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The crosspropagation of 1-ethylcyclopentyl methacrylate (ECPMA) and methyl methacrylate (MMA) has been studied using a combination of quantum chemistry calculations and experiment. Our computational work utilizes a trimer-to-tetramer reaction model, coupled with an ONIOM (B3LYP/6-31G(2df,p): B3LYP/6-31G(d)) method for geometry optimization and an M06-2X/6-311+G(2df,p) method plus SMD solvation model for single point energy calculations. The results show several trends: the identity of the ultimate unit of a trimer radical affects not only the preferred conformation of the region where the reaction takes place, but also the reactivity of the radical; the addition of an ECPMA monomer to the radicals is generally favored compared to an MMA monomer; the pen-penultimate unit of a trimer radical shows a nonnegligible entropic effect; the penultimate unit effect is implicit for the ECPMA-MMA copolymer system. Finally, terminal model reactivity ratios fitted based on the explicit rate coefficients calculated from the quantum chemical results are compared with those from experimental measurements. The computations not only agree qualitatively with experimentally derived results in terms of the selectivity of ECPMA-MMA crosspropagation, but also give reasonable quantitative predictions of reactivity ratios. [ABSTRACT FROM AUTHOR]

Sodium ions, one of the natural inorganic constituents in lignocellulosic biomass, significantly alter pyrolysis behavior and resulting chemical speciation. Here, experiments were conducted using a micropyrolyzer to investigate the catalytic effects of NaCl on fast pyrolysis of glucose-based carbohydrates (glucose, cellobiose, maltohexaose, and cellulose), and on a major product of cellulose pyrolysis, levoglucosan (LVG). A mechanistic model that addressed the significant catalytic effects of NaCl on the product distribution was developed. The model incorporated interactions of Na+ with cellulosic chains and low molecular weight species, reactions mediated by Na+ including dehydration, cyclic/Grob fragmentation, ring-opening/closing, isomerization, and char formation, and a degradation network of LVG in the presence of Na+. Rate coefficients of elementary steps were specified based on Arrhenius parameters. The mechanistic model for cellulose included 768 reactions of 222 species, which included 252 reactions of 150 species comprising the mechanistic model of glucose decomposition in the presence of NaCl. © 2015 American Institute of Chemical Engineers AIChE J, 62: 766-777, 2016 [ABSTRACT FROM AUTHOR]

This study aimed at investigating the performance of a series of basis sets, density functional theory (DFT) functionals, and the IEF-PCM solvation model in the accurate calculation of ¹H and 13C NMR chemical shifts in toluene-d8. We demonstrated that, on a test set of 37 organic species with various functional moieties, linear scaling significantly improved the calculated shifts and was necessary to obtain more accurate results. Inclusion of a solvation model produced larger deviations from the experimental data as compared to the gas-phase calculations. Moreover, we did not find any evidence that very large basis sets were necessary to reproduce the experimental NMR data. Ultimately, we recommend the use of the BMK functional. For the 1H shifts the use of the 6-311G(d) basis set gave linearly scaled mean unsigned (MU) and root-mean-square (rms) errors of 0.15 ppm and 0.21 ppm, respectively. For the calculation of the 13C chemical shifts the 6-31G(d) basis set produced MUE of 1.82 ppm and RMSE of 3.29 ppm. [ABSTRACT FROM AUTHOR]

A variety of quantum mechanical (QM) methods, basis sets and solute cavity descriptions using the conductor-like polarisable continuum model for the modelling of reaction free energies in solution have been evaluated and compared. In order to test the performance of each QM level of theory and cavity model, five common types of organic reactions in different solvents have been considered. The study shows that the hybrid metageneralised-gradient approximation M05-2X functional, in conjunction with the MG3S basis set and UA0 or universal force field cavities, produces results in the best overall agreement with experimental data. In addition, within the UA0 formalism, explicit cavities should be built on the hydrogen atoms that undergo transformation during chemical reaction. [ABSTRACT FROM AUTHOR]

Abstract: A detailed mechanistic model for polystyrene pyrolysis was created that built on a modeling framework developed in our previous work and was used to probe three competing pathways to dimer formation: benzyl radical addition, 1,3-hydrogen shift, and 7,3-hydrogen shift, based on recent literature reports. To incorporate the chemistry involved in the 7,3-hydrogen shift pathway, the 1,7- and 7,3-hydrogen shift reaction families were added to the model. The updated version of the model tracks 75 species and over 3500 reactions. Rate parameters for all families were specified based on our previous work, more recent literature reports, and regression against limited experimental data. The model was able to accurately predict the experimental results for polystyrene pyrolysis for different reactor configurations for a temperature range of 100°C and two orders of magnitude of initial molecular weight for experimental data collected in our own lab and from Bouster and coworkers and Bockhorn and coworkers. The results from our model were studied using net rate analysis to gain insight into the competitiveness of the various reaction pathways to dimer formation. The net rate analysis demonstrated that 7,3-hydrogen shift is the dominant reaction pathway to dimer formation at the temperatures studied. Benzyl radical addition becomes a more competitive reaction pathway as the temperature increases, which is caused predominantly by an increase in the benzyl radical concentration with increasing temperature. Overall, it is quantitatively shown that both 7,3-hydrogen shift and benzyl radical addition are important pathways for dimer formation, with their relative competitiveness influenced by temperature. [Copyright &y& Elsevier]

Describes the general elements of kinetic modeling of complex reaction networks. Use of quantum chemistry as a computational method to uncover details of species and reactions that are part of a complex reaction network; Information on the calculation of thermodynamic properties from quantum chemistry; Concept behind the transition state theory.

An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism. [ABSTRACT FROM AUTHOR]

Abstract: The steric effects of a metal-organic framework (MOF) on the enantioselectivity of a (salen)Mn were studied using classical atomistic modeling. Rotational energy profiles for the approach of 2,2-dimethyl-2H-chromene to the active site of (salen)Mn were mapped for the homogeneous catalyst and the catalyst immobilized as a linker in a MOF. The model corroborated that the Re enantioface is favored by the homogeneous catalyst. It was shown that the predicted enantioselectivity when chromene approaches the more accessible (salen)Mn in the MOF is highly sensitive to the distance between the (salen)Mn linkers of the interpenetrated frameworks. Calculated rotational energy profiles for a hypothetical non-interpenetrated MOF revealed that this MOF catalyst should exhibit enantioselectivity intermediate to the interpenetrated MOF and the homogeneous catalyst. Finally, the continuous chirality measure of the catalyst was found to correlate well with the energy of the homogeneous catalyst–reactant complex, suggesting that high chirality content is related to high enantioselectivity. This correlation, however, did not apply for some of the MOF catalysts. For heterogeneous catalysts, the mechanism of asymmetric induction depends on the steric environment in addition to the chirality of the catalyst. [Copyright &y& Elsevier]

Thin films (~115 μm thick) of milled wood lignin from hybrid poplar and acid-washed hybrid poplar were pyrolyzed at 500 °C and ~55 °C/s at five pressures (4, 250, 500, 750, and 1000 mbar) to determine the impact of secondary liquid intermediate reactions on the product distribution. For both milled wood lignin extracted from poplar and acid-washed hybrid poplar wood, pressure had a significant effect on the product distribution for thin film pyrolysis between 4 and 1000 mbar. For lignin, lowering the pressure from 1000 mbar to 4 mbar reduced the char yield from 36 to 23% and enhanced production of large cluster pyrolytic lignin. However, the pressure did not dramatically impact the gas yield (CO2, CO, methane, H2, ethane, propane, and butane), nor did it significantly impact the release of monomeric phenolic compounds. ICR-MS shows limited changes in the composition of lignin oligomers. The increase in the production of large lignin oligomers observed by UV fluorescence and the reduction of char yield with vacuum confirm the importance of oligomeric combination reactions to form large polyaromatic structures in the liquid intermediate. For hybrid poplar, lowering the pressure from 1000 mbar to 4 mbar decreased the char yield from 19 to 7% and enhanced production of heavy sugars (cellobiosan and cellotriosan). ICR-MS results clearly show the importance of dehydration reactions in the liquid intermediate. Lowering the pressure also enhanced production of CO, CO2, and methane due to heterogeneous catalysis by residual alkali and alkaline earth metals in the solid wood matrix. However, it also decreased production of levoglucosan from 10 to 6.1 wt %. The yields of levoglucosan and cellobiosan obtained for hybrid poplar were higher and lower, respectively, compared with those expected if the pyrolysis products were the result of the additive contribution of hybrid poplar constituents. This result could be explained by the tendency of lignin liquid intermediate to bubble vigorously, contributing in this way to the removal of cellulose oligomers from the liquid intermediate. [ABSTRACT FROM AUTHOR]

Advances in computational modeling tools have allowed for the construction of detailed chemical models of oxidation processes to enhance the understanding of mechanisms and answer questions of interest in diverse fields such as DNA damage, lubricant oxidation, food chemistry, and art conservation. The construction of detailed kinetic models is facilitated by the use of kinetic correlations, such as Evans-Polanyi relationships, where the activation energy, EA, is related linearly to the heat of reaction, ΔHR: EA = E0 + α ΔHR. In this work, we present an Evans-Polanyi relationship based on properties determined from hybrid G4 quantum chemical calculations for an epoxidation reaction of peroxy species. We explore a broader chemical space at a higher level of theory than previous reports, and as a result, the importance of several key structural features, such as alkylhydroperoxy functional groups, that can strongly influence the trends observed was revealed. We suggest a subdivision of the reaction family into separate Evans-Polanyi relationships to accurately capture EA values quantitatively. We also quantified the impact of local unsaturation during the epoxidation reaction, demonstrating that it raises the energy barrier by 6.6 kcal/mol on average when compared to that of an alkyl radical counterpart. [ABSTRACT FROM AUTHOR]

Epoxide ring-opening is a key reaction in organic chemistry. We have previously shown that B(C 6 F 5) 3 , a strongly Lewis acidic arylborane, exhibited high rates and unusual selectivities for catalyzing the ring-opening of aliphatic epoxides with alcohols. Here we compare catalysts of the form B(C 6 H 5−X F X) 3 (x = 5, 4, 3, and 0) and determine that moderately Lewis acidic arylboranes have higher regioselectivity, but slower rates in this reaction. At high temperatures, these arylboranes can also hydrolyze into inactive species. However, deactivation is suppressed in the presence of co-catalytic amounts of 1,2-propanediol, and DFT calculations suggest a role for arylborane-H 2 O-diol complexes. Thermal stabilization and regioselectivity enhancement by diol are both more pronounced for B(C 6 F 5) 3 than for less Lewis acidic B(C 6 HF 4) 3 and B(C 6 H 2 F 3) 3 catalysts. These results further demonstrate the catalytic relevance of H-bound networks of arylboranes and diols and enable their use at higher temperatures and greatly increased rates. [Display omitted] • Arylborane catalysts hydrolyze above 90 oC, which decreases rates and selectivity in epoxide ring-opening. • Co-catalytic glycol stabilizes the catalyst against hydrolytic decomposition for > 1 h, while also increasing selectivity. • Glycol-mediated stabilization is higher for more Lewis acidic catalysts such as tris(pentafluorophenyl)borane. [ABSTRACT FROM AUTHOR]

Abstract: Experimental results in the literature show that two metal-organic frameworks (MOFs) containing copper and cobalt nodes are active for hydroperoxide decomposition, which is an important reaction in auto-oxidation processes. Density functional theory (DFT) calculations reported here for these systems suggest that the metal sites in the interior of these MOFs are not the active sites for this type of reaction due to the steric effects of the adjacent linkers. This implies that the experimental catalysis observed may occur on the exterior surface of the MOF crystals. Additional calculations with a copper paddlewheel node show that, despite being able to form complexes with hydroperoxides, the metal sites in copper paddlewheels do not catalyze hydroperoxide decomposition. Preliminary calculations involving undercoordinated metal atoms as a model for metal sites on the MOF exterior crystal surface suggest that these sites could be catalytically active. [Copyright &y& Elsevier]

Abstract: The binary degradation of polystyrene (PS) and polypropylene (PP) was modeled at the mechanistic level by combining the individual component models developed in previous modeling work [T.M. Kruse, O.S. Woo, H.-W. Wong, S.S. Khan, L.J. Broadbelt, Macromolecules 35 (2002) 7830; T.M. Kruse, H.-W. Wong, L.J. Broadbelt, Macromolecules 36 (2003) 9594] and adding interactions between PS- and PP-derived species. The full binary model developed for the pyrolysis of PS/PP mixtures consisted of over 37,000 reactions and tracked 277 species. Within the binary model, interactions between polymeric species of different polymer types were not allowed since PS and PP are immiscible. However, a fraction of low molecular weight radicals (LMWR) of each polymer type was allowed to diffuse into the other polymer type. This was the only adjustable parameter in the model. Based on experimental data for a 50/50wt% PS/PP mixture at 380°C, we found that allowing 0.037% of the LMWR derived from PS to diffuse into PP captured the enhancement of nearly a factor of four in the PP degradation rate that was observed experimentally at these conditions. To increase the enhancement in the PP degradation rate, solid-state shear pulverization (SSSP) and changes in the PS/PP weight ratio were used to manipulate the interfacial area between PS and PP during binary pyrolysis (no premixing was performed during the conventional binary experiments). Using SSSP to blend PS and PP resulted in a 25% increase in the enhancement in the PP degradation rate compared to no premixing. In order to model this enhancement, the fraction of low molecular weight PS radicals that could diffuse into PP was increased to 0.10%. [Copyright &y& Elsevier]