Computational Kinetics of Hydroperoxybutylperoxy Isomerizations and Decompositions: A Study of the Effect of Hydrogen Bonding.

Hydroperoxyalkylperoxy (OOQOOH) radicals are important intermediates in combustion chemistry. The conventional isomerization of OOQOOH radicals to form ketohydroperoxides has been long believed to be the most important chain branching reaction under the low-temperature combustion conditions. In this work, the kinetics of competing pathways (alternative isomerization, concerted elimination, and H-exchange pathways) to the conventional isomerization of different ß-, γ- and Δ-OOQOOH butane isomers are investigated. Six- and seven-membered ring conventional isomerizations are found to be the dominant pathways, whereas alternative isomerizations are more important than conventional isomerization, when the latter proceeded via a more strained transition state ring. The oxygen atoms in OOQOOH radicals introduce intramolecular hydrogen bonding (HB) that significantly affects the energies of reacting species and transition states, ultimately influencing chemical kinetics. Conceptually, HB has a dual effect on the stability of chemical species, the first being the stabilizing effect of the actual intramolecular HB force, and the second being the destabilizing effect of ring strain imposed by the HB conformer. The overall effect can be quantified by determining the difference between the minimum energy conformers of a chemical species or transition state that have HB and that do not have HB (non-hydrogen bonding (NHB)). The stabilization effect of HB on the species and transition sates is assessed, and its effect on the calculated rate constants is also considered. Our results show that, for most species and transition states, HB stabilizes their energies by as much as 2.5 kcal/mol. However, NHB conformers are found to be more stable by up to 2.7 kcal/mol for a few of the considered species. To study the effect of HB on rate constants, reactions are categorized into two groups ( groups one and two) based on the structural similarity of the minimum energy conformers of the reactant and transition state, for a particular reaction. For cases where the reactant and transition state conformers are similar (i.e., both HB or NHB structures), group one, the effect of HB on reaction kinetics is major only if the magnitudes of the stabilization energy of the reactant and transition state are quite different. Meanwhile, for group two, where the reactant and transition state prefer different conformers (one HB and the other NHB), HB affects the kinetics when the stabilization energy of the reactant or transition state is significant or the entropy effect is important. This information is useful in determining corrections accounting for HB effects when assigning rate parameters for chemical reactions using estimation and/or analogy, where analogies usually result in inaccuracies when modeling atmospheric and combustion processes.

High-Pressure Limit Rate Rules for α-H Isomerization of Hydroperoxyalkylperoxy Radicals.

Hydroperoxyalkylperoxy (OOQOOH) radical isomerization is an important low-temperature chain branching reaction within the mechanism of hydrocarbon oxidation. This isomerization may proceed via the migration of the α-hydrogen to the hydroperoxide group. In this work, a combination of high level composite methods-CBS-QB3, G3, and G4-is used to determine the high-pressure-limit rate parameters for the title reaction. Rate rules for H-migration reactions proceeding through 5-, 6-, 7-, and 8-membered ring transitions states are determined. Migrations from primary, secondary and tertiary carbon sites to the peroxy group are considered. Chirality is also investigated by considering two diastereomers for reactants and transition states with two chiral centers. This is important since chirality may influence the energy barrier of the reaction as well as the rotational energy barriers of hindered rotors in chemical species and transition states. The effect of chirality and hydrogen bonding interactions in the investigated energies and rate constants is studied. The results show that while the energy difference between two diastereomers ranges from 0.1-3.2 kcal/mol, chirality hardly affects the kinetics, except at low temperatures (atmospheric conditions) or when two chiral centers are present in the reactant. Regarding the effect of the H-migration ring size, it is found that in most cases, the 1,5 and 1,6 H-migration reactions have similar rates at low temperatures (below ∼830 K) since the 1,6 H-migration proceeds via a cyclohexane-like transition state similar to that of the 1,5 H-migration.

Hydroxyalkoxy radicals: importance of intramolecular hydrogen bonding on chain branching reactions in the combustion and atmospheric decomposition of hydrocarbons.

During both the atmospheric oxidation and combustion of volatile organic compounds, sequential addition of oxygen can lead to compounds that contain multiple hydrogen-bonding sites. The presence of two or more of these sites on a hydrocarbon introduces the possibility of intramolecular H-bonding, which can have a stabilizing effect on the reactants, products, and transition states of subsequent reactions. The present work compares the absolute energies of two sets of conformations, those that contain intramolecular H-bonds and those that lack intramolecular H-bonds, for each reactant, product, and transition state species in the 1,2 through 1,7 H-migrations and Cα-Cß, Cα-H, and Cα-OH-bond scission reactions in the n-hydroxyeth-1-oxy through n-hydroxyhex-1-oxy radicals, for n ranging from 1 to 6. The difference in energy between the two conformations represents the balance between the stabilizing effects of H-bonds and the steric cost of bringing the two H-bonding sites together. The effect of intramolecular H-bonding and the OH group is assessed by comparing the net intramolecular H-bond stabilization energies, the reaction enthalpies, and barrier heights of the n-hydroxyalkoxy radical reactions with the corresponding alkoxy radicals values. The results suggest that there is a complex dependence on the location of the two H-bonding groups, the location of the abstraction or bond scission, and the shape of the transition state that dictates the extent to which intramolecular H-bonding effects the relative importance of H-migration and bond scission reactions for each n-hydroxyalkoxy radical. These findings have important implications for future studies on hydrocarbons with multiple H-bonding sites.

Computational study of the combustion and atmospheric decomposition of 2-methylfuran.

There is a growing interest in alkylfurans as potential biofuels. Recent work has highlighted the need for further study of the atmospheric oxidation mechanism of 2-methylfuran (2MF). This study utilizes the high level composite computational methods, G4 and CBS-QB3, to determine the bond dissociation energies for the C-H bond in 2MF and the reaction enthalpies and barrier heights of several of the known possible initiation reaction pathways. This study also investigates the possible subsequent low temperature reaction pathways following the addition of OH and then O2 onto the 2MF ring. The placement of the OH and O2 on the ring, either cis or trans to each other, dictates the viability of subsequent reactions. Of particular interest is the observation that 1,4 H-migrations that abstract the hydrogen bound to the same carbon as the OH have abnormally low barrier height. This dramatic decrease puts the reaction barrier lower than concerted eliminations and 6-membered ring Waddington-type reactions. In addition, a novel reaction type, described as a Waddington concerted elimination, is reported herein. This reaction, when viable, is generally more favorable than other reactions. The results presented here are of interest to combustion modelers and atmospheric chemists, particularly those working on aromatic hydrocarbons and systems with conjugated double bonds.

Hydrogen migrations in alkylcycloalkyl radicals: implications for chain-branching reactions in fuels.

A thorough understanding of the oxidation chemistry of cycloalkanes is integral to the development of alternative fuels and improving current fuel performance. An important class of reactions essential to this chemistry is the hydrogen migration; however, they have largely been omitted from the literature for cycloalkanes. The present work investigates all of the hydrogen migration reactions available to methylcyclopentane, ethylcyclopentane, methylcyclohexane, and ethylcyclohexane. The kinetic and thermodynamic parameters have been studied by a combination of computational methods and compared to their corresponding n-alkyl and methylalkyl counterparts to determine the effect that the cycloalkane ring has on these reactions. In particular, although the alkylcycloalkyl activation energies for the dominant 1,4, 1,5, and 1,6 H-migration are higher than in n-alkyl and methylalkyl radicals, because several of the rotors needed to form the transition state are locked into place as part of the cycloalkane ring, the A-factors are higher for the alkylcycloalkyl reactions, making the rates closer to the noncyclic systems, at higher temperatures. The results presented here suggest that the relative importance of each H-migration pathway differs from the trends predicted by either the n-alkyl or methylalkyl radical systems. Of particular interest is the observation that since the barrier height of the 1,4 H-migration is only 3-5 kcal mol(-1) higher than the 1,5 H-migration in the methyl and ethylcycloalkyl radicals, compared to a difference of roughly 7 kcal mol(-1) in similar reactions for both the n-alkyl and methylalkyl radicals, the 1,4 H-migrations in alkylcycloalkyl radicals will be more important in the overall mechanism than would be predicted based on the n-alkyl and methylalkyl radicals. These results have important combustion model implications, particularly for fuels with high cycloalkane content.

Ab initio study of chain branching reactions involving second generation products in hydrocarbon combustion mechanisms.

sec-Alkyl radicals are key reactive intermediates in the hydrocarbon combustion and atmospheric decomposition mechanisms that are formed by the abstraction of hydrogen from an alkane, or as a second generation product of n-alkyl H-migrations, C-C bond scissions in branched alkyl radicals, or the bimolecular reaction between olefins and n-alkyl radicals. Since alkanes and branched alkanes, which the sec-alkyl radicals are derived from, make up roughly 40-50% of traditional fuels an understanding of their chemistry is essential to improving combustion systems. The present work investigates all H-migration reactions initiated from an sec-alkyl radical that involve the movement of a secondary hydrogen, for the 2-butyl through 4-octyl radicals, using the CBS-Q, G2, and G4 composite methods. The resulting thermodynamic and kinetic parameters are compared to similar reactions in n-alkyl radicals in order to determine underlying trends. Particular attention is paid to the effect of cis/trans and 1,3-diaxial interactions on activation energies and rate coefficients. When combined with our previous work on n-alkyl radical H-migrations, a complete picture of H-migrations in unbranched alkyl radicals is obtained. This full data set suggests that the directionality of the remaining branched chains has a minimal effect on the rate coefficients for all but the largest viable transition states, which is in stark contrast to the differences predicted by the structurally similar dimethylcycloalkanes. In fact the initial location of the secondary radical site has a greater effect on the rate than does the directionality of the remaining alkyl chains. The activation energies for secondary to secondary reactions are much closer to those of the secondary to primary H-migrations. However, the rate coefficients are found to be closer to the corresponding primary to primary reaction values. A significant ramification of these results is that there will be multiple viable reaction pathways for these reactions instead of only one dominant pathway as previously believed.

Reactivity trends within alkoxy radical reactions responsible for chain branching.

Alkoxy radicals are a key component in both the atmospheric and combustion oxidation pathways of traditional and alternative fuels. An accurate description of their chemistry as it alters with reaction conditions is essential to understanding atmospheric and combustion processes involving hydrocarbons. Experimental and theoretical data on alkoxy radicals and their reactions are scarce, especially for larger chain systems and high temperatures. The present work investigates all unimolecular reactions of the methoxy through heptoxy radicals using the CBS-Q, G2, and G4 composite computational methods. After analysis of the resulting thermodynamic and kinetic parameters, discussions about the relative importance of each reaction group and their effects on chain branching in the oxidation reaction pathways of hydrocarbons are presented. These results are then compared to similar processes in alkyl and alkylperoxy radicals. Where discrepancies are found among these three radical systems, discussions about possible causes are presented. Of particular interest is the observation that 1,6 H-migration reactions are not the dominant pathway in alkoxy radicals, as they are in both alkyl and alkylperoxy radicals, at low temperatures. However, these H-migrations are expected to play a larger role in reaction mechanisms than previously believed, particularly at atmospherically relevant temperatures. This will lead to greater diversity in the intermediate and end product species, which will in turn add complexity to other atmospheric processes, such as aerosol formation and tropospheric ozone production. The current work significantly extends the range of alkoxy radicals that are relevant to models for new fuel systems. Based on the results of this study, recommendations regarding the selection of model systems for future studies are presented.

Ab initio study of key branching reactions in biodiesel and Fischer-Tropsch fuels.

Many biologically and Fischer-Tropsch synthesized fuels contain branched alkanes which, during their combustion and atmospheric oxidation mechanism, produce methylalkyl radicals. As a result, an accurate description of the chemistry of these species is essential to integrating these fuels into our energy systems. Even though branched alkanes make up roughly one-third of the compounds in gasoline and diesel fuels, both experimental and theoretical data on methylalkyl radicals and their reactions are scarce, especially for larger chain systems and combustion conditions. The present work investigates all the hydrogen migration reactions available to the n-methylprop-1-yl through n-methylhept-1-yl radicals, for n = 2-6, using the CBS-Q, G2, and G4 composite computational methods, over a wide temperature range. The resulting thermodynamic and kinetic parameters are used to determine the effect that the presence of the methyl group has on these important unimolecular, chain branching reactions, for the reactions involving not only a tertiary abstraction site but also all the primary and secondary sites. The activation energies of hydrogen migration reactions with the methyl group, either within or immediately outside the ring, are found to be roughly 0.8-1.6 kcal mol(-1) lower in energy than expected on the basis of analogous reactions in n-alkyl radicals. An important implication of this result is that the current method of using rate parameters derived from n-alkyl radicals to predict the chain branching characteristics of methylated alkyl radicals significantly underpredicts the importance of these reactions in atmospheric and combustion processes. Discussion of a possible cause for this phenomenon and its effect on the overall combustion mechanism of branched hydrocarbons is presented. Of particular concern is that 2,2,4,4,6,8,8-heptamethylnonane, which is currently used to model branched alkanes in diesel fuel surrogates, is predicted to have a much lower activation energy, by as much as 3 kcal mol(-1), for the dominant, 1,5 H-migration reactions than for the same reaction in many of the less branched alkanes that it is meant to represent. Also, counter to the currently accepted theory, the 3-methylalk-1-yl radical 1,4 and 1,5 H-migrations involving the movement of a secondary hydrogen are found to have higher rate coefficients than the corresponding reactions involving a tertiary hydrogen. The results presented here have significant implications for future experimental, computational, and combustion modeling studies.

Ab initio study of hydrogen migration across n-alkyl radicals.

A thorough ab initio investigation is conducted on all possible hydrogen migration pathways for the 1-ethyl, 1-propyl, 1-butyl, 1-pentyl, 1-hexyl, 1-heptyl, and 1-octyl radicals in order to determine underlying trends in reaction enthalpies, activation energies, Arrhenius A-factors, tunneling, and rate coefficients. The G4, G2, and CBS-Q composite methods are used to determine the enthalpy of reaction and activation energy barrier for each reaction. Each method shows excellent agreement with eight experimental enthalpy of reaction values, with root mean squared values of 0.8, 0.9, and 0.6 kcal mol(-1) for CBS-Q, G2, and G4, respectively. Differences in barrier heights, A-factors, tunneling, and rate coefficients are observed for axial and equatorial arrangements as well as between secondary hydrogen migration sites, depending on the location of the secondary site relative to the terminal carbon. The validity of using cycloalkane model systems to estimate rate parameters is also assessed. The failure of two key assumptions inherent to the cycloalkane models, resulting in a breakdown in the accuracy of these methods for larger transition states, is discussed. This study has significant ramifications for future theoretical, experimental, and modeling studies involving the decomposition of n-alkanes.

Ab initio study of hydrogen migration in 1-alkylperoxy radicals.

Alkylperoxy and hydroperoxyalkyl radicals are key reactive intermediates in hydrocarbon oxidation mechanisms. An understanding of the interconversion of these two species via a hydrogen migration reaction is of fundamental importance to the prediction of chain branching reactions and end product composition. An extensive ab initio investigation of the hydrogen migration reaction in 1-ethyl, 1-propyl, 1-butyl, 1-pentyl, and 1-hexylperoxy radicals is conducted to assess the validity of using cycloalkanes to model the ring strain of their transition states as well as the effect of both location of the migrating hydrogen and directionality of the remaining alkyl chain in the transition state of the reaction involving a secondary hydrogen. The G2 and CBS-Q composite methods are used to determine the activation energy and enthalpy of reaction relative to the alkylperoxy radical. Both methods show good agreement with five experimentally determined reaction enthalpies, having root mean squared deviations of 0.7 and 1.3 kcal mol(-1) for the CBS-Q and G2 methods, respectively. The effect of hydrogen abstraction site and transition state geometry, particularly axial and equatorial geometries of the remaining alkyl chain, on the activation energy, Arrhenius A-factor, tunneling, and rate coefficient are discussed. Differences between terminal adjacent and nonterminal adjacent secondary sites result in small but consistent differences in barrier height. Failure of key assumptions within the cycloalkane based estimation method leads to the break down in the accuracy for both small and large transition states. For large transition states, the breakdown of these assumptions also results in the failure of the current cycloalkane method as a conceptual model. Of great interest is the observed alteration in the preferred H-migration from the 1,5 to the 1,6 H-migration within the temperature region where these reactions are particularly important to the combustion mechanism.

Primary steps in the reaction of OH radicals with peptide systems: perspective from a study of model amides.

This study reports on an ab initio investigation into the effects of radical attack on peptide backbones using eight model amides. The eight model amides are divided into two subcategories, formamide and acetamide. Within each subcategory, there are four unique systems which include the parent, cis and trans methyl, and the dimethyl structures. The mechanism for hydrogen abstraction shows alpha-C abstraction is kinetically and thermodynamically favorable for all formamide systems. The addition of a methyl group on the nitrogen results in a secondary competitive pathway at the gamma-C site. In the parent acetamide, beta-abstraction is preferred. The addition of a methyl group on the amino group of acetamide results in the introduction of a secondary pathway that will outcompete beta-abstraction, both thermodynamically and kinetically. For all systems, H-abstraction off the nitrogen is the least preferred path. With the addition of a methyl group on the nitrogen, H-abstraction off the nitrogen becomes more favorable. To explain site preference, geometry structures and stabilizations are examined. The results of this study have implications for future studies on radical attack of peptide and protein systems.

Effects of increasing acidity on metal(loid) bioprecipitation in groundwater: column studies.

Large-scale column experiments were carried out over a period of 545 days to assess the effect of increasing acidity on bacterial denitrification, sulfate reduction, and metal(loid) bioprecipitation in groundwater affected by acid mine drainage. At a groundwater pH of 5.5, denitrification and Cu2+ removal, probably via malachite (Cu2(OH)2CO3) precipitation, were observed in the ethanol-amended column. Sulfate reduction, sulfide production, and Zn2+ removal were also observed, with Zn2+ removal observed in the zone of sulfate reduction, indicating likely precipitation as sphalerite (ZnS). Se6+ removal was also observed in the sulfate reducing zone, probably as direct bioreduction to elemental selenium via ethanol/acetate oxidation or sulfide oxidation precipitating elemental sulfur. A step decrease in groundwater pH from 5.5 to 4.25 resulted in increased denitrification and sulfate reduction half-lives, migration of both these redox zones along the ethanol-amended column, and the formation of an elevated Cu2+ plume. Additionally, an elevated Zn2+ plume formed in the previous sulfate reducing zone of the ethanol-amended column, suggesting dissolution of precipitated sphalerite as a result of the reduction in groundwater pH. As Cu2+ passed through the zone of sphalerite dissolution, SEM imaging and EDS detection suggested that Cu2+ removal had occurred via chalcocite (Cu2S) or covellite (CuS) precipitation.

Modeling of microbial dynamics and geochemical changes in a metal bioprecipitation experiment.

A biogeochemical transport modeling study was carried out to analyze large-scale laboratory column experiments in which ethanol was used as an electron donor to create favorable conditions for the immobilization of selected trace metals (Zn and Cu) in groundwater. Microbial activity was explicitly simulated to capture the dynamic changes of the redox zonation within the column (i) in the early phase of the experiment (microbial lag) and (ii) in response to a significant decrease in the pH of the feed solution introduced after 188 days. The simulated redox dynamics agreed well with the observations after the pH-dependency of microbial growth was incorporated into the microbial model. The study showed that residual minerals may have buffered the pH for a period after the pH of the feed solution was decreased. Where the buffering capacity was exhausted, the pH decreased, leading to a successive downstream movement of the redox boundaries. The simulations reproduced the Zn immobilization within the sulfate-reducing zone as well as its partial remobilization after this zone moved further downstream. The immobilization of Cu within the denitrifying zone could also be well explained by incorporating malachite (Cu2(OH)2CO3) precipitation in the simulations.