Unimolecular Reaction Pathways Research Articles

Atmospheric Fate of the CH3SOO Radical from the CH3S + O2 Equilibrium.

The atmospheric oxidation mechanisms of reduced sulfur compounds are of great importance in the biogeochemical sulfur cycle. The CH3S radical represents an important intermediate in these oxidation processes. Under atmospheric conditions, CH3S will predominantly react with O2 to form the peroxy radical CH3SOO. The formed CH3SOO has two competing unimolecular reaction pathways: isomerization to CH3SO2, which further decomposes into CH3 and SO2, or a hydrogen shift followed by HO2 loss, leading to CH2S. Previous theoretical calculations have suggested that CH2S formation should be the dominant pathway, in disagreement with existing experimental results. Our large active space multireference configuration interaction calculations agree with the experimental results that the formation of CH3 and SO2 is the dominant route and the formation of CH2S and HO2 can, at most, be a minor pathway. We support the calculations with new experiments starting from the OH + CH3SH reaction for CH3S formation under low NOx conditions and find a SO2 yield of 0.86 ± 0.18 within our reaction time of 7.9 s. Model simulations of our experiments show that the SO2 yield converges to 0.98. This combined theoretical and experimental study thus furthers the understanding of the general oxidation mechanisms of sulfur compounds in the atmosphere.

KinBot: Automated stationary point search on potential energy surfaces

KinBot is a Python code that automatically characterizes kinetically important stationary points on reactive potential energy surfaces and arranges the results into a form that lends itself easily to master equation calculations. This version of KinBot tackles C, H, O and S atom containing species and unimolecular (isomerization or dissociation) reactions. KinBot iteratively changes the geometry of the reactant to obtain initial guesses for reactive saddle points defined by KinBot’s reaction types, which are then optimized by a third-party quantum chemistry package. KinBot verifies the connectivity of the saddle points with the reactant and identifies the products through intrinsic reaction coordinate calculations. New calculations can be automatically spawned from the products to obtain complete potential energy surfaces. The utilities of KinBot include conformer searches, projected frequency and hindered rotor calculations, and the automatic determination of the rotational symmetry numbers. Input files for popular RRKM master equation codes are automatically built, enabling an automated workflow all the way to the calculation of pressure and temperature dependent rate coefficients. Four examples are included. (i) [1,3]-sigmatropic H-migration reactions of unsaturated hydrocarbons and oxygenates are calculated to assess the relative importance of suprafacial and antrafacial reactions. (ii) Saddle points on three products of gamma-valerolactone thermal decomposition are studied and compared to literature potential energy surfaces. (iii) The previously published propene+OH reaction is reproduced to show the capability of building an entire potential energy surface. (iv) All species up to C4 in the Aramco Mech 2.0 are subjected to a KinBot search. Program summaryProgram title: KinBotProgram files doi:http://dx.doi.org/10.17632/hsh6dvv2zj.1Licensing provisions: BSD 3-ClauseProgramming language: PythonSupplementary material:1. A static version of the source code (KinBot.tar),2. The manual for the static version (KinBot_Manual.pdf)3. Geometries and energies of the stationary points on the potential energy surface of the sigmatropic reaction search (sigmatropic_H_shift.out)4. Geometries and energies of the stationary points on the potential energy surface of the propene+ OH central and terminal addition reaction (propene+oh central addition.out, propene+oh terminal addition.out)5. Geometries and energies of the stationary points on the potential energy surface of gamma valerolactone, 4-pentenoic acid and 3-pentenoic acid (GVL energies and geometries.out, 4PA energies and geometries.out, 3PA energies and geometries.out)6. Example runs including all input and output files for a one-well search for propanol radical, full PES search for the n-pentyl radical, a search for all homolytic scission in propanol, and the reaction searches for GVL (output.zip)7. Results of symmetry calculations for a literature benchmark dataset (Symmetry_correct.pdf, Symmetry_wrong.pdf)Nature of problem: Automatic discovery of unimolecular reaction pathways (isomerization and dissociation) for molecules and radicals relevant in gas-phase combustion and atmospheric chemistry, including oxidation and pyrolytic processes for structures including carbon, oxygen, sulfur and hydrogen atoms. The reactants, products, and transition states are characterized using a suite of tools coupled to electronic structure codes, and the results are provided in a format that lends itself easily to calculating rate coefficients based on statistical rate theories with other external codes.Solution method: Reaction pathways are identified using heuristic searches starting from a reactant by iteratively altering its geometry toward a good guess for a transition state for reactions with barriers. The transition state is identified as a first-order saddle point on the potential energy surface, which is located using local optimization methods of third-party quantum chemistry codes. We use intrinsic reaction coordinate calculations to verify the direct connectivity of the saddle point to the reactant and to identify the product species. Conformational searches, hindered rotor potentials, frequency calculations, and high-level optimizations yield the necessary data for RRKM master equation calculations.Additional comments including restrictions and unusual features: KinBot is designed to run on Unix clusters, and is written in Python, compatible with versions 2.7 and 3. It communicates with a PBS or SLURM workload manager to submit quantum chemistry calculations to third-party software. It makes use of a modified fork of ASE for the input writing, calling and output parsing of the quantum chemistry software which has been tested with Gaussian (G09RevD.01). OpenBabel (2.4.1) and RDKit (2018.09.01) are used to convert smiles to internal species representations and for species comparison and results visualization. The output of KinBot can be visualized with the PESViewer script, and graph structures are drawn using NetworkX. The master equation solvers MESS or MESMER are needed to calculate rate coefficients at the end of a given run. This version of KinBot can handle H, C, S, and O atom-containing molecules, and searches for isomerization and dissociation pathways.

Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods.

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The present joint approach significantly outperforms previous manual and automated transition-state searches - 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Overall, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).

Substituent effects in the decarboxylation reactions of coordinated arylcarboxylates in dinuclear copper complexes, [(napy)Cu2(O2CC6H4X)]+ †.

A combination of gas-phase ion trap mass spectrometry experiments and density functional theory (DFT) calculations have been used to examine the role of substituents on the decarboxylation of 25 different coordinated aromatic carboxylates in binuclear complexes, [(napy)Cu2(O2CC6H4X)]+, where napy is the ligand 1,8-naphthyridine (molecular formula, C8H6N2) and X = H and the ortho ( o), meta ( m) and para ( p) isomers of F, Br, CN, NO2, CF3, OAc, Me and MeO. Two competing unimolecular reaction pathways were found: decarboxylation to give the organometallic cation [(napy)Cu2(C6H4X)]+ or loss of the neutral copper benzoate to yield [(napy)Cu]+. The substituents on the aryl group influence the branching ratios of these product channels, but decarboxylation is always the dominant pathway. Density functional theory calculations reveal that decarboxylation proceeds via two transition states. The first enables a change in the coordination mode of the coordinated benzoate in [(napy)Cu2(O2CC6H4X)]+ from the thermodynamically favoured O, O-bridged form to the O-bound form, which is the reactive conformation for the second transition state which involves extrusion of CO2 with concomitant formation of the CO2 coordinated organometallic cation, [(napy)Cu2(C6H4X)(CO2)]+, which then loses CO2 in the final step to yield [(napy)Cu2(C6H4X)]+. In all cases the barrier is highest for the second transition state. The o-substituted benzoates show a lower activation energy than the m-substituted ones, while the p-substituted ones have the highest energy, which is consistent with the experimentally determined normalised collision energy required to induce fragmentation of [(napy)Cu2(O2CC6H4X)]+.

Kinetic barriers, rate constants and branching ratios for unimolecular reactions of methyl octanoate peroxy radicals: A computational study of a mid-sized biodiesel fuel surrogate

Towards the goal of establishing kinetic database for low-temperature combustion (T < 1000K) of mid-sized biodiesel surrogates, the study uses quantum chemistry and statistical kinetic methods to investigate three primary unimolecular reaction pathways of methyl octanoate peroxy radicals, including dissociation, isomerization and concerted elimination. We calculate kinetic barriers and pressure-dependent rate constants at 500–1000K. The comparison between our computed and previously estimated rate constants offers further insight into how transition state structures and molecular mechanics are correlated with reaction kinetics. In the branching ratio analysis, we investigate the proposed unimolecular reactions and factors affecting these kinetic characteristics. For the first time, the previously measured oxidation rates of methyl octanoate under the cool flame regime (560–1000K) are computationally verified by kinetic modeling that reflects the contribution of the present submodel to an existing detailed mechanism of methyl octanoate. Consequently, the rate-of-production analysis reveals the significance of newly proposed reaction pathways.

The contribution of tunnelling to the 1,5 H-shift isomerisation reaction of alkoxyl radicals

Theoretical models have been used to derive rate coefficients for the unimolecular reaction pathways of two prototypical alkoxyl radicals (1-butoxyl and 2-pentoxyl) which can undergo 1,5 H-shift isomerisation yielding the corresponding delta-hydroxy alkyl radical. Special emphasis has been given to the contribution of tunnelling in the isomerisation channels which has not been accounted for in previous theoretical studies. The combination of high level ab initio calculations with a fully coupled multiple channel master equation (ME) treatment resulted in a significant increase of the isomerisation rates by about a factor of 2.7 for the 1-butoxyl and 2.3 for the 2-pentoxyl radical, respectively, as compared to calculations in which tunnelling was neglected, even at 298 K. The corresponding Arrhenius energies in the temperature range from 200 up to 1000 K are significantly smaller when tunnelling is accounted for and differ from previous results which focused only on temperatures around 298 K. The rate expressions derived for the 1,5 H-shift isomerisation reactions are: k(iso,1but) = 1.58 x 10(12)(T/300 K)(-2.30) exp(-4679 K/T) s(-1) and k(iso,2pent) = 4.65 x 10(12)(T/300 K)(-3.22) exp(-4782 K/T) s(-1) valid for p = 1013 mbar and temperatures between 200 K < or = T < or = 1000 K. Our results are strongly supported by recent experiments of Cox and co-workers, (D. Johnson, P. Cassanelli, and R. A. Cox, J. Phys. Chem. A, , 2004, 108, 519 and P. Cassanelli, D. Johnson, and R. A. Cox, Phys. Chem. Chem. Phys. 2005, 7, 3702, 18) which are among the very few studies performed in a temperature regime (250 < or = T < or = 320 K) where tunnelling is thought to be effective. Since tunnelling has been neglected so far in the theoretical analysis of experimental data, the reliability of existing extrapolations to higher and lower temperatures is discussed in detail.

Unimolecular Reactions of Vibrationally Excited CF2ClCHFCH3 and CF2ClCHFCD3: Evidence for the 1,2-FCl Interchange Pathway

Chemically activated CF2ClCHFCH3 and CF2ClCHFCD3 molecules were prepared with 94 kcal mol-1 of vibrational energy by the recombination of CF2ClCHF and CH3(CD3) radicals at room temperature. The unimolecular reaction pathways were 2,3-FH(FD) elimination, 1,2-ClF interchange and 1,2-ClH elimination; the interchange produces CF3CHClCH3(CF3CHClCD3) with 105 kcal mol-1 of vibrational energy. Rate constants for CF2ClCHFCH3 [CF2ClCHFCD3] were (3.1+/-0.4)x10(6) s-1 [(1.0+/-0.1)x10(6) s-1] for 2,3-FH [FD] loss, (1.5+/-0.2)x10(6) s-1 [(8.3+/-0.9)x10(5) s-1] for 1,2-ClF interchange, and (8.2+/-1.0)x10(5) s-1 [(5.3+/-0.6)x10(5) s-1] for 1,2-ClH [DCl] loss. These correspond to branching fractions of 0.55+/-0.06 [0.43+/-0.04] for 2,3-FH [FD] loss, 0.29+/-0.03 [0.35+/-0.04] for 1,2-ClF interchange, and 0.16+/-0.02 [0.22+/-0.02] for 1,2-ClH [ClD] loss. Kinetic-isotope effects were 3.0+/-0.6 for 2,3-FH [FD] loss, 1.6+/-0.3 for 1,2-ClH loss, and 1.8+/-0.4 for 1,2-ClF interchange. The CF3CHClCH3 (CF3CHClCD3) molecules formed by 1,2-FCl interchange react by loss of HCl [DCl] with rate constants of (5.6+/-0.9)x10(7) s-1 [(2.1+/-0.4)x10(7)] s-1 for an isotope effect of 2.7+/-0.4. Density functional theory was employed to calculate vibrational frequencies and moments of inertia for the molecules and for the transition-state structures. These results were used with RRKM theory to assign threshold energies from comparison of computed and experimental unimolecular rate constants. The threshold energy for ClF interchange is 57.5 kcal mol-1, and those for HF and HCl channels are 2-5 kcal mol-1 higher. Experiments with vibrationally excited CF2ClCF2CF3, CF2ClCF2CF2Cl, and CF2ClCF2Cl, which did not show evidence for ClF interchange, also are reported.

Quantum Chemical Study of Low Temperature Oxidation Mechanism of Dibenzofuran

A density functional theory (DFT) study of the reaction of dibenzofuranyl radical with oxygen molecule has been made. The geometries, energies, and vibrational frequencies of the reactant, transition states, intermediates, and products have been calculated at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level of theory. The initial reaction of dibenzofuran (DBF) with molecular oxygen results in the formation of the 1-dibenzofuranylperoxy radical. The stability of this adduct toward decomposition at low to intermediate temperatures results in it undergoing several possible rearrangements. The lowest energy pathway with a barrier of 24.2 kcal/mol involves a rearrangement to the 1,1-dioxadibenzofuran radical. The next lowest energy pathway involves fission of the O-O linkage whose reaction energy was found to be 37.6 kcal/mol. Transition state theory (TST) calculations indicate that the lowest energy pathway should predominate at temperatures up to about 1200 K. Two other unimolecular reaction pathways with barriers of 45.5 and 91.1 kcal/mol have also been discovered. The latter pathway leads to the formation of a para-quinone (dibenzofuran quinone) which has been detected experimentally in the low-temperature oxidation of DBF [Marquaire, P. M.; Worner, R.; Rambaud, P.; Baronnet, F. Organohalogen Compd. 1999, 40, 519]. Our quantum calculations, however, do not support this latter pathway to quinone formation. Instead, the quinone is most probably formed as a consequence of recombination of the 1-dibenzofuranyloxy radical (produced by peroxy fission) with an O atom in the para position. Each of the unimolecular reaction pathways have been subjected to detailed quantum chemical investigation and transition states and intermediates leading to the final products (principally CO, CO2, and C2H2 with traces of benzofuran and benzene) have been identified. For certain stable intermediates, their possible reactions with molecular oxygen have been further investigated quantum chemically. The present work therefore presents a detailed quantum chemical investigation of the reaction pathways in the low-temperature oxidation mechanism of DBF. Since the dibenzofuran moiety is present in the polychlorinated DBFs, our conclusions should be generally applicable to this family of compounds.

Theoretical studies on unimolecular reactions of thioacetaldehyde

Taking thioacetaldehyde as an example, the purpose of this work is to investigate the reactivity difference between carbonyl compounds and thiocarbonyl compounds. Five possible unimolecular reaction pathways for ground-state thioacetaldehyde have been investigated in this work with MP2 and B3LYP methods in conjugation with cc-pVDZ basis set. The present calculations predict that the unimolecular reactions for ground-state thioacetaldehyde are quite different from those for ground-state acetaldehyde. In addition, it is found that this is mainly due to the larger size of sulfur atom than oxygen and the less stability of compounds containing sulfur with respect to the corresponding carbonyl compounds.

Charge Separation and Charge Distribution in Rearrangement Reactions of β-(Phosphatoxy)alkyl Radicals

Unimolecular reaction pathways for the 2-(dimethylphosphatoxy)-2-(p-methoxyphenyl)-1,1,-dimethylethyl radical 1 have been studied with several different hybrid density functional methods. The most reliable prediction has been obtained through combination of relative energies calculated at the BHLYP/6-311+G(d,p)//Becke3LYP/6-31G(d) level of theory with solvation free energies calculated with the PCM (polarizable continuum) model for THF. All reaction pathways characterized in detail have mixed homolytic/heterolytic character with a dominating heterolytic component. Concerted reaction pathways for 1,2- and 3,2-migration of the phosphate group lead to rearranged benzylic radical 2 that is more stable than 1 by about 30 kJ/mol. Also, a flat region of the potential energy surface has been identified that contains intermediates of nonintegral charge separation. This region of the potential energy surface can be reached from the reactant radical 1, the rearranged radical 2, and the phosphoric acid elimination pr...

Theoretical study on unimolecular reactions of thioformyl cyanide

Seven possible unimolecular reaction pathways of thioformyl cyanide in its ground state have been investigated at the HF/cc-pVDZ, B3LYP/cc-pVDZ, MP2/cc-pVDZ, and MP2/6-31G** levels of theory. The theoretical analysis indicates that thioformyl cyanide is rather stable at room temperature in the case of unimolecular reactions, which is consistent with the experimental findings.

1,2-Chlorine atom migration in 3-chloro-2-butyl radicals: a computational study.

The structure as well as several unimolecular reaction pathways of the 3-chloro-2-butyl radical 1 have been studied at several different theoretical levels (B3LYP/aug-cc-pVDZ, BHLYP/aug-cc-pVDZ, G3(ROMP2)B3). The symmetrically chlorine-bridged structure is a transition state at all levels of theory and the most favorable ground state structure is the unbridged beta-chloroalkyl radical. Reaction barriers for the 1,2-chlorine migration process are higher than those for rotation around the central C-C bond. 1,2-migration of the chlorine atom is accompanied by an increase in chlorine negative charge as well as chlorine spin density. This hybrid homo-/heterolytic process is well known from rearrangement reactions in beta-(dialkoxyphosphoryloxy)alkyl radicals and suggests that chlorine migration can be influenced by polar substituent effects.

A G2 ab initio study of C 2H 5S isomers: Structures, energetics, and unimolecular reaction pathways

The potential energy surface of C 2H 5S isomers has been studied with the G2 ab initio method. The structures and G2 heats of formation of the six stable isomers/conformers, CH 3CH 2S ( 1), syn-CH 3CHSH ( 2), anti-CH 3CHSH ( 3), CH 3SCH 2 ( 4), gauche-HSCH 2CH 2 ( 5), and anti-HSCH 2CH 2 ( 6), have been reported previously (Chem. Phys. Lett., 213 (1993) 250; J. Chem. Phys., 104 (1996) 130). Their structural properties upon change of conformation can be rationalized by the perturbative molecular orbital model. The C 2H 5S radicals are very flexible due to low-energy barriers for rotations and inversions. Unimolecular rearrangements are exclusively 1,2- and 1,3-H shifts with large G2 activation energies at 0 K: E a (1 → 3) = 147.0 kJ mol −1, E a (1 → 5) = 140.0 kJ mol −1, E a (2 → 5) = 187.2 kJ mol −1, E a (3 → 6) = 191.7 kJ mol −1, and E a (4 → 4) = 176.9 kJ mol −1. The TS structures for the unimolecular decompositions: 5 → C 2 H 4 + SH (6), 1 → CH 3 + H 2 CS (7), and 4 → CH 3 + H 2 CS (8) are loose and product-like. Their UHF determinant functions have considerable spin contamination (〈 S 2〉 ≈ 0.96–1.08). Energy barriers for the analogous reactions of 6 and 7 for the oxygen analogs were also computed and compared to the observed rate parameters. In general, it is found that the G2 method is still reliable to estimate the reaction barriers for systems with 〈 S 2〉 ≤ 0.96. Correction with spin projection is required for systems with 〈 S 2〉 > 1.0. Among the reactions of C 2H 5S studied in this work, the pathway with the lowest energy is 6. The G2 E a = 41.7 kJ mol −1 for 6 at 700 K is in good agreement with Shum and Benson's (Int. J. Chem. Kinet., 17 (1985) 277, 749) estimated value (46 kJ mol −1). At the same temperature, the calculated E a ′ s for 7 and 8, after spin-projection corrections, are 158.9 kJ mol −1 and 109.0 kJ mol −1, respectively, in agreement with the estimated E a ' s (145.5 kJ mol −1 for 7 and 101.3 kJ mol −1 for 8). The addition reaction CH 3 + H 2CS → 4 ( 8) is predicted to be negative temperature dependent with an E a of −3.0 kJ mol −1 at 700 K. This is in line with the lower bound of the estimated E a (ca. 11.7 kJ mol −1 ± 12.6 kJ mol −1) for 8 at 644 K as reported by Shum and Benson.

Theoretical study on unimolecular reactions of formyl cyanide

The possible unimolecular reactions of formyl cyanide (CHOCN) in its ground state have been investigated with ab initio method, at the level of MP4 (SDTQ)/6-31G *//HF/6-31G *. Our theoretical analysis indicated that in the case of unimolecular reaction pathways, CHOCN is rather stable at room temperature. However, at higher temperature this compound can decompose into HCN and CO. All of these are in agreement with the experimental identifications.

Thermal reactions of decalin. II. A mass spectrometric study

The very low pressure pyrolysis of trans-decalin (⩽1450 K, 10 −3 s, 10 −5 mbar) has been studied under real-time conditions by mass spectrometry. The results obtained confirm the existence of several unimolecular reaction pathways: (i) CC bond ruptures (not only the preferential transannular CC cleavage); thereupon, (ii) a reaction course resulting in olefinic C/H isomeric hydrocarbons; and subsequently, (iii) thermal conversion of these reaction intermediates formed via routes (i) and (ii). The observed reaction pattern for the decomposition of decalin is similar to that for the thermal rearrangement of cyclohexane.