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Porous aluminosilicates such as zeolites are ubiquitous catalysts for the production of high-value and industrially relevant commodity chemicals, including the conversion of hydrocarbons, amines, alcohols, and others. Bimolecular reactions are an important subclass of reactions that can occur on Brønsted acid sites of a zeolite catalyst. Kinetic modeling of these systems at the process scale requires the interaction energetics of reactants and the active sites to be described accurately. It is generally known that adsorption is a coverage-dependent phenomenon, with lower heats of adsorption observed for molecules at higher coverage. However, few studies have systematically investigated the coadsorption of molecules on a single active site, specifically focusing on the strength of interaction of the second adsorbate after the initial adsorption step. In this work, we quantify the unimolecular and bimolecular adsorption energies of varying adsorbates, including paraffins, olefins, alcohols, amines, and noncondensible gases in the acidic and siliceous ZSM-5 frameworks. As a special case, olefin adsorption was examined for physisorption and chemisorption regimes, characterized by π-complex, framework alkoxide and carbenium ion adsorption, respectively. The effects of functional groups and molecular size were quantified, and correlations that relate the adsorption of the second adsorbate identity to that of the first adsorbate are provided.

Pyrolysis of polyolefins has been proposed as a potential resource recovery strategy by converting macromolecules into valuable fuels and chemicals. Due to variations in possible backbone structures, chain-length distributions, and arrangements of pendant groups, their decomposition behavior via pyrolysis can be complex. In the present work, a review of historical data and empirical models for two distinct polyolefins, polyethylene (PE) and polypropylene (PP), is provided followed by a comparison to recent mechanistic models. The characteristic sigmoidal behavior of linear polymer decomposition is captured with global, lumped-species, and mechanistic models of high-density polyethylene. The PE model was extended to simulate PP using the same reaction families and reaction family parameters, but with distinct rate coefficients that accounted for the difference in the structure of PP with its pendant methyl groups compared to PE as manifested through heats of reaction embedded in the Evans–Polanyi relationship, Ea= E0 + γ×ΔHreacn. The change in structure and its associated kinetic parameters resulted in no sigmoidal conversion, consistent with experimental reports for atactic PP. This suggests that mechanistic modeling could be an important complement to global model studies to understand when other effects are at play in the pyrolytic decomposition of polymers such as PP.

Sourcing polymers from biobased materials is desirable for a transition to a more sustainable world. However, finding new monomers sourced from biobased molecules requires extensive experimental ef...

The microkinetic modelling methodology that we developed previously to describe Bronsted acid-catalyzed propene oligomerization on medium-pore MFI zeolites has been extended successfully to large-pore Beta zeolites. The extension of the model was supported by the identification of the key descriptors that account for the different topologies and acid strengths of the zeolite frameworks (physisorption enthalpies, stabilization enthalpies, frequency factors). The model is validated with experimental conversion and selectivity data measured in a plug-flow reactor on a commercial Beta zeolite over a range of operating conditions. Analysis of net reaction rates allowed identifying the preferred pathways that increase oligomerization selectivity toward C9 species with increasing propene pressure. The model was additionally used to investigate how the stabilization enthalpies of chemisorbed intermediates, an important catalyst descriptor, influenced the selectivity and surface coverage at iso-conversion. This analysis provides mechanistic insights into the propene oligomerization reaction network and its dependence on zeolite topology, and demonstrates how microkinetic models can describe catalyst behaviour and aid in catalyst and process optimization.

Lignin liquefaction microkinetics is a move toward a more first-principles (i.e., ab initio)-based understanding at the molecular level in reaction engineering. While the microkinetic modeling of r...

Density functional theory (DFT) calculations, experimental data, and microkinetic modeling are used to extend a triple-pathway (Lewis acid, water-mediated, and alcohol-mediated) mechanism for tris(...

Epoxide alcoholysis is extensively employed in the synthesis of polymers and chemical intermediates, and it generally requires an acid catalyst for high rates and selectivity. Tris(pentafluoropheny...

In a noncontact catalytic system, intermediaries derived from Au-catalyzed cyclooctene epoxidation effects ethylbenzene oxidation., Traditionally, a catalyst functions by direct interaction with reactants. In a new noncontact catalytic system (NCCS), an intermediate produced by one catalytic reaction serves as an intermediary to enable an independent reaction to proceed. An example is the selective oxidation of ethylbenzene, which could not occur in the presence of either solubilized Au nanoclusters or cyclooctene, but proceeded readily when both were present simultaneously. The Au-initiated selective epoxidation of cyclooctene generated cyclooctenyl peroxy and oxy radicals that served as intermediaries to initiate the ethylbenzene oxidation. This combined system effectively extended the catalytic effect of Au. The reaction mechanism was supported by reaction kinetics and spin trap experiments. NCCS enables parallel reactions to proceed without the constraints of stoichiometric relationships, offering new degrees of freedom in industrial hydrocarbon co-oxidation processes.

A nonconventional, water-mediated catalytic mechanism was proposed to explain the effects of residual water on the reactivity and regioselectivity of tris(pentafluorophenyl)borane catalyst in the ring-opening reaction of 1,2-epoxyoctane by 2-propanol. This nonconventional mechanism was proposed to operate in parallel with conventional Lewis acid-catalyzed ring-opening. Microkinetic modeling was conducted to validate the proposed reaction mechanism, with all kinetic and thermodynamic parameters derived from density functional theory (DFT) calculations. Experimental data at a variety of temperatures and water contents were captured by the model after adjustments within reasonable limits set by experimental benchmarking and accuracy of theory of a small subset of parameters. In addition, the microkinetic model was able to generate accurate predictions at reaction conditions that were not used for parameter estimation. Detailed analysis of the net reaction rates showed that >95% of the reaction flux passed th...

The construction of mechanistic models for the autoxidation of fatty acid or ester substrates found in oil paint binders is a challenging undertaking due to the complexity of the large crosslinked species that form, and the small molecules that volatilize. Building models that capture this product diversity are made possible by automating the process of network generation. This work presents a microkinetic model for the autoxidation of ethyl linoleate catalyzed by cobalt(II) 2-ethyl hexanoate. The mechanism size was controlled by using a rate-based criterion to include the most kinetically relevant reactions from among the millions of possible reactions generated. The resulting model was solved and compared to experimental metrics. Quantities such as hexanal production and the consumption of unsaturated moieties were in good agreement with experiment. Finally, the model was used to explore the effect of the catalyst concentration and temperature on key measurables.

Small gold nanoparticles (AuNPs) have recently shown potential to act as a catalyst for oxidation reactions mediated by free radicals, with their role postulated to be facilitating hydrogen abstraction by gold superoxo species and/or activation of hydroperoxides. Cyclooctene oxidation using molecular oxygen as the oxidant at 373 K showed high selectivity to the epoxide product, cyclooctene oxide, with either tert-butyl hydroperoxide as an initiator or in the presence of small AuNPs (5–8 atoms). While previous studies have investigated the mechanism leading to high epoxide selectivity using density functional theory, a full microkinetic model was developed in this work using automated network generation to determine the relative contributions of elementary reactions and the role of AuNPs. A cycle of radical addition of peroxy and alkoxy radicals with subsequent epoxidation reactions can justify the observed activity and selectivity to epoxide at multiple temperatures and initiator concentrations. The alcoh...

Lignocellulosic biomass is a promising feedstock for renewable fuels and chemical intermediates; in particular, lignin attracts attention for its favorable chemical composition. One obstacle to lignin utilization and valorization is the unknown chemical mechanism that gives rise to the complex product distributions observed upon deconstruction. Among possible deconstruction chemistries, fast pyrolysis is promising due to its short residence time, thus enabling high-volume production. However, the chemistry is inherently complex, thereby hampering the creation of detailed kinetic models describing pathways to specific low molecular products. To this end, we created a detailed kinetic model of lignin decomposition via pyrolysis comprised of 4313 reactions and 1615 species based on pathways suggested by pyrolysis of model compounds in the literature. Using a rule-based reaction network generation approach, a pathways-level reaction network is proposed to predict the evolution of macromolecular species and th...

Hemicellulose is one of the major components of lignocellulosic biomass, which is an abundant source of renewable carbon on the Earth and has potential for the production of renewable drop-in transportation fuels and multiple commodity chemicals. In this work, a structure for hemicellulose extracted from corn stover was proposed to capture the experimentally characterized structural properties. A mechanistic model for hemicellulose pyrolysis was constructed based on the reaction family approach that we used for cellulose pyrolysis before. The model described the decomposition of hemicellulose chains, reactions of intermediates, and formation of a range of low molecular weight products (LMWPs) at the mechanistic level and specified rate constants for all the reactions in the network. Overall, 504 reactions of 114 species were included in the mechanistic model for fast pyrolysis of extracted hemicellulose. The mechanistic model closely matched experimental yields of various products with mass yield ≥1 wt%. Modeling results show that both the degree of polymerization and the polydispersity index of hemicellulose have an insignificant effect on the pyrolysis product distribution. Then, the mechanistic model of extracted hemicellulose is further extended to simulate the fast pyrolysis of native hemicellulose. Comparison of the model results showed that fast pyrolysis of native hemicellulose from corn stalk yielded more char, gaseous species, acetol, and much more acetic acid than that of extracted hemicellulose from corn stover, while yielding less 1,2-anhydroxylopyranose, 1,2;3,4-dianhydroxylopyranose and glycolaldehyde.

The mechanisms responsible for the production of small volatile aldehydes during low temperature condensed phase oxidation have been the subject of extensive research, and many pathways have been proposed in the literature. However, many of these mechanisms have yet to be explored quantitatively in the context of a kinetic model. A variety of mechanistic postulates for the formation of the volatile species hexanal, such as direct β-scission of alkoxy radicals, Korcek-like decomposition reactions, intramolecular hydrogen shifts, intramolecular reactions of allylic peroxy species, and scission reactions of higher order oligomeric species, were assembled, and quantum chemical calculations were performed where necessary to obtain estimates of kinetic parameters to test each reaction’s kinetic relevance in a microkinetic model for the oxidation of a cobalt-catalyzed ethyl linoleate system. Under atmospheric conditions, scission of chain ends from dimeric species was the largest contributor of hexanal, with an ...

Light alkene oligomerization on heterogeneous acidic catalysts is widely and successfully used in current commercial processes. However, ethylene oligomerization remains inefficient due to ethylene’s inability to form reaction intermediates to a sufficient extent on acid sites. Adding Ni(II) on solid acids can more efficiently catalyze ethylene oligomerization and selectively produce butenes to fuel range products. The review proposes a complete and detailed mechanism of heterogenous Ni-catalyzed oligomerization, whose structures are supported by combining various studies throughout recent literature, and focuses on the bifunctional effects of the nickel and acid sites on ethylene oligomerization. Using experiments, first-principles calculations, and kinetic modeling, Ni2+ has been shown to selectively oligomerize ethylene to light, linear alkenes via the Cossee-Arlman mechanism, while Bronsted H+ sites catalyze further alkylation, cracking, and isomerization reactions. The effects of reaction conditions and catalyst properties on selectivity and activity for oligomerization are systematically discussed. Tuning the relative nickel-to-acid site ratio and the framework support can allow for an optimal catalyst design directed towards desirable products.

The modeling of the molecular weight distribution of polymers is critical in polymerization modeling. Moment-based models and kinetic Monte Carlo are two methods used to calculate the number and weight average molecular weight during simulation of polymerization. While these two methods are commonly considered to yield equivalent results in the molecular weight distribution, we show that there can be significant differences between these two methods when copolymerization of multiple monomers is modeled. In particular, clear differences in results exist for low molecular weight polymers where the molar mass of one monomer is two or more times greater than the others. Detailed analysis is provided for the cause of the difference, and we demonstrate the importance of tracking the exact number of each type of monomer in every polymer chain when calculating the moments of molecular weight.

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 wit...

The economic viability of the biofuel industry has been plagued in part by the incomplete valorization of lignin, which is currently being burned for process heat. One of the roadblocks to effectively converting lignin into usable fuels and chemicals is that the structure of lignin has yet to be entirely understood owing to its polydispersity, complexity, and hyper-branched topology. Libraries of structural representations of lignin accounting for these facets have recently been proposed for wheatstraw, an herbaceous biomass, based on a stochastic generation method that creates lignin molecules that collectively conform to properties measured experimentally. We have extended this stochastic method to accommodate more complexity and any type of biomass, i.e., softwood, hardwood, or herbaceous. The unique mechanistic details for several of the new lignin bond types are essential in deciding rules for bond formation in the algorithm. Further, we present two successful methods of decreasing the degrees of fre...

The homogeneous partial oxidation of 1,3-propanediol using oxygen at relatively mild conditions (430 K) has been observed to result in high selectivity to acrolein at low to moderate conversion with minor formation of formaldehyde and acetaldehyde (Diaz, E. ChemSusChem 2010, 3, 1063−1070, DOI: 10.1002/cssc.201000142). In this work, various competing mechanistic postulates for the selective conversion of 1,3-propanediol to acrolein were tested quantitatively using mechanistic modeling. Specifically, mechanisms based on free-radical chemistry and concerted pathways, both of which have been postulated in the literature, were evaluated. Automated mechanism generation was used to comprehensively create detailed reaction mechanisms based on reaction families relevant to free-radical or concerted chemistries. A mechanism based on free-radical reactions alone was unable to account for the rate of conversion and high selectivity to acrolein that were observed experimentally. Concerted pathways based on both unimol...

Current methods for processing lignocellulosic biomass fail to take full advantage of the phenolic chemicals available in lignin, the third most common polymer on the planet. The complexity of the lignin polymer structure, the lack of knowledge of the mechanisms by which it breaks down, and the difficulties in predicting and controlling the reaction product distribution make improvement in processing methods challenging. The use of model compounds, which contain only a few key features of the native polymer, allow the reactivity of the overall polymer to be investigated more simply by isolating key elements. In our previous work, we examined the mechanism of acidolysis for two α-O-4 lignin model compounds, benzylphenyl ether (BPE) and 1-(phenoxyethyl)benzene (PEB). In the present work, we examine the rate-limiting step of this mechanism, a nucleophilic attack on the α-carbon commensurate with protonation of the ether oxygen, for other α-O-4 model compounds that contain features more reminiscent of native ...

Fast pyrolysis is a promising thermochemical technology that breaks down renewable and abundant lignocellulosic biomass into a primary liquid product (bio-oil) in seconds. The bio-oil can then be potentially catalytically upgraded into transportation fuels and multiple commodity chemicals. Hemicellulose is one of the three major components of lignocellulosic biomass and is characterized as a group of cell wall polysaccharides that are neither cellulose nor pectin. The composition and structural features of hemicellulose (mixture of different heterogeneous polysaccharides) and different specific hemicellulose polysaccharides are reviewed. Particular focus is then given to reviewing the status of hemicellulose pyrolysis in terms of experimental investigations, reaction mechanisms, and kinetic modeling. For each aspect, recent results, challenges, and future prospects are addressed.

Efforts to derive value-added chemicals from lignin are hindered in part because of its great structural complexity and heterogeneity. Lignin is a polydisperse, random copolymer with varying proportions of monomers and interunit linkage types, forming a hyperbranched topology. Structural models comprising a single macromolecular representation have been proposed for specific biomass sources; these representations, although consistent with experimental observations, are not unique. Alternative models consisting of populations of representations whose average properties match experiment have also been proposed. Expanding on this latter approach, we have developed a stochastic method of generating libraries of diverse and complex structural representations of lignin that is generally applicable to any biomass source. For demonstration purposes, the method is applied to create libraries of wheat straw lignin, a representative herbaceous lignin. The libraries are statistically validated through the χ2 goodness...

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.

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

A mechanistic model considering the significant catalytic effects of Na+ on fast pyrolysis of glucose-based carbohydrates was developed in Part 1 of this study. A computational framework based on continuous distribution kinetics and mass action kinetics was constructed to solve the mechanistic model. Agreement between model yields of various pyrolysis products with experimental data from fast pyrolysis of glucose-based carbohydrates dosed with NaCl ranging from 0–0.34 mmol/g at 500 °C validated the model and demonstrated the robustness and extendibility of the mechanistic model. The model was able to capture the yields of major and minor products as well as their trends across NaCl concentrations. Modeling results showed that Na+ accelerated the rate of decomposition and reduced the time for complete thermoconversion of carbohydrates. The sharp reduction in the yield of levoglucosan (LVG) from fast pyrolysis of cellulose in the presence of NaCl was mainly caused by reduced decomposition of cellulose chains via end-chain initiation and depropagation due to Na+ favoring competing dehydration reactions. Analysis of the contributions of reaction pathways showed that the decomposition of LVG made a minor contribution to its yield reduction and contributed less than 0.5% to the final yield of glycolaldehyde from fast pyrolysis of glucose-based carbohydrates in the presence of NaCl. © 2015 American Institute of Chemical Engineers AIChE J, 62: 778–791, 2016

The glass transition temperature (Tg) of a polystyrene (PS) nanolayer is shown to be strongly tuned by the presence of neighboring immiscible polymer layers over a 100 °C range spanning temperatures above and below the bulk PS Tg. Fluorescence spectroscopy is used to measure the glass transition temperature (Tg) of the ultrathin dye-labeled PS layers at specific regions within multilayer films of immiscible polymers. The Tg of a 14-nm-thick PS layer is 45 °C atop poly(n-butyl methacrylate) and 144 °C atop poly(4-vinyl pyridine). Additionally, the Tg of an 11- to 14-nm thick PS layer is shown to be the same as that reported by a near-infinitely-dilute PS blend component [Evans and Torkelson Macromolecules 2012, 45, 8319] with the same neighboring polymer, which indicates a common physical origin of Tg perturbations in both systems. The magnitude of Tg-confinement effects depends not only on the Tg of the neighboring domain but is also strongly correlated with neighboring domain fragility, a fundamental property of glass formers which provides a link between medium-range structural order and dynamics.

Kinetic Monte Carlo (KMC) has become a well-established technique for simulating the kinetics of free radical polymerization, both to generate polymer molecular weight distributions and, more recently, to track the explicit monomer sequence in every chain. However, KMC simulations require a minimal number of molecules in order to accurately describe monomer conversion and macromolecular quantities, which can render them computationally prohibitive. In this work, we propose a novel approach for accelerating KMC simulations through scaling relationships that allow the number of molecules simulated to be reduced. Using the concept of the minimal number of molecules and an explicit expression we derived for copolymerization, we propose a factor that is used to scale the reaction rate constants which results in an acceleration of KMC simulations by a factor of ∼100. Furthermore, we demonstrate the limits of this scaling approach, revealing the absolute lower bound for the number of molecules used in KMC simula...

Lignocellulosic biomass offers a vast, renewable resource for the sustainable production of fuels and chemicals. To date, a commonly employed approach to depolymerize the polysaccharides in plant cell walls employs mineral acids, and upgrading strategies for the resulting sugars are under intense development. Although the behavior of cellulose and hemicellulose is reasonably well characterized, a more thorough understanding of lignin depolymerization mechanisms in acid environments is necessary to predict the fate of lignin under such conditions and ultimately to potentially make lignin a viable feedstock. To this end, dilute acid hydrolysis experiments were performed on two lignin model compounds containing the α-O-4 ether linkage at two temperatures concomitant with dilute acid pretreatment. Both primary and secondary products were tracked over time, giving insight into the reaction kinetics. The only difference between the two model compounds was the presence or absence of a methyl group on the α-carbo...

Historical models for cellulose pyrolysis and mathematical approaches to kinetic analysis are reviewed with the objective of identifying the correct global chemical kinetic models and parameters for cellulose pyrolysis. In most recent experiments, cellulose pyrolysis clearly has sigmoidal reaction character, which is consistent with one of a sequential, nucleation–growth, or random-scission global model. The apparent activation energy of ∼47 kcal/mol is consistent with mechanistic modeling if one allows catalytic acceleration of the concerted initiation reaction. There is a possibility that part of the sigmoidal character is due to adsorption effects at low pyrolysis temperatures, but further work is required to resolve this issue. Reasons are given for why fitting data at a single heating rate to a first-order reaction model gives incorrect results.

Density functional theory (DFT) calculations were used to study the mechanism of CO2 hydrolysis by Co-(1,4,7,10-tetrazacyclododecane), also referred to as cobalt-cyclen, and evaluate the associated thermodynamic and kinetic parameters. A microkinetic model was then built based on the kinetics and thermodynamics derived from first principles. The intrinsic reaction rate constant was calculated to be 10572 M−1 s−1, three times larger than that of zinc-cyclen. The high activity was ascribed to a very large pKa value of 13.3. The monodentate structure of a key intermediate along the reaction coordinate, [Cyclen-Co-HCO3]+, was more stable than the bidentate isomer, due to a hydrogen bond formed between bicarbonate and the ligand. The reaction rate constant decreased significantly over 0–12 ms, which was attributed to the fast decrease of the concentration of the catalytic form, Co OH−. The conversion of CO2 at 1000 ms as a function of pH was calculated to compare the relative activity of zinc-cyclen and cobalt-cyclen, and zinc-cyclen was found to be a much better catalyst. Through calculating the ratio of the net rate to the forward rate of each elementary reaction, the rate-limiting step of the catalytic cycle was identified as the adsorption of CO2, which was the same as that for zinc-cyclen, though the product-releasing step was regarded as more difficult in cobalt-cyclen, compared to zinc-cyclen.

Fluorinated Fe-porphyrins, especially [tetrakis(pentafluorophenyl)porphyrinato]iron(III) chloride (tetrakis(pentafluorophenyl)porphyrinato = TPFPP) (TPFPP)FeCl (Fepor-2a), were found to be highly efficient for catalyzing the double epoxidation of divinylbenzene (DVB) to divinylbenzene dioxide (DVBDO), a novel component of epoxy resin formulation. The electronic properties of the catalysts are highly dependent on the substituents on the phenyl groups of these metalloporphyrins. The electron-rich fluorinated Fe-porphyrins are more selective toward epoxidation but are more vulnerable toward decomposition in H2O2. On the other hand, the electron deficient Fe-porphyrins are more stable, yet more Lewis acidic, which facilitates the formation of byproducts such as epoxide ring opening and overoxidation.

Motivation: The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may exceed 1 million compounds. To alleviate this limitation, we report two methods—SimIndex (SI) and SimZyme—which use chemical similarity of 2D chemical fingerprints to efficiently navigate large metabolic networks and propose enzymatic connections between the constituent nodes. We also report a Byers–Waterman type pathway search algorithm for further paring down pertinent networks. Results: Benchmarking tests run with SI show it can reduce the number of nodes visited in searching a putative network by 100-fold with a computational time improvement of up to 105-fold. Subsequent Byers–Waterman search application further reduces the number of nodes searched by up to 100-fold, while SimZyme demonstrates ∼90% accuracy in matching query substrates with enzymes. Using these modules, we have designed and annotated an alternative to the methylerythritol phosphate pathway to produce isopentenyl pyrophosphate with more favorable thermodynamics than the native pathway. These algorithms will have a significant impact on our ability to use large metabolic networks that lack annotation of promiscuous reactions. Availability and implementation: Python files will be available for download at http://tyolab.northwestern.edu/tools/. Contact: k-tyo@northwestern.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Biomass pyrolysis is a promising technology for the production of renewable fuels and chemicals from nonfood biomass. Given the potential of pyrolysis as a viable, cost-effective biomass deconstruction method, there is active interest in understanding the chemical transformations at the heart of the technology. It has long been known that the presence of alkali- and alkaline-earth-metal ions in biomass, such as Na+, significantly alters product yields of biomass pyrolysis, but the mechanism behind this effect has not been elucidated. In this work, we employ density functional theory (DFT) to reveal the stereoelectronic basis of the effect of sodium ions on several key glucose thermal decomposition reactions, such as the formation of levoglucosan and 5-hydroxymethylfurfural (5-HMF). β-d-Glucose is of interest for pyrolysis, as it is the monomer of cellulose and a key intermediate in cellulose pyrolysis. α-d-Glucose is included in this study, as the two anomers can readily interconvert under pyrolysis condi...

In this work, we carried out a comprehensive density functional theory (DFT) study on the basis of a trimer-to-tetramer radical reaction model to assess a cost-effective approach to perform the calculation of kinetic and thermodynamic properties of methyl methacrylate (MMA) free-radical homopolymerization. By comparing results from several different functionals (PBE, M06-2X, wB97XD, KMLYP, and MPW1B95), in conjunction with a series of basis sets (6-31G(d,p), 6-31+G(d,p), 6-31G(2df,p), 6-311G(d,p), 6-311+G(d,p), 6-311+G(2df,p), 6-311+G(2df,2p)), we show that calculations using M06-2X/6-311+G(2df,p)//B3LYP/6-31G(2df,p) provide an activation energy of 5.25 kcal mol(-1) for the homopropagation step, which is within 1 kcal mol(-1) of the experimental value. However, this method predicts a heat of polymerization of 17.37 kcal mol(-1) that is larger than the experimental value by 3.5 kcal mol(-1). MPW1B95/6-311+G(2df,p) on the B3LYP/6-31G(2df,p) geometries produces a heat of polymerization value within 1 kcal mol(-1) of experimental data, yet overestimates the activation energy by 3 kcal mol(-1). In addition, we evaluated the performance of ONIOM MO:MO calculations on the geometry optimization of species comprising our MMA polymerization model and found that ONIOM(B3LYP/6-31G(2df,p):B3LYP/6-31G(d)) is capable of producing geometries in very good agreement with the full B3LYP/6-31G(2df,p) calculations. Subsequent calculations of energies using M06-2X/6-311+G(2df,p) based on the ONIOM geometries provided an activation energy value comparable to that based on the full B3LYP/6-31G(2df,p) geometries.

It is challenging to track explicit copolymer sequences and related measures using continuum kinetic models. We developed a generalized framework based on kinetic Monte Carlo (KMC) to model free radical polymerization of any number of monomers to obtain the explicit sequence and its distribution. The KMC framework was applied to copolymerization of butyl acrylate/methyl methacrylate (BA/MMA) and methyl acrylate/methyl methacrylate (MA/MMA), and the simulation output was compared with experimental results. Sequence characteristics that were not accessible via experiments were then predicted. Explicit monomer sequence information was used to construct operating diagrams to design a representative copolymer recipe with a specific sequence target as a function of molecular weight and monomer conversion.

Fast pyrolysis of lignocellulosic biomass, utilizing moderate temperatures ranging from 400 to 600 °C, produces a primary liquid product (pyrolytic bio-oil), which is potentially compatible with existing petroleum-based infrastructure and can be catalytically upgraded to fuels and chemicals. In this work, experiments were conducted with a micropyrolyzer coupled to a gas chromatography–mass spectrometry/flame ionization detector system to investigate fast pyrolysis of neat cellulose and other glucose-based carbohydrates. A detailed mechanistic model building on our previous work was developed for fast pyrolysis of neat glucose-based carbohydrates by integrating updated findings obtained through experiments and theoretical calculations. The model described the decomposition of cellulosic polymer chains, reactions of intermediates, and formation of a range of low molecular weight compounds at the mechanistic level and specified each elementary reaction step in terms of Arrhenius parameters. The mechanistic m...

A computational framework based on continuous distribution kinetics was constructed to solve the mechanistic model that was developed for fast pyrolysis of glucose-based carbohydrates in the first part of this study [Zhou et al. Ind. Eng. Chem. Res. 2014, 53. DOI 10.1021/ie502259w]. Comparing modeling results with experimental yields from fast pyrolysis over a wide range of reaction conditions validates the model. Agreement between model yields of final pyrolysis products with experimental data of fast pyrolysis of cellulose at temperatures ranging from 400 to 600 °C and maltohexaose, cellobiose, and glucose at 500 °C showed that the mechanistic model was robust and extendable. In comparison to our previous model [Vinu, R.; Broadbelt, L. J. Energy Environ. Sci. 2012, 5, 9808–9826], the mechanistic model presented in this work incorporating new findings from experiments and theoretical calculations showed enhanced performance in capturing experimental yields of major products such as levoglucosan-pyranose,...

As biomass pyrolysis is a promising technology for producing renewable fuels, mechanistic descriptions of biomass thermal decomposition are of increasing interest. While previous studies have demonstrated that glucose is a key primary intermediate and have elucidated many important elementary mechanisms in its pyrolysis, key questions remain. For example, there are several proposed mechanisms for evolution of an important product and platform chemical, 5-hydroxymethylfurfural (5-HMF), but evaluation with different methodologies has hindered comparison. We evaluated a host of elementary mechanisms using a consistent quantum mechanics (QM) level of theory and reveal a mechanistic understanding of this important pyrolysis pathway. We also describe a novel route as a target for catalyst design, as it holds the promise of a more selective pathway to 5-HMF from glucose. We further demonstrate the effect of conformational and structural isomerization on dehydration reactivity. Additionally, we combined QM and ex...

The three-point model and molecular simulation are used to understand the enantioselective adsorption of a homologous series of chiral compounds on a common chiral selector that is incorporated on a solid surface. We demonstrate how the enantioselectivity of homologous chiral compounds may go down, go up, remain the same, or even reverse. Conditions that lead to consistent enantioselectivity for homologous chiral compounds are also proposed.

Pyrolysis is a promising thermochemical technique to convert polymers such as waste plastics and lignocellulosic biomass to liquid products that are valuable either directly as or are potentially upgraded to liquid fuels and fine chemical intermediates. Mechanistically, polymer pyrolysis involves a complex set of free radical, concerted, and/or ionic reactions that occur via numerous competing pathways. Engineering these pathways to produce the required molecules warrant a thorough understanding of kinetics of the reactions under different conditions. In this critical review, after emphasizing the need for resource and energy recovery from polymers, the elementary reactions involved in the pyrolysis of polyolefins to various products are discussed along with an elucidation of detailed kinetic modeling. The reactions involved in oxidative pyrolysis of polymers are also discussed with polystyrene autoxidation as an example case. The influence of catalysts such as zeolites in altering the product distribution from pyrolysis of synthetic polymers is discussed. As lignocellulosic biomass is more complex in structure compared to synthetic polymers, the challenges and methodology involved in modeling the degradation of its basic constituents, viz. cellulose, hemicellulose, and lignin, to various organics are discussed. After elucidating the influence of various concerted reactions involved in cellulose pyrolysis on product yields, the effect of catalysts on biomass fast pyrolysis and bio-oil upgradation are discussed. The review concludes with a note on advantages of copyrolysis of synthetic polymers and biomass to enhance the quality of bio-oil that can be easily converted to biofuel with minimal upgradation.

Experiments and microkinetic modeling were used to investigate the reaction mechanism of cis-cyclooctene oxidation with H2O2 on heterogeneous manganese 1,4,7-trimethyl-1,4,7-triazacyclononane (Mn–tmtacn) catalysts. A mechanism based on literature reports and model discrimination was identified that captured experimental data well, including data at reaction conditions that were not used for parameter estimation. H2O2 activation on the heterogeneous catalytic complex was identified as the rate-determining step (RDS), and a simple analytical rate expression was derived using the RDS and the pseudo-steady-state approximation for all intermediates. Predicted reaction orders for cis-cyclooctene, water, H2O2, catalyst, and diol and epoxide products are also consistent with experimental observations and can be rationalized according to the derived rate expression. In addition, the ratio of productive to unproductive H2O2 use is analyzed, and catalyst deactivation is found to be an important step in the reaction mechanism that is highly sensitive to temperature.

The mechanism of the NOx reduction reaction on BaNaY zeolite using acetic acid/acetate as a reductant has been explored using density functional theory. The elementary steps, the reaction intermediates, and the transition states were identified on a zeolite cluster consisting of 10 tetrahedral atoms (10T). The hydrogen abstraction reaction of acetic acid/acetate was identified as the rate-determining elementary step at 473 K. The long-range electrostatic effect of the lattice on the rate-determining step was studied on expanded 24T, 30T, 34T, 40T, 44T, and 50T zeolite clusters. It was found that while acetate may be greatly stabilized on the expanded clusters with additional Na+ cations and Al atoms, the stabilization of acetic acid is much less affected by the long-range lattice effect. The reaction barrier of the hydrogen abstraction reaction, on the other hand, is less sensitive to the long-range lattice effect. The results of this paper highlight the importance of long-range electrostatic effects on t...

Conventional continuum mechanistic models for polymer degradation typically involve thousands of coupled differential-algebraic equations, requiring an efficient solver to solve the complex set of stiff model equations. This can be overcome by formulating the problem in terms of a stochastic simulation procedure, requiring only iterative operations to solve the model. The present work describes the detailed mechanistic modeling of pyrolysis of poly(styrene peroxide) (PSP) using kinetic Monte Carlo (KMC) simulation to predict the product yields and gain a better understanding of the product evolution pathways. The traditionally accepted mechanism of PSP pyrolysis proposed by Mayo and Miller, which involves the key reaction steps of peroxide bond fission, alkoxy radical recombination and disproportionation, and end chain β-scission, was initially tested using the KMC model to predict the peroxide concentration profile and the product yields. This model was only qualitatively able to predict the major products, benzaldehyde and formaldehyde, while the formation of minor products like α-hydroxy acetophenone, phenyl glycol, and phenyl glyoxal was not captured at all. Hence, a new mechanism that also incorporated hydrogen abstraction and β-scission was proposed and implemented in KMC. The final model tracked 949 reactions of 83 species. The rate coefficients for all the reaction steps were based on the existing literature reports, and hence no parameter estimation was done to fit the model against the experimental data. The revised model was quantitatively able to predict all the products of PSP pyrolysis, which was attributed to the stabilization of the alkoxy radicals by hydrogen abstraction, and the subsequent generation of additional alkoxy radicals by β-scission. KMC allowed the dominant pathways for the formation of minor products and dimers to be identified explicitly. Finally, the implications of this study in understanding the effect of trace peroxide bonds on poly(styrene) pyrolysis are outlined.

The discovery of biochemical reaction pathways consisting of both known and novel reactions to synthesize carbon-based compounds is of tremendous interest for the production of biofuels. One attractive target is energy-rich alcohols that can be produced via a series of enzymatic transformations. Computational tools for generating networks of reactions to produce alcohols have been demonstrated, yet the number of potential pathways was still too large to be explored experimentally. Here we present the results of high-level quantum chemical calculations to predict the thermodynamic feasibility of various reactions. The conversion of pyruvic acid to 1-butanol was used as an example system. The free energy landscapes generated using ab initio methods were compared against group contribution analysis for a reaction network of ABE fermentation of pyruvic acid. Secondly, detailed reaction energetics were calculated for Ehrlich’s pathway for the conversion of 2-keto acids to alcohols. Finally, the energetics for the conversion of non-native keto acids such as 2-keto-butanoic acid, 2-keto-valeric acid and 2-keto-isovaleric acid to their corresponding alcohols were evaluated, and the thermodynamic landscapes were compared to that of the native substrate, pyruvic acid.

Kinetic parameters for the dominant pathways during the addition of the four Si(2)H(2) isomers, i.e., trans-HSiSiH, SiSiH(2), Si(H)SiH, and Si(H(2))Si, to monosilane, SiH(4), and disilane, Si(2)H(6), have been calculated using G3//B3LYP, statistical thermodynamics, conventional and variational transition state theory, and internal rotation corrections. The direct addition products of the multifunctional Si(2)H(2) isomers were monofunctional substituted silylenes, hydrogen-bridged species, and silenes. During addition to monosilane and disilane, the SiSiH(2) isomer was found to be most reactive over the temperature range of 800 to 1200 K. Revised parameters for the Evans-Polanyi correlation and a representative pre-exponential factor for multifunctional silicon hydride addition and elimination reaction families under pyrolysis conditions were regressed from the reactions in this study. This revised kinetic correlation was found to capture the activation energies and rate coefficients better than the current literature methods.

Because of the complexity of monomer sequence formation during polymerization, it is necessary to employ programmed synthesis to prepare copolymers with well-defined sequences. We introduce a computational tool that can generate recipes to synthesize copolymers with pre-designed monomer sequences. An efficient design strategy was crafted based on analyzing the impact of varying multiple synthesis factors in forced gradient copolymerization on the targeted properties. Finally, the proposed design tool was applied to generate recipes for several different structural gradient copolymers as case studies. It was shown that a recipe that meets certain targets can be designed in minutes. The recipes that are designed can also be tailored according to different application requirements.

A molecular modeling strategy to screen the capacity of known enzymes to catalyze the reactions of non-native substrates is presented. The binding of pyruvic acid and non-native ketoacids in the active site of pyruvate ferredoxin oxidoreductase was examined using docking analysis, and our results suggest that enzyme-non-native ketoacid-bound species are feasible. Quantum mechanics/molecular mechanics methods were then used to study the geometry of the covalent intermediate formed from the enzyme and the various ketoacids. Finally, quantum mechanical methods were used to study the decarboxylation reaction of 2-keto acids at the mechanistic level. This hierarchical screening ranked the substrates from those that cannot be accommodated by the enzyme (phenyl pyruvate) to those whose conversion rate would most closely approach that of the native substrate (2-ketobutanoic acid and 2-ketovaleric acid). Most notably, our investigation suggests that novel pathways generated using generalized enzyme actions may be screened using the hierarchical approach employed here.

The effects of the reactive center connectivity and internal rotations on the reactivity of hydrogenated silicon nanostructures toward cyclization and ring opening pathways have been investigated. Rate coefficients for 25 cyclization and ring opening reactions for hydrides containing up to eight silicon atoms have been calculated using G3//B3LYP. The overall reactions exhibit two elementary steps. Overcoming the first barrier results in the formation of a hydrogen-bridged cyclic intermediate from a substituted silylene. Passing over the second barrier converts this intermediate into a cyclic silicon hydride. The rate-determining step varied according to the ring size formed and the temperature. Assuming a rate-determining step, values for the single-event Arrhenius pre-exponential factor, $$ \tilde{A}$$ , and the activation energy, E a, were calculated from G3//B3LYP rate coefficients corrected for internal rotations, and a group additivity scheme was developed to predict $$ \tilde{A}$$ and E a. The values predicted by group additivity are more accurate than structure–reactivity relationships currently used in the literature, which rely on a representative $$ \tilde{A}$$ value for each reaction class and the Evans-Polanyi correlation to predict E a. Internal rotation corrections played a prominent role in cyclization pathways, impacting $$ \tilde{A}$$ values for larger ring formation reactions more strongly than any variations in the connectivity of the reactive center.

The impact of the synthesis conditions on the formation of the monomer sequences of styrene (S) and methyl methacrylate (MMA) gradient copolymers synthesized by forced gradient copolymerization with nitroxide-mediated controlled radical polymerization (NM-CRP) was investigated using kinetic Monte Carlo (KMC) simulations. The factors affecting the formation of the individual segments, arrangement of these segments along the chain, and the uniformity of monomer sequences were investigated. It was shown that instantaneous segment lengths increase exponentially as a function of monomer composition. The concentration of nitroxyl radicals also plays a key role in the formation of segment lengths. In addition, the arrangement of the segments mainly depends on the feed profile of the second monomer. A constant feed profile, which is widely used in current syntheses of gradient copolymers, is shown to not be suitable to make a structural gradient along the chain. It was also demonstrated that the uniformity of seq...