catalyst in the temperature range 175–350 °C was investigated with the use of parahydrogen-induced polarization (PHIP) technique. Activation energies for both pairwise and non-pairwise H₂ addition routes were estimated. It was found that at 175–275 °C the activation energies for hydrogen addition to the triple bond of propyne have similar values (about 60–70 kJ/mol) for both routes of hydrogen addition. At higher temperatures (275–350 °C), the rate constant for pairwise hydrogen addition reaches a maximum value while the rate constant for non-pairwise hydrogen addition continues to increase with increasing temperature.     

A periodic density functional theory study of the dehydrogenation of methanol over CuCl(1 1 1) surface

The decomposition of methanol on clean and oxygen-precovered CuCl(1 1 1) surface have been studied with the method of density functional theory-generalized gradient approximation (DFT-GGA) and the periodic slab models. The effects of different methanol coverages up to one monolayer are investigated. The activation of the O-H bond of methanol to form the methoxide intermediate, the activation of the C-H bond to form the hydroxymethyl intermediate and the activation of the C-O bond to form methyl are examined. These intermediates can subsequently react to form methoxide, hydroxymethyl, methyl, formaldehyde, formyl, and finally CO on the surface. The chemisorption energies of CH₃OH, CH₃O, H₂COH, CH₃, H₂CO, HCO, OH and CO at their most favorable adsorption sites are predicted to be −57.9, −235.3, −172.9, −170.5, −67.8, −192.4, −309.5 and −105.7 kJ/mol, respectively. We also confirm that the O-H bond-breaking paths have lower energy barrier, compared to the C-O and C-H bond-breaking paths. However, these reactions need a lower energy barrier when precovered oxygen atoms participate in these reactions.     

Direct ab initio dynamics calculations of the reaction rate for the hydrogen abstraction reaction of NCO with CH4 and C2H6

The kinetics of the hydrogen abstraction reactions NCO + CH₄ (R1) and NCO + C₂H₆ (R2) have been studied over a wide temperature range. The minimum energy paths (MEPs) were calculated at the MP2/cc-pVDZ level and single-point calculations were refined at the G3MP2 level. The rate constants for the title reactions were calculated using canonical variational transition state theory (CVT) with small-curvature tunneling (SCT) contributions. The fitted three-parameter formulae are k ₁ = 2.52 × 10^?22 T ^3.46 exp(2466/T) and k ₂ = 9.8 × 10^?22 T ^3.2 exp(411.8/T) cm³ molecule^?1 s^?1 for (R1) and (R2), respectively. The calculated rate constants were found to be in good agreement with the available experimental data. Deuterium kinetic isotope effects were also investigated. Both reactions show a significant kinetic isotope effect in the low-temperature range.     

Theoretical investigation on H abstraction reaction mechanisms and rate constants of Isoflurane with the OH radical

The mechanism of H abstraction reactions for Isoflurane with the OH radical was investigated using density functional theory and G3(MP2) duel theory methods. The geometrical structures of all the species were fully optimised at B3LYP/6-311++G** level of theory. Thermochemistry data were obtained by utilising the high accurate model chemistry method G3(MP2) combined with the standard statistical thermodynamic calculations. Gibbs free energies were used for the reaction channels analysis. All the reaction channels were confirmed throughout the intrinsic reaction coordinate analysis. The results show that two channels were obtained, which correspond to P(1) and P(2) with the respective activation barriers of 63.03 and 54.82 kJ/mol. The rate constants for the two channels over a wide temperature range of 298.15–2000 K were predicted and the calculated data are in agreement with the experimental one. The results show that P(2) is the dominant reaction channel under 800 K and above 800 K, it can be found that P(1) will be more preferable reaction channel.     

The production of prop-2-ynylideneamine by thermolysis of N-chloropropargylamine,N-fluoropropargylamine and N-hydroxypropargylamine: a computational study

Ab initio molecular orbital calculations using MP2 and DFT/B3LYP methods at the 6-311++G(d,p) and aug-cc-pvdz basis sets were applied to characterise the kinetics of the thermal dissociation of HC≡CCH₂NHX [where X = OH(I), F(II) and Cl(III)] to produce Z- and E-prop-2-ynylideneamines (HC≡CCH=NH) (IV and V, respectively), which tautomerise to vinyl cyanide (CH₂=CHC≡N) (VI). The optimised geometries and electronic energies of reactants, transition states and products were estimated and discussed. A concerted proton migration and HX abstraction mechanism was proposed for the imine formation. The reliance of these properties on the elected levels of theory was discussed. The activation energies and barrier heights for the Z- and E-forms and their vinyl cyanide tautomers were estimated and analysed. The Z-form was computed to be more stable than the E-form. Using natural bond orbital calculations, the origin of the preference of the Z-form was attributed mainly to the N lone pair delocalisations. Vinyl cyanide was located to have a lower energy (33–35 kcal/mol) than prop-2-ynylideneamine. The provenance of the preference of the former and its tautomerisation mechanism will be addressed in a separate publication.