A quantitative curve-crossing model for radical fragmentation

The kinetics of bond fragmentation for a series of N-methoxypyridyl radicals are analyzed in terms of a simple curve-crossing model that includes bond stretching and bond bending coordinates. The model accurately reproduces the reaction surfaces calculated using density functional theory (DFT) and also the experimental reaction energy barriers. The reactions proceed on the ground state surface by avoidance of a conical intersection, which is clearly illustrated by the model. A value for the electronic coupling matrix element responsible for splitting the upper and lower surfaces of 0.9 eV is obtained. The model illustrates the molecular features that allow barrierless fragmentation from a formally pi radical.     

Density functional theory predicts the barriers for radical fragmentation in solution

[reaction: see text] N-Methoxypyridyl radicals formed by one-electron reduction of the corresponding cationic heterocycles undergo N-O bond cleavage. Experimental activation free energies for a series of these bond fragmentations are compared to corresponding barriers determined from electronic structure calculations. The DFT barriers agree well with those from experiment, being smaller than the latter values by an average value of ca. 1 kcal/mol, for rate constants varying over almost 3 orders of magnitude, or within ca. 3 kcal/mol over 8 orders of magnitude of rate constant. For a model compound, the B3PW91/6-31+G hybrid density functional method is also found to be in good agreement with the MCSCF-MRMP2 method. One of the reactions is found by DFT to have no minimum for the reactant radical, consistent with a truly barrierless reaction.     

Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA

Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.     

Mimicking the silicon surface: reactivity of silyl radical cations toward nucleophiles

Radical cations of selected low molecular-weight silicon model compounds were obtained by photoinduced electron transfer. These radical cations react readily with a variety of nucleophiles, regularly used in monolayer fabrication onto hydrogen-terminated silicon. From time-resolved kinetics, it was concluded that the reactions proceed via a bimolecular nucleophilic attack to the radical cation. A secondary kinetic isotope effect indicated that the central Si-H bond is not cleaved in the rate-determining step. Apart from substitution products, also hydrosilylation products were identified in the product mixtures. Observation of the substitution products, combined with the kinetic data, point to an bimolecular reaction mechanism involving Si-Si bond cleavage. The products of this nucleophilic substitution can initiate radical chain reactions leading to hydrosilylation products, which can independently also be initiated by dissociation of the radical cations. Application of these data to the attachment of organic monolayers onto hydrogen-terminated Si surfaces via hydrosilylation leads to the conclusion that the delocalized Si radical cation (a surface-localized hole) can initiate the hydrosilylation chain reaction at the Si surface. Comparison to monolayer experiments shows that this reaction only plays a significant role in the initiation, and not in the propagation steps of Si-C bond making monolayer formation.     

Mechanistic analysis of oxidative C-H cleavages using inter- and intramolecular kinetic isotope effects

A series of monodeuterated benzylic and allylic ethers were subjected to oxidative carbon-hydrogen bond cleavage to determine the impact of structural variation on intramolecular kinetic isotope effects in DDQ-mediated cyclization reactions. These values are compared to the corresponding intermolecular kinetic isotope effects that were accessed through subjecting mixtures of non-deuterated and dideuterated substrates to the reaction conditions. The results indicate that carbon-hydrogen bond cleavage is rate determining and that a radical cation is most likely a key intermediate in the reaction mechanism.     

Interpretation of the gas-phase solvent deuterium kinetic isotope effects in the S(N)2 reaction mechanism: Comparison of theoretical and experimental results in the reaction of microsolvated fluoride ions with methyl halides

We carried out a comprehensive ab initio calculation and transition-state theory analysis of the solvent and secondary deuterium kinetic isotope effects in the SN2 reactions of microsolvated fluoride ions with methyl halides. Water, methanol, and hydrogen fluoride were used as solvents, and the results are compared with recent experiments. Kinetic isotope effects were dissected into contributions from translations, rotations, and different vibration modes, and the validity of such analysis is also discussed. Excellent agreement was found for some reactions, whereas the agreement was poor for other reactions. We showed that the deviation between theory and experiments is related to the reaction kinetics; a faster reaction produced a kinetic isotope effect that was systematically larger (less inverse) than the calculated value. In addition, we also found that the magnitude of the deviation is proportional to the reaction efficiency. We rationalize the disagreement as a failure of the transition-state theory to model barrierless reactions, and we propose a very simple scheme to interpret these findings and predict the deviation between experimental and theoretical values in those reactions.     

Variational analysis of the phenyl + O2 and phenoxy + O reactions

Variational transition state analysis was performed on the barrierless phenyl + O2 and phenoxy + O association reactions. In addition, we also calculated rate constants for the related vinyl radical (C2H3) + O2 and vinoxy radical (C2H3O) + O reactions and provided rate constant estimates for analogous reactions in substituted aromatic systems. Potential energy scans along the dissociating C-OO and CO-O bonds (with consideration of C-OO internal rotation) were obtained at the O3LYP/6-31G(d) density functional theory level. The CO-O and C-OO bond scission reactions were observed to be barrierless, in both phenyl and vinyl systems. Potential energy wells were scaled by G3B3 reaction enthalpies to obtain accurate activation enthalpies. Frequency calculations were performed for all reactants and products and at points along the potential energy surfaces, allowing us to evaluate thermochemical properties as a function of temperature according to the principles of statistical mechanics and the rigid rotor harmonic oscillator (RRHO) approximation. The low-frequency vibrational modes corresponding to R-OO internal rotation were omitted from the RRHO analysis and replaced with a hindered internal rotor analysis using O3LYP/6-31G(d) rotor potentials. Rate constants were calculated as a function of temperature (300-2000 K) and position from activation entropies and enthalpies, according to canonical transition state theory; these rate constants were minimized with respect to position to obtain variational rate constants as a function of temperature. For the phenyl + O2 reaction, we identified the transition state to be located at a C-OO bond length of between 2.56 and 2.16 A (300-2000 K), while for the phenoxy + O reaction, the transition state was located at a CO-O bond length of 2.00-1.90 A. Variational rate constants were fit to a three-parameter form of the Arrhenius equation, and for the phenyl + O2 association reaction, we found k(T) = 1.860 x 1013T-0.217 exp(0.358/T) (with k in cm3 mol-1 s-1 and T in K); this rate equation provides good agreement with low-temperature experimental measurements of the phenyl + O2 rate constant. Preliminary results were presented for a correlation between activation energy (or reaction enthalpy) and pre-exponential factor for heterolytic O-O bond scission reactions.     

Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark‐ and Light‐Adapted States of a Blue‐Light YtvA LOV Photoreceptor

The dark‐ and light‐adapted states of YtvA LOV domains exhibit distinct excited‐state behavior. We have employed high‐level QM(MS‐CASPT2)/MM calculations to study the photochemical reactions of the dark‐ and light‐adapted states. The photoreaction from the dark‐adapted state starts with an S₁→T₁ intersystem crossing followed by a triplet‐state hydrogen transfer from the thiol to the flavin moiety that produces a diradical intermediate, and a subsequent internal conversion that triggers a barrierless C−S bond formation in the S₀ state. The energy profiles for these transformations are different for the four conformers of the dark‐adapted state considered. The photochemistry of the light‐adapted state does not involve the triplet state: photoexcitation to the S₁ state triggers C−S bond cleavage followed by recombination in the S₀ state; both these processes are essentially barrierless and thus ultrafast. The present work offers new mechanistic insights into the photoresponse of flavin‐containing blue‐light photoreceptors.     

Role of O2 + QOOH in low-temperature ignition of propane. 1. Temperature and pressure dependent rate coefficients

The kinetics of the reaction of molecular oxygen with hydroperoxyalkyl radicals have been studied theoretically. These reactions, often referred to as second O(2) addition, or O(2) + QOOH reactions, are believed to be responsible for low-temperature chain branching in hydrocarbon oxidation. The O(2) + propyl system was chosen as a model system. High-level ab initio calculations of the C(3)H(7)O(2) and C(3)H(7)O(4) potential energy surfaces are coupled with RRKM master equation methods to compute the temperature and pressure dependence of the rate coefficients. Variable reaction coordinate transition-state theory is used to characterize the barrierless transition states for the O(2) + QOOH addition reactions as well as subsequent C(3)H(6)O(3) dissociation reactions. A simple kinetic mechanism is developed to illustrate the conditions under which the second O(2) addition increases the number of radicals. The sequential reactions O(2) + QOOH → OOQOOH → OH + keto-hydroperoxide → OH + OH + oxy-radical and the corresponding formally direct (or well skipping) reaction O(2) + QOOH → OH + OH + oxy-radical increase the total number of radicals. Chain branching through this reaction is maximized in the temperature range 600-900 K for pressures between 0.1 and 10 atm. The results confirm that n-propyl is the smallest alkyl radical to exhibit the low-temperature combustion properties of larger alkyl radicals, but n-butyl is perhaps a truer combustion archetype.     

Radical-Pair Formation in Hydrocarbon (Aut)Oxidation

The reaction profiles for the uni- and bimolecular decomposition of benzyl hydroperoxide have been studied in the context of initiation reactions for the (aut)oxidation of hydrocarbons. The unimolecular dissociation of benzyl hydroperoxide was found to proceed through the formation of a hydrogen-bonded radical-pair minimum located +181 kJ mol⁻¹ above the hydroperoxide substrate and around 15 kJ mol⁻¹ below the separated radical products. The reaction of toluene with benzyl hydroperoxide proceeds such that O−O bond homolysis is coupled with a C−H bond abstraction event in a single kinetic step. The enthalpic barrier of this molecule-induced radical formation (MIRF) process is significantly lower than that of the unimolecular O−O bond cleavage. The same type of reaction is also possible in the self-reaction between two benzyl hydroperoxide molecules forming benzyloxyl and hydroxyl radical pairs along with benzaldehyde and water as co-products. In the product complexes formed in these MIRF reactions, both radicals connect to a centrally placed water molecule through hydrogen-bonding interactions.     

Explicit and implicit solvation of radical ions: the cycloreversion of CPD dimers

The electron transfer catalyzed cycloreversion of cyclobutane pyrimidine dimers is the key step in repair of light-induced DNA lesions catalyzed by the enzyme CPD photolyase. The formation of the CPD radical anion was found to be strongly solvent dependent due to a specific hydrogen bond that stabilizes the valence bound state over the dipole bound state of the additional electron. The effect of solvation on the vertical and adiabatic electron affinity of uracil and uracil dimers as well as on the mechanism of the cycloreversion of the uracil dimer radical anion is explored for three model systems that include explicit solvent molecules at the B3LYP/6-311++G^∗∗/B3LYP/6-31+G^∗ level of theory. The second solvation shell is described using the implicit C-PCM solvation model. These calculations indicate an effectively barrierless mechanism. These results are in agreement with the available experimental data for the reaction energies and isotope effects. It is also shown that a single hydrogen bond donor is a sufficient minimal model for the first solvation shell by adequately describing the stabilization of the valence bound state of the radical anion through hydrogen bonding. The relationship of these model systems with the enzymatic reaction catalyzed by DNA photolyase is also discussed.     

Screening gas-phase chemical kinetic models: Collision limit compliance and ultrafast timescales

Detailed gas-phase chemical kinetic models are widely used in combustion research, and many new mechanisms for different fuels and reacting conditions are developed each year. Recent works have highlighted the need for error checking when preparing such models, but a useful community tool to perform such analysis is missing. In this work, we present a simple online tool to screen chemical kinetic mechanisms for bimolecular reactions exceeding collision limits. The tool is implemented on a user-friendly website, cloudflame.kaust.edu.sa, and checks three different classes of bimolecular reactions; (ie, pressure independent, pressure-dependent falloff, and pressure-dependent PLOG). In addition, two other online modules are provided to check thermodynamic properties and transport parameters to help kinetic model developers determine the sources of errors for reactions that are not collision limit compliant. Furthermore, issues related to unphysically fast timescales can remain an issue even if all bimolecular reactions are within collision limits. Therefore, we also present a procedure to screen ultrafast reaction timescales using computational singular perturbation. For demonstration purposes only, three versions of the rigorously developed AramcoMech are screened for collision limit compliance and ultrafast timescales, and recommendations are made for improving the models. Larger models for biodiesel surrogates, tetrahydropyran, and gasoline surrogates are also analyzed for exemplary purposes. Numerical simulations with updated kinetic parameters are presented to show improvements in wall-clock time when resolving ultrafast timescales.     

Toluene combustion: reaction paths, thermochemical properties, and kinetic analysis for the methylphenyl radical + O2 reaction

Aromatic compounds such as toluene and xylene are major components of many fuels. Accurate kinetic mechanisms for the combustion of toluene are, however, incomplete, as they do not accurately model experimental results such as strain rates and ignition times and consistently underpredict conversion. Current kinetic mechanisms for toluene combustion neglect the reactions of the methylphenyl radicals, and we believe that this is responsible, in part, for the shortcomings of these models. We also demonstrate how methylphenyl radical formation is important in the combustion and pyrolysis of other alkyl-substituted aromatic compounds such as xylene and trimethylbenzene. We have studied the oxidation reactions of the methylphenyl radicals with O2 using computational ab initio and density functional theory methods. A detailed reaction submechanism is presented for the 2-methylphenyl radical + O2 system, with 16 intermediates and products. For each species, enthalpies of formation are calculated using the computational methods G3 and G3B3, with isodesmic work reactions used to minimize computational errors. Transition states are calculated at the G3B3 level, yielding high-pressure limit elementary rate constants as a function of temperature. For the barrierless methylphenyl + O2 and methylphenoxy + O association reactions, rate constants are determined from variational transition state theory. Multichannel, multifrequency quantum Rice-Ramsperger-Kassel (qRRK) theory, with master equation analysis for falloff, provides rate constants as a function of temperature and pressure from 800 to 2400 K and 1 x 10(-4) to 1 x 10(3) atm. Analysis of our results shows that the dominant pathways for reaction of the three isomeric methylphenyl radicals is formation of methyloxepinoxy radicals and subsequent ring opening to methyl-dioxo-hexadienyl radicals. The next most important reaction pathway involves formation of methylphenoxy radicals + O in a chain branching process. At lower temperatures, the formation of stabilized methylphenylperoxy radicals becomes significant. A further important reaction channel is available only to the 2-methylphenyl isomer, where 6-methylene-2,4-cyclohexadiene-1-one (ortho-quinone methide, o-QM) is produced via an intramolecular hydrogen transfer from the methyl group to the peroxy radical in 2-methylphenylperoxy, with subsequent loss of OH. The decomposition of o-QM to benzene + CO reveals a potentially important new pathway for the conversion of toluene to benzene during combustion. A number of the important products of toluene combustion proposed in this study are known to be precursors of polyaromatic hydrocarbons that are involved in soot formation. Reactions leading to the important unsaturated oxygenated intermediates identified in this study, and the further reactions of these intermediates, are not included in current aromatic oxidation mechanisms.     

Model of the radical addition reaction as the superposition of three potential curves

A new semiempirical model of the reaction of radical addition to molecules with multiple bonds has been developed. In the framework of this model, the transition state (TS) of the reaction X^. + Y=Z → XYZ^. is considered as the result of the intersection of the potential curve of the stretching vibration of the forming bond X-Y with the curve that is the difference between the amplitudes of stretching vibrations of the Y-Z and Y=Z bonds and the stretching vibrations are considered harmonic. The kinetic parameters describing the activation energy as a function of the enthalpy of the reaction were calculated for 34 classes of addition reactions using the new model. The factors determining the activation energy of the addition reactions are analyzed: triplet repulsion in the TS, the π electrons in the α position to the reaction center, the electronegativity of atoms of the reaction center of the TS, the steric factor, the interaction of polar groups in the TS, and the force constants of the reacting bonds. The increments characterizing the contribution of these factors to the activation energy are calculated. The model is also used to describe the energy of 12 classes of cyclization reactions and 16 classes of radical decomposition reactions. The parameters that make it possible to estimate the activation energy of the reaction from its enthalpy are calculated for these classes of reactions.     

Theoretical mechanistic study on the reaction of CN radical with HNCN

The mechanism for the reaction of the cyanogen radical (CN) with the cyanomidyl radical (HNCN) has been investigated theoretically. The electronic structure information of the singlet and triplet potential energy surfaces (PESs) is obtained at the B3LYP/6-311+G(3df,2p) level, and the single-point energies are refined at the CCSD(T)/6-311+G(3df,2p) level as well as by multilevel MCG3-MPWB method. The calculations show that the C atom of CN additions to middle- and end-N atoms of HNCN are two barrierless association processes leading to the energy-rich intermediates IM1 HN(CN)CN and IM2 HNCNCN, respectively, on the singlet PES. The higher barriers of the subsequent isomerization and dissociation channels from IM1 and IM2 indicate that these two intermediates, which have considerably thermodynamic and kinetic stability, are the dominant product at high pressure. While at low pressure, the most favorable product is P(2) H + NCNCN, which will be formed from both IM1 and IM2 via direct dissociation processes by the H-N bond rupture, and the secondary feasible product is P(4) HCN + (1) NCN, while P(5) HCCN + N(2) and P(6) HCNC + N(2) are the least competitive products. On the triplet PES, P(14) NCNC + HN may be a comparable competitive product at high temperature. In addition, the comparison between the mechanisms of the CN + HNCN and OH + HNCN reactions is made. The present results will enrich our understanding of the chemistry of the HNCN radical in combustion processes and interstellar space.     

Mechanism and kinetics of the atmospheric degradation of perfluoropolymethylisopropyl ether by OH radical: a theoretical study

In the present work, the mechanism and kinetics of the reaction of perfluoropolymethylisopropyl ether (PFPMIE) with OH radical are studied. The reaction between PFPMIE and OH radical is initiated through breaking of C–C or C–O bond of PFPMIE. These reactions lead to the formation of COF₂ molecules and alkyl radical. The pathways corresponding to the reaction between PFPMIE and OH radical have been modelled using density functional theory methods M06-2X and MPW1K with 6-31G(d,p) basis set. It is found that the C–C bond breaking reaction is most favourable than the C–O bond breaking reaction. The subsequent reactions of the alkyl radicals, formed from the C–C bond breaking reactions, are studied in detail. The rate constant for the initial oxidation reactions is calculated using canonical variational transition state theory with small curvature tunnelling corrections over the temperature range of 278–350 K. From the calculated reaction, potential energy surface and rate constant, the lifetime and global warming potential of PFPMIE are studied.     

Kinetic scheme and rate constants for methyl methacrylate synthesis occurring via the radical–coordination mechanism

Two kinetic schemes of the bulk radical–coordination polymerization of methyl methacrylate initiated by the benzoyl peroxide–ferrocene system are considered from the standpoint of formal kinetics. The most likely kinetic scheme is the one that includes the reactions characteristic of classical radical polymerization and, additionally, reactions of controlled radical polymerization proceeding via the Organometallic Mediated Radical Polymerization mechanism, a reaction generating a coordination active site, and a chain propagation reaction in the coordination sphere of the metal. The temperature dependences of the rate constants for the reactions of this kinetic scheme at temperatures typical of commercial poly(methyl methacrylate) production (313–353 K) have been determined by solving the inverse kinetic problem.     

Mechanism and regioselectivity for the reactions of propylene oxide with X(100)-2x1 surfaces (X = C, Si, Ge): a density functional cluster model investigation

We have performed density functional cluster model calculations to explore the mechanism and regioselectivity for the reactions of propylene oxide with X(100)-2x1 surfaces (X = C, Si, and Ge). The computations reveal the following: (i) the reactions on Si(100) and Ge(100) are barrierless and highly exothermic; (ii) the reactions on X(100) (X = Si and Ge) are initiated by the formation of a dative-bonded precursor state followed by regioselective cleavage of the C2-O bond (C2 directly connected to the methyl-substituent) in propylene oxide, giving rise to a five-membered ring surface species; and (iii) the reaction on C(100), although highly exothermic, requires a large activation energy and would be kinetically forbidden at room temperature.     

Barrierless Single‐Electron‐Induced cis–trans Isomerization

Lowering the activation energy of a chemical reaction is an essential part in controlling chemical reactions. By attaching a single electron, a barrierless path for the cis–trans isomerization of maleonitrile on the anionic surface is formed. The anionic activation can be applied in both reaction directions, yielding the desired isomer. We identify the microscopic mechanism that leads to the formation of the barrierless route for the electron‐induced isomerization. The generalization to other chemical reactions is discussed.     

Mechanistic and kinetic study of the O + CH2OH reaction

The mechanism for the O + CH2OH reaction was investigated by various ab initio quantum chemistry methods. For the chemical activation mechanism, that is, the addition/elimination path, the couple-cluster methods including CCSD and CCSD(T) were employed with the cc-pVXZ (X = D, T, Q, 5) basis sets. For the abstraction channels, multireference methods including CASSCF, CASPT2, and MRCISD were used with the cc-pVDZ and cc-pVTZ basis sets. It has been shown that the production of H + HCOOH is the major channel in the chemical activation mechanism. The minor channels include HCO + H2O and OH + CH2O. The hydrogen abstraction by an O atom from the CH2OH radical produces either OH + CH2O or OH + HCOH. Moreover, the two abstraction reactions are essentially barrierless processes. The rate constants for the association of O with CH2OH have been calculated using the flexible transition state theory. A weak negative temperature dependence of the rate constants is found in the range 250-1000 K. Furthermore, it is estimated that the abstraction processes also play an important role in the O + CH2OH reaction. Additionally, the falloff behavior for the OCH2OH --> H + HCOOH reaction has been investigated. The present theoretical results are compared to the experimental measurements to understand the mechanism and kinetic behavior of the O + CH2OH reaction and the unimolecular reaction of the OCH2OH radical.