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Geminal (gem−) disubstitution in heterocyclic monomers is an effective strategy to enhance polymer chemical recyclability by lowering their ceiling temperatures. However, the effects of specific substitution patterns on the monomer's reactivity and the resulting polymer's properties are largely unexplored. Here we show that, by systematically installing gem‐dimethyl groups onto ϵ‐caprolactam (monomer of nylon 6) from the α to ϵ positions, both the redesigned lactam monomer's reactivity and the resulting gem‐nylon 6's properties are highly sensitive to the substitution position, with the monomers ranging from non‐polymerizable to polymerizable and the gem‐nylon properties ranging from inferior to far superior to the parent nylon 6. Remarkably, the nylon 6 with the gem‐dimethyls substituted at the γ position is amorphous and optically transparent, with a higher Tg (by 30 °C), yield stress (by 1.5 MPa), ductility (by 3×), and lower depolymerization temperature (by 60 °C) than conventional nylon 6. [ABSTRACT FROM AUTHOR]

A kinetic Monte Carlo model of polyurethane polymerization which explicitly tracks the polymer sequences is developed and shared. This model is benchmarked against theoretical and experimental polyurethane data and used to investigate the effect on oligomer distributions of unequal reactivity of the first and second isocyanate to react. The reverse reactions using thermodynamic consistency are then added to the framework, and analogous to the addition polymerization concept of ceiling temperature, equilibrium chain length distributions at various temperatures are calculated. For a mixture of three monomers AA, BB, and CC, where BB and CC do not react with one another, are present in stoichiometric proportions, and have different enthalpies of reaction with AA, an odd‐even effect emerges. Odd length chains are more likely than even length chains for temperatures at which BB and CC have significantly different equilibrium conversions. The concept of ceiling temperature that is typically cited for addition polymers is extended here to provide a measure of conditions under which depolymerization for recycling is favored. [ABSTRACT FROM AUTHOR]

Biobased chemicals will inevitably be an important part of a sustainable organic chemical industry. Current efforts in biobased chemicals are largely driven by opportunistic chemical product targets requiring complete technology development from feedstock to final product for a specific molecule. To enhance the development of biobased chemicals, it is important to create strategies that can be more systematic and can leverage advancements across multiple final products. Discussed here is the concept of bioprivileged molecules, which are chemical intermediates that have the potential to be efficiently converted into a range of product molecules that can both directly replace existing petrochemicals and are novel molecules that impart enhanced performance properties in end‐use applications. [ABSTRACT FROM AUTHOR]

Kinetic Monte Carlo (KMC) has been widely used in the simulation of polymeric reactions. The power of KMC is highlighted by its ability to keep track of the length and sequence of every radical or polymer chain, while it is computationally more expensive than deterministic kinetic models. This paper introduces an acceleration method that significantly reduces the computational cost of KMC simulations, while keeping the same features as the full kinetic Monte Carlo simulations. Case studies are used to demonstrate the general applicability of this method to free radical copolymerization. © 2017 American Institute of Chemical Engineers AIChE J, 63: 4013-4021, 2017 [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

ABSTRACT Chemicals with aldehyde moieties are useful in the synthesis of polymerization reagents, pharmaceuticals, pesticides, flavors, and fragrances because of their high reactivity. However, chemical synthesis of aldehydes from carboxylic acids has unfavorable thermodynamics and limited specificity. Enzymatically catalyzed reductive bioaldehyde synthesis is an attractive route that overcomes unfavorable thermodynamics by ATP hydrolysis in ambient, aqueous conditions. Carboxylic acid reductases (Cars) are particularly attractive, as only one enzyme is required. We sought to increase the knowledge base of permitted substrates for four Cars. Additionally, the Lys2 enzyme family was found to be mechanistically the same as Cars and two isozymes were also tested. Our results show that Cars prefer molecules where the carboxylic acid is the only polar/charged group. Using this data and other published data, we develop a support vector classifier (SVC) for predicting Car reactivity and make predictions on all carboxylic acid metabolites in iAF1260 and Model SEED. Biotechnol. Bioeng. 2016;113: 944-952. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

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]

Industrial biotechnology provides an efficient, sustainable solution for chemical production. However, designing biochemical pathways based solely on known reactions does not exploit its full potential. Enzymes are known to accept non-native substrates, which may allow novel, advantageous reactions. We have previously developed a computational program named Biological Network Integrated Computational Explorer (BNICE) to predict promiscuous enzyme activities and design synthetic pathways, using generalized reaction rules curated from biochemical reaction databases. Here, we use BNICE to design pathways synthesizing propionic acid from pyruvate. The currently known natural pathways produce undesirable by-products lactic acid and succinic acid, reducing their economic viability. BNICE predicted seven pathways containing four reaction steps or less, five of which avoid these by-products. Among the 16 biochemical reactions comprising these pathways, 44% were validated by literature references. More than 28% of these known reactions were not in the BNICE training dataset, showing that BNICE was able to predict novel enzyme substrates. Most of the pathways included the intermediate acrylic acid. As acrylic acid bioproduction has been well advanced, we focused on the critical step of reducing acrylic acid to propionic acid. We experimentally validated that Oye2p from Saccharomyces cerevisiae can catalyze this reaction at a slow turnover rate (10−3 s−1), which was unknown to occur with this enzyme, and is an important finding for further propionic acid metabolic engineering. These results validate BNICE as a pathway-searching tool that can predict previously unknown promiscuous enzyme activities and show that computational methods can elucidate novel biochemical pathways for industrial applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:303-311, 2016 [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]

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 [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

ABSTRACT Density functional theory (DFT) calculations were used to study the mechanism of CO2 hydrolysis by Zn-(1,5,9-triazacyclododecane) and Zn-cyclam and evaluate the associated thermodynamic and kinetic parameters. Microkinetic models were then built based on the kinetics and thermodynamics derived from first principles. Both catalysts showed very similar behavior to Zn-cyclen, which we have reported previously, but with multiple distinctions. The intrinsic reaction rate constants for Zn-(1,5,9-triazacyclododecane) and Zn-cyclam were calculated to be 2693 and 4623 M−1 s−1, respectively, which is in reasonable agreement with experimental values reported or estimated. The CO2 adsorption step was found to be a rate-limiting step for all three catalysts. Zn-cyclam has the lowest barrier for this step due to the highest p Ka or nucleophilicity of the Zn-OH− form, and, therefore, the highest intrinsic activity. However, the observed reaction rate constant also depends on the availability of the catalyst. The decrease in the observed reaction rate constant over 0-12 ms was ascribed to the decrease in the concentration of the catalytic form, Zn-OH−, which was primarily converted to Zn-HCO3−. The reaction rate constant of Zn-cyclam dropped much faster than those of Zn-cyclen and Zn-(1,5,9-triazacyclododecane) due to lower energy of the Zn-HCO3− form. The conversion of CO2 at 1000 ms as a function of pH was calculated to compare the relative activity of these catalysts, and Zn-cyclen was found to be the best catalyst. [ABSTRACT FROM AUTHOR]

Live-cell assays to measure cellular function performed within 3D cultures have the potential to elucidate the underlying processes behind disease progression and tissue formation. Cells cultured in 3D interact and remodel their microenvironment and can develop into complex structures. We have developed a transcription factor (TF) activity array that uses bioluminescence imaging (BLI) of lentiviral delivered luminescent reporter constructs that allows for the non-invasive imaging of TF activity in both 2D and 3D culture. Imaging can be applied repeatedly throughout culture to capture dynamic TF activity, though appropriate normalization is necessary. We investigated in-well normalization using Gaussia or Renilla luciferase, and external well normalization using firefly luciferase. Gaussia and Renilla luciferase were each unable to provide consistent normalization for long-term measurement of TF activity. However, external well normalization provided low variability and accounted for changes in cellular dynamics. Using external normalization, dynamic TF activities were quantified for five TFs. The array captured expected changes in TF activity to stimuli, however the array also provided dynamic profiles within 2D and 3D that have not been previously characterized. The development of the technology to dynamically track TF activity within cells cultured in both 2D and 3D can provide greater understanding of complex cellular processes. Biotechnol. Bioeng. 2013; 110: 563-572. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

1,5-Hydrogen transfer reactions in methyl acrylate and butyl acrylate free-radical polymerization are studied using quantum chemistry and transition state theory to estimate the kinetic parameters ( ktr, Ea, and A) with tetrameric radicals, requiring a number of atoms that ranks among the largest polymeric mimics to date. A two-step transformation accounted for the overall reaction: rotation from an extended conformation to a coiled conformation and abstraction of the fifth hydrogen atom by the end-chain radical. UB3LYP/6-31G(d) was used for geometry optimization, validation of the transition states, and calculation of frequencies that were used to obtain thermodynamic properties. The more computationally demanding level of theory, MPWB1K/6-31G(d,p), was used for calculation of the electronic energy. [ABSTRACT FROM AUTHOR]

A variety of metal-organic frameworks (MOFs) with varying linkers, topologies, pore sizes, and metal atoms were screened for xenon/krypton separation using grand canonical Monte Carlo (GCMC) simulations. The results indicate that small pores with strong adsorption sites are desired to preferentially adsorb xenon over krypton in multicomponent adsorption. However, if the pore size is too small, it can significantly limit overall gas uptake, which is undesirable. Based on our simulations, MOF-505 was identified as a promising material due to its increased xenon selectivity over a wider pressure range compared with other MOFs investigated. © 2010 American Institute of Chemical Engineers AIChE J, 2011 [ABSTRACT FROM AUTHOR]

A multiscale modeling approach was developed to capture concentration variations in the fluid in two dimensions for catalytic flow reactors. The methodology couples continuum descriptions of the fluid phase and kinetic Monte Carlo simulations of the catalyst domain. A number of catalytic domains, placed as patches along the length of the reactor, were solved using kinetic Monte Carlo (kMC) and linked with a finite difference (FD) solver for the fluid phase. Patch dynamics concepts, such as lifting, restriction and interpolation, were employed to provide the complete set of boundary conditions to the continuum solver. A simple kinetic mechanism involving adsorption, desorption and a single-step surface reaction was used to validate the approach by comparing the solution obtained using the multiscale scheme with a model solved using a wholly implicit solution. Solutions from a mean-field model and the multiscale scheme for a system in which surface diffusion was low were then contrasted. [ABSTRACT FROM AUTHOR]

Modeling and simulation at different scales were used to study mass transport and residence times of particles in nanostructured membranes with uniform cylindrical pores of 10-150 nm diameter and up to 5 µm long. Analytical equations of the possible mass-transport mechanisms inside the pores were used to determine that diffusion dominates over convection under the conditions of interest for selective oxidation: 700 K and pressure near atmospheric. Molecular dynamics simulations showed that surface diffusion is present only at temperatures < 700 K. Knudsen diffusion was identified as the dominant mechanism. Simulations based on its principles were performed using an ensemble of particles in a boundary-driven simulation cell, providing the average number of hits between a particle and the pore wall and the dependency of the residence time on the pore dimensions. The differences between operating a nanostructured membrane reactor in sweep-gas and pass-through modes were also investigated. [ABSTRACT FROM AUTHOR]

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.

Biomass pyrolysis—a sustainable way to produce renewable fuels and chemicals: The cover image depicts a sustainable world where green fuels and chemicals will be produced from renewable, abundant, and cheap biomass by using a variety of technologies (e.g., biological, thermochemical, and catalytic). Hemicellulose, one of the three major components of biomass, receives scarce attention compared to cellulose and lignin; however, it deserves much more. Herein, this contribution highlights the progress in characterizing the composition and structural features of hemicellulose and particularly focuses on salient experimental investigations, reaction mechanisms, and kinetic modeling of hemicellulose pyrolysis through a critical literature analysis. Challenges and future prospects are also discussed. More details can be found in the Review by X. Zhou, W. Li, R. Mabon, L. J. Broadbelt from Northwestern University and Exxon Mobil (DOI: 10.1002/ente.201600327). [ABSTRACT FROM AUTHOR]

A correction to the article "A Critical Review on Hemicellulose Pyrolysis" is presented.

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]