Modeling the kinetics of hydrogen abstraction reactions in nitrogen-containing compounds via group additivity.

New group additivity values are presented to enable the modeling of a broad range of intermolecular hydrogen abstraction reactions involving nitrogen-containing compounds. From a dataset of 316 reaction rate coefficients calculated at the CBS-QB3 level of theory in the high-pressure limit, 76 group additivity values and 14 resonance corrections have been estimated. The influence of substituents on both the attacked hydrogen and attacking radical, being a carbon or nitrogen atom, has been investigated systematically. The new group additivity models can be applied to approximate the Arrhenius parameters of hydrogen abstraction reactions of nitrogen-containing compounds by hydrogen atoms, carbon-centered and nitrogen-centered radicals in the 300-1800 K temperature range. Complementary to the group additivity model, correlations for the tunneling coefficients, which depend on both the temperature and the activation energy of the reaction in the exothermic direction, have been generated. The good performance of the new group additivity schemes has been demonstrated using a test set of reactions. At 1000 K, the rate coefficients for all test set reactions are approximated on average within a factor of 1.45, 1.47 and 1.34, for the hydrogen abstractions with a reactive center of the type H-H-N, N-H-N and C-H-N respectively.

Modeling the thermochemistry of nitrogen-containing compounds via group additivity.

First-principles based kinetic modeling is essential to gain insight into the governing chemistry of nitrogen-containing compounds over a wide range of technologically important processes, e.g. pyrolysis, oxidation and combustion. It also enables the development of predictive, fundamental models key to improving understanding of the influence of nitrogen-containing compounds present as impurities or process additives, considering safety, operability and quality of the product streams. A prerequisite for the generation of detailed fundamental kinetic models is the availability of accurate thermodynamic properties. To address the scarcity of thermodynamic properties for nitrogen-containing compounds, a consistent set of 91 group additive values and three non-nearest-neighbor interactions has been determined from a dataset of CBS-QB3 calculations for 300 species, including 104 radicals. This dataset contains a wide range of nitrogen-containing functionalities, i.e. imine, nitrile, nitro, nitroso, nitrite, nitrate and azo functional groups. The group additivity model enables the approximation of the standard enthalpy of formation and standard entropy at 298 K as well as the standard heat capacities over a large temperature range, i.e. 300-1500 K. For a test set of 27 nitrogen-containing compounds, the group additivity model succeeds in approximating the ab initio calculated values for the standard enthalpy of formation with a MAD of 2.3 kJ mol-1. The MAD for the standard entropy and heat capacity is lower than 4 and 2 J mol-1 K-1, respectively. For a test set of 11 nitrogen-containing compounds, the MAD between experimental and group additivity approximated values for the standard enthalpy of formation amounts to 2.8 kJ mol-1.

Computational prediction of the molecular configuration of three-dimensional network polymers.

The three-dimensional arrangement of natural and synthetic network materials determines their application range. Control over the real-time incorporation of each building block and functional group is desired to regulate the macroscopic properties of the material from the molecular level onwards. Here we report an approach combining kinetic Monte Carlo and molecular dynamics simulations that chemically and physically predicts the interactions between building blocks in time and in space for the entire formation process of three-dimensional networks. This framework takes into account variations in inter- and intramolecular chemical reactivity, diffusivity, segmental compositions, branch/network point locations and defects. From the kinetic and three-dimensional structural information gathered, we construct structure-property relationships based on molecular descriptors such as pore size or dangling chain distribution and differentiate ideal from non-ideal structural elements. We validate such relationships by synthesizing organosilica, epoxy-amine and Diels-Alder networks with tailored properties and functions, further demonstrating the broad applicability of the platform.

Ab-Initio-Based Kinetic Modeling to Understand RAFT Exchange: The Case of 2-Cyano-2-Propyl Dodecyl Trithiocarbonate and Styrene.

Ab-initio-calculated rate coefficients for addition and fragmentation in reversible-addition fragmentation chain transfer (RAFT) polymerization of styrene with 2-cyano-2-propyl dodecyl trithiocarbonate initiated by azobisisobutyronitrile allow the reliable simulation of the experimentally observed conversion, number average chain length, and dispersity. The rate coefficient for addition of a macroradical Ri to the macroRAFT agent Ri X at 333 K (6.8 104 L mol-1 s-1 ) is significantly lower than to the initial RAFT agent R0 X (3.2 106 L mol-1 s-1 ), mainly due to a difference in activation energy (15.4 vs 3.0 kJ mol-1 ), which causes the dispersity to spike in the beginning of the polymerization.

Ab initio derived group additivity model for intramolecular hydrogen abstraction reactions.

A set of group additivity values for intramolecular hydrogen abstraction reactions of alkanes, alkenes and alkynes is reported. Calculating 448 reaction rate coefficients at the CBS-QB3 level of theory for 1-2 up to 1-7 hydrogen shift reactions allowed the estimation of ΔGAV° values for 270 groups. The influence of substituents on (1) the attacking radical, (2) the attacked carbon atom, and (3) the carbon chain between the attacking and attacked reactive atom has been systematically studied. Substituents have been varied between hydrogen atoms and sp3, sp2 and sp hybridized carbon atoms. It has been assumed that substituents further away from the reactive atoms or their connecting carbon chain have negligible influences on the kinetics. This group additivity model is applicable to a wide variety of reactions in the 300-1800 K temperature range. Correlations for tunneling coefficients have been generated which are complementary to the ΔGAV°'s to obtain accurate rate coefficients without the need for imaginary frequencies or electronic energies of activation. These correlations depend on the temperature and activation energy of the exothermic step. The group additivity model has been successfully applied to a test set of reactions also calculated at the CBS-QB3 level of theory. A mean absolute deviation of 1.18 to 1.71 has been achieved showing a good overall accuracy of the model.

Computational Investigation of the Aminolysis of RAFT Macromolecules.

This work presents a detailed computational study and kinetic analysis of the aminolysis of dithioates, dithiobenzoates, trithiocarbonates, xanthates, and thiocarbamates, which are frequently used as chain-transfer agents for reversible addition-fragmentation chain-transfer (RAFT) polymerization. Rate coefficients were obtained from ab initio calculations, taking into account a diffusional contribution according to the encounter pair model. A kinetic model was constructed and reveals a reaction mechanism of four elementary steps: (i) formation of a zwitterionic intermediate, (ii) formation of a complex intermediate in which an assisting amine molecule takes over the proton from the zwitterionic intermediate, (iii) breakdown of the complex into a neutral tetrahedral intermediate with release of the assisting amine molecule, and (iv) amine-assisted breakdown of the neutral intermediate to the products. Furthermore, a comparative analysis indicates that the alkanedithioates and dithiobenzoates react the fastest, followed, respectively, by xanthates and trithiocarbonates, which react almost equally fast, and dithiocarbamates, which are not reactive at typical experimentally used conditions.

Quantitative First-Principles Kinetic Modeling of the Aza-Michael Addition to Acrylates in Polar Aprotic Solvents.

This work presents a detailed computational study and kinetic analysis of the aza-Michael addition of primary and secondary amines to acrylates in an aprotic solvent. Accurate rate coefficients for all elementary steps in the various competing mechanisms are calculated using an ONIOM-based approach in which the full system is calculated with M06-2X/6-311+G(d,p) and the core system with CBS-QB3 corrected for solvation using COSMO-RS. Diffusional contributions are taken into account using the coupled encounter pair model with diffusion coefficients calculated based on molecular dynamics simulations. The calculated thermodynamic and kinetic parameters for all forward and reverse elementary reactions are fed to a microkinetic model giving excellent agreement with experimental data obtained using GC analysis. Rate analysis reveals that for primary and secondary amines, the aza-Michael addition to ethyl acrylate occurs preferentially according to a 1,2-addition mechanism, consisting of the pseudoequilibrated formation of a zwitterion followed by a rate controlling amine assisted proton transfer toward the singly substituted product. The alternative 1,4-addition becomes competitive if substituents are present on the amine or double bond of the acrylate. Primary amines react faster than secondary amines due to increased solvation of the zwitterionic intermediate and less sterically hindered proton transfer.

Insights into the Reaction Mechanism of Ethanol Conversion into Hydrocarbons on H-ZSM-5.

Ethanol dehydration to ethene is mechanistically decoupled from the production of higher hydrocarbons due to complete surface coverage by adsorbed ethanol and diethyl ether (DEE). The production of C3+ hydrocarbons was found to be unaffected by water present in the reaction mixture. Three routes for the production of C3+ hydrocarbons are identified: the dimerization of ethene to butene and two routes involving two different types of surface species categorized as aliphatic and aromatic. Evidence for the different types of species involved in the production of higher hydrocarbons is obtained via isotopic labeling, continuous flow and transient experiments complemented by UV/Vis characterization of the catalyst and ab initio microkinetic modeling.

Symmetry calculation for molecules and transition states.

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three-dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label-stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules.

Computational Study and Kinetic Analysis of the Aminolysis of Thiolactones.

The aminolysis of three differently α-substituted γ-thiolactones (C4H5OSX, X = H, NH2, and NH(CO)CH3) is modeled based on CBS-QB3 calculated free energies corrected for solvation using COSMO-RS. For the first time, quantitative kinetic and thermodynamic data are provided for the concerted path and the stepwise path over a neutral tetrahedral intermediate. These paths can take place via an unassisted, an amine-assisted, or a thiol-assisted mechanism. Amine assistance lowers the free energy barriers along both paths, while thiol assistance only lowers the formation of the neutral tetrahedral intermediate. Based on the ab initio calculated rate coefficients, a kinetic model is constructed that is able to reliably describe experimental observations for the aminolysis of N-acetyl-dl-homocysteine thiolactone with n-butylamine in THF and CHCl3. Reaction path analysis shows that for all conditions relevant for applications in polymer synthesis and postpolymer modification, an assisted stepwise mechanism is operative in which the formation of the neutral tetrahedral intermediate is rate-determining and which is mainly amine-assisted at low conversions and thiol-assisted at high conversions.

Improved Livingness and Control over Branching in RAFT Polymerization of Acrylates: Could Microflow Synthesis Make the Difference?

The superior capabilities of structured microreactors over batch reactors are demonstrated for reversible addition-fragmentation chain transfer (RAFT) solution polymerization of n-butyl acrylate with the aid of simulations, explicitly accounting for the chain length distribution of all macrospecies types. Since perfect isothermicity can be established in a microreactor, less side products due to backbiting and ß-scission are formed compared to the batch operation in which ineffective heat removal leads to an undesirable temperature spike. For a given RAFT chain transfer agent (CTA), additional microstructural control results under microflow conditions by optimizing the reaction temperature, lowering the dilution degree, or decreasing the initial molar ratio of monomer to RAFT CTA.

Group Additive Kinetics for Hydrogen Transfer Between Oxygenates.

Hydrogen abstraction reactions involving oxygenates in gaseous phase play an important role in many biomass-related conversion processes. In this work, group additivity is used to provide Arrhenius parameters in a temperature range of 300-2500 K for hydrogen abstractions between oxygenate compounds such as alcohols, ethers, esters, acids, ketones, diketones, aldehydes, hydroxyperoxides, alkyl peroxides, and unsaturated ethers and ketones. The group additive values for Arrhenius parameters of hydrogen transfer reactions of the type O--H--C and O--H--O are derived from CBS-QB3 calculations in the high-pressure limit. From a total set of 118 reactions, 43 group additivity values are determined. Inclusion of an additional 37 corrections accounting for cross-resonance effects in the transition state further improves the accuracy of the model. For a set of 25 ab initio calculated and 60 experimental rate coefficients, group additive modeling reproduces rate coefficients within a mean factor of deviation of ∼3. Hence, the developed group additive models can be reliably used for an accurate and fast prediction of the kinetics of hydrogen abstractions involving oxygenates.

Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by carbon-centered radicals.

Hydrogen abstractions are important elementary reactions in a variety of reacting media at high temperatures in which oxygenates and hydrocarbon radicals are present. Accurate kinetic data are obtained from CBS-QB3 ab initio (AI) calculations by using conventional transition-state theory within the high-pressure limit, including corrections for hindered rotation and tunneling. From the obtained results, a group-additive (GA) model is developed that allows the Arrhenius parameters and rate coefficients for abstraction of the α-hydrogen from a wide range of oxygenate compounds to be predicted at temperatures ranging from 300 to 1500 K. From a training set of 60 hydrogen abstractions from oxygenates by carbon-centered radicals, 15 GA values (ΔGAV°s) are obtained for both the forward and reverse reactions. Among them, four ΔGAV°s refer to primary contributions, and the remaining 11 ΔGAV°s refer to secondary ones. The accuracy of the model is further improved by introducing seven corrections for cross-resonance stabilization of the transition state from an additional set of 43 reactions. The determined ΔGAV°s are validated upon a test set of AI data for 17 reactions. The mean absolute deviation of the pre-exponential factors (log A) and activation energies (E(a)) for the forward reaction at 300 K are 0.238 log(m(3) mol(-1) s(-1)) and 1.5 kJ mol(-1), respectively, whereas the mean factor of deviation <ρ> between the GA-predicted and the AI-calculated rate coefficients is 1.6. In comparison with a compilation of 33 experimental rate coefficients, the <ρ> between the GA-predicted values and these experimental values is only 2.2. Hence, the constructed GA model can be reliably used in the prediction of the kinetics of α-hydrogen-abstraction reactions between a broad range of oxygenates and oxygenate radicals.

Thermodynamic study of benzene and hydrogen coadsorption on Pd(111).

Periodic density functional theory (DFT) has been used to study the coadsorption of hydrogen and benzene on Pd(111). The most stable coverages are predicted by constructing the thermodynamic phase diagram as a function of gas-phase temperature and pressure. The common approximation that neglects vibrational contributions to the surface Gibbs free energy, using the PW91 functional, is compared to the one that includes vibrational contributions. Higher coverages are predicted to be thermodynamically the most stable including vibrational frequencies, mainly due to the different entropy contributions. The first approach is also compared to the one using a (optPBE-vdW) vdW-DF functional without vibrational contributions, which predicts higher benzene coverages for benzene adsorption, and lower hydrogen coverages for hydrogen adsorption and coadsorption with a fixed benzene coverage. Inclusion of vibrational contributions using the vdW-DF method has not been implemented due to computational constraints. However, an estimate of the expected result is proposed by adding PW91 vibrational contributions to the optPBE-vdW electronic energies, and under typical hydrogenation conditions high coverages of about θH = 0.89 are expected. Inclusion of vibrational contributions to the surface Gibbs free energy and a proper description of van der Waals interaction are recommended to predict the thermodynamically most stable surface coverage.

Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by hydrogen atoms.

Hydrogen-abstraction reactions play a significant role in thermal biomass conversion processes, as well as regular gasification, pyrolysis, or combustion. In this work, a group additivity model is constructed that allows prediction of reaction rates and Arrhenius parameters of hydrogen abstractions by hydrogen atoms from alcohols, ethers, esters, peroxides, ketones, aldehydes, acids, and diketones in a broad temperature range (300-2000 K). A training set of 60 reactions was developed with rate coefficients and Arrhenius parameters calculated by the CBS-QB3 method in the high-pressure limit with tunneling corrections using Eckart tunneling coefficients. From this set of reactions, 15 group additive values were derived for the forward and the reverse reaction, 4 referring to primary and 11 to secondary contributions. The accuracy of the model is validated upon an ab initio and an experimental validation set of 19 and 21 reaction rates, respectively, showing that reaction rates can be predicted with a mean factor of deviation of 2 for the ab initio and 3 for the experimental values. Hence, this work illustrates that the developed group additive model can be reliably applied for the accurate prediction of kinetics of α-hydrogen abstractions by hydrogen atoms from a broad range of oxygenates.

Group additive values for the gas-phase standard enthalpy of formation, entropy and heat capacity of oxygenates.

A complete and consistent set of 60 Benson group additive values (GAVs) for oxygenate molecules and 97 GAVs for oxygenate radicals is provided, which allow to describe their standard enthalpies of formation, entropies and heat capacities. Approximately half of the GAVs for oxygenate molecules and the majority of the GAVs for oxygenate radicals have not been reported before. The values are derived from an extensive and accurate database of thermochemical data obtained by ab initio calculations at the CBS-QB3 level of theory for 202 molecules and 248 radicals. These compounds include saturated and unsaturated, α- and ß-branched, mono- and bifunctional oxygenates. Internal rotations were accounted for by using one-dimensional hindered rotor corrections. The accuracy of the database was further improved by adding bond additive corrections to the CBS-QB3 standard enthalpies of formation. Furthermore, 14 corrections for non-nearest-neighbor interactions (NNI) were introduced for molecules and 12 for radicals. The validity of the constructed group additive model was established by comparing the predicted values with both ab initio calculated values and experimental data for oxygenates and oxygenate radicals. The group additive method predicts standard enthalpies of formation, entropies, and heat capacities with chemical accuracy, respectively, within 4 kJ mol(-1) and 4 J mol(-1) K(-1) for both ab initio calculated and experimental values. As an alternative, the hydrogen bond increment (HBI) method developed by Lay et al. (T. H. Lay, J. W. Bozzelli, A. M. Dean, E. R. Ritter, J. Phys. Chem.- 1995, 99, 14514) was used to introduce 77 new HBI structures and to calculate their thermodynamic parameters (Δ(f)H°, S°, C(p)°). The GAVs reported in this work can be reliably used for the prediction of thermochemical data for large oxygenate compounds, combining rapid prediction with wide-ranging application.

Kinetics of homolytic substitutions by hydrogen atoms at thiols and sulfides.

Thermodynamic and kinetic data in the temperature range 300-1500 K are calculated for 94 homolytic substitution reactions by a hydrogen atom at thiols and sulfides with the CBS-QB3//BMK/6-311G(2d,d,p) method. The studied reactions were found to proceed according to a one-step mechanism. A group additivity (GA) method is presented to model the Arrhenius parameters of this reaction family. The required GA values were derived from data obtained for a set containing 58 reactions. By using the developed GA scheme, rate coefficients at 300 K for 26 substitution reactions by the hydrogen atom are reproduced within a factor of 2.2. Mean absolute deviations on the activation energy and pre-exponential factor are limited to 1.1 kJ mol(-1) and 0.19, respectively. Rate coefficients for the reverse reactions, that is, substitution reactions by C- and S-centered radicals with expulsion of a hydrogen atom, are reproduced within a factor of 6 by using thermodynamic consistency. At 1000 K, group additive and calculated rate coefficients for the forward and reverse reactions agree within a factor of 1.8 and 4, respectively. Experimental rate coefficients in the temperature range 300-400 K are reproduced within a factor of 5. Discrepancies between calculated and experimental data are discussed.

Kinetic modeling of hydrogen abstractions involving sulfur radicals.

One of the requisites for the development of detailed reaction networks is the availability of accurate kinetic data. Group additivity based models linking the Arrhenius parameters to structural characteristics of the transition state have proven to be a valuable tool to obtain those data. In this work, group additivity values are presented to allow a broad range of CH and SH hydrogen abstraction reactions by S radicals to be modeled. Rate coefficients in the temperature range from 300 to 1500 K are obtained by using the CBS-QB3 method in the high-pressure limit and are corrected for tunneling and anharmonicity of rotation about the transitional bond. A total of 149 reactions are studied. From these reactions, a total of 52 group additivity values and 35 resonance corrections are derived. The general applicability of the group additivity method is demonstrated for a test set containing 25 reactions. At 300 K, rate coefficients are on average reproduced within a factor of 2.8. The mean absolute deviations on the Arrhenius parameters are 2 kJ mol(-1) for the activation energy and 0.38 for log A in which A is the pre-exponential factor.

Benzene adsorption on binary Pt3M alloys and surface alloys: a DFT study.

Benzene adsorption on Pt3M/Pt(111) surfaces and Pt3M(111) bulk alloys (M = Fe, Co, Ni, Cu, Pd, Ag, Au) is analyzed using density functional theory calculations on 4-layered slabs in the framework of catalyst development for aromatics hydrogenation. Segregation in the top layers was allowed for, accounting for the actual stoichiometric composition of the top layers rather than using simplified 'skin' or 'sandwich' structures. On the surfaces that do not segregate (M = Pd, Ag, Au), the preferred benzene adsorption site is the hollow Pt3-hcp(0) site. On antisegregated "Pt-skin" surfaces (M = Fe, Co, Ni, Cu, Pd), which have a top layer composed entirely of Pt, benzene prefers bridge sites with a maximized number of solute atoms M in the subsurface layers. Benzene adsorption is weaker than on pure Pt(111), by 0.1-0.5 eV on the surface alloys and by 0.6-1.0 eV on bulk alloys, except for Pt3Pd alloys, which behave similarly to pure Pt. On the fully segregated Pt3Ag and Pt3Au alloys, which have a Ag resp. Au monolayer on top, only physisorption occurs. Benzene adsorption does not change the segregation state of the catalyst. From various DOS-based catalyst descriptors, the occupied d-band center of the clean catalyst slab shows the best correlation with benzene adsorption energies, allowing the prediction of benzene adsorption energies on a range of other Pt-based bimetallic alloys.

Kinetics of α hydrogen abstractions from thiols, sulfides and thiocarbonyl compounds.

Hydrogen abstraction reactions involving organosulfur compounds play an important role in many industrial, biological and atmospheric processes. Despite their chemical relevance, little is known about their kinetics. In this work a group additivity model is developed that allows predicting the Arrhenius parameters for abstraction reactions of α hydrogen atoms from thiols, alkyl sulfides, alkyl disulfides and thiocarbonyl compounds by carbon-centered radicals at temperatures ranging from 300 to 1500 K. Rate coefficients for 102 hydrogen abstractions were obtained using conventional transition state theory within the high-pressure limit. Electronic barriers were calculated using the CBS-QB3 method and the rate coefficients were corrected for tunneling and hindered rotation about the transitional bond. Group additivity values for 46 groups are determined. To account for resonance and hyperconjugative stabilization in the transition state, 8 resonance corrections were fitted to a set of 32 reactions. The developed group additivity scheme was validated using a test set containing an additional 30 reactions. The group additivity scheme succeeds in reproducing the rate coefficients on average within a factor of 2.4 at 300 K and 1.4 at 1000 K. Mean absolute deviations of the Arrhenius parameters amount to, respectively, 2.5 kJ mol(-1) for E(a) and 0.13 for log A, both at 300 and 1000 K. This work hence illustrates that the recently developed group additivity methods for Arrhenius parameters extrapolate successfully to hetero-element containing compounds.