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Abstract: Molecular simulations were used to screen a diverse collection of eight homochiral metal–organic frameworks (MOFs) for their ability to separate 19 chiral compounds by enantioselective adsorption. The simulation model was validated by comparison with available experimental data. It was found that high enantioselectivity is strongly correlated with a close match between the size of the pore and the size of the chiral sorbate molecule. However, there is also a possibility of no enantioselectivity even when the size of the pore matches with the size of the chiral sorbate molecule. A four-point model was used to explain this observation, and a solution to promote high enantioselectivity has been proposed. [Copyright &y& Elsevier]

Abstract: Reaction progress kinetic analysis of the proline-mediated intermolecular aldol reaction shows that the rate depends on the concentrations of both the donor ketone1 and the electrophilic aldehyde 2, implying that enamine formation cannot be rate-determining. The observed kinetics and deuterium isotope effects are consistent with formation of the product iminium species as the rate-determining step. [Copyright &y& Elsevier]

Abstract: A detailed, mechanistic model for high-density polyethylene pyrolysis was created based on the modeling framework developed in our previous work and was used to study the time evolution of low molecular weight products formed. Specifically, the role that unzipping, backbiting, and random scission reaction pathways play in the evolution of low molecular weight species was probed. The model tracked 151 species and included over 11,000 reactions. Rate parameters were adapted from our previous work, literature values, and regression against experimental data. The model results were found to be in excellent agreement with experimental data for the evolution of condensable low molecular weight products. The time evolution curves of specific low molecular weight products indicated that the random scission pathway was important for all species, while the backbiting pathway played a complementary role. Net rate analysis was used to further elucidate the competition between the pathways. Net rate analysis of end-chain radicals showed that the unzipping pathway was not competitive with the other pathways, as expected based on experimental yields of ethylene. The random scission pathway was found to be controlling, with the backbiting pathway playing a more minor role for product formation. By comparing the net rates for formation of specific mid-chain radicals via intramolecular hydrogen shift reactions, the contribution of the backbiting pathway was shown to vary, with radicals formed via the most facile x,x +4-intramolecular hydrogen transfer reactions being favored. [Copyright &y& Elsevier]

Abstract: Quantum chemical calculations were employed to develop a better understanding of the adsorption properties of BaNaY interacting with molecules relevant to deNO x catalysis. First, various basis sets and levels of theory were tested for barium-containing species and gas-phase reactions, and it was shown that the choice of the basis set for barium is critical. Density functional theory (DFT) with the B3LYP functional and SDD as the basis set was selected based on its combination of relative accuracy and speed. This level of theory was then used to calculate energies, geometries, and frequencies for acetaldehyde, acetic acid, nitromethane, and water adsorbed and in the gas phase. The predicted properties were compared to experiment where available and reasonable agreement was found. To study the effect of the zeolite framework on the adsorption properties, the size of the zeolite cluster was increased from 6T to 36T to 96T using the embedded ONIOM method. Inclusion of van der Waals interactions with increasing cluster size only changed the adsorption enthalpy by a small amount for all of the adsorbates studied. It was found that the interaction between the empty 6s orbital of Ba and the lone pair orbital of the oxygen atom in the adsorbed state, revealed by natural bond orbital analysis, correlates with the adsorption enthalpy and the gas-phase charge of the oxygen atom that interacts with Ba. [Copyright &y& Elsevier]

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]

Knudsen dynamics simulations were performed in cylindrical pores with multiple sections of different diameters. The number and location of hits between particles and the pore walls can be related to the known distributions in the uniform diameter cases. Both sweep-gas and pass-through modes of operation were examined. The contact of the particles traveling inside the pores with the pore walls can be regulated by adjusting the aspect ratio (section length/section diameter) of the pore sections and the ratio of their cross-sectional areas. The results were found to be independent of the transition angle between sections except for very smooth transitions. Analytical expressions were developed to relate the transmission probability in pores of multiple sections to the transmission probabilities of the constituent sections. [Copyright &y& Elsevier]

Quantum chemistry and transition state theory were used to study 10 different radical reactions of peroxy radicals abstracting the phenolic hydrogen of several antioxidants. The B3LYP functional with a 6-31G(d) basis set was used to characterize transition states with as many as 20 heavy atoms. The impact of quantum tunneling was investigated for a representative reaction, and it was shown that the Wigner correction provides a good approximation to more advanced semi-classical transmission coefficients. A kinetic correlation was developed that is suitable for use in kinetic modeling, allowing antioxidant chemistry to be included in large mechanistic models of hydrocarbon oxidation. [Copyright &y& Elsevier]

Photolysis is an important loss process of carbonyl, peroxy, and nitrate species in the atmosphere. In general, photolysis rate coefficients depend on the intensity of radiation, wavelength, temperature, and the specific molecule reacting. One key source of differences in rate coefficients between different molecules is the absorption cross-section, σ, which is specific to the reactive molecule under consideration. In order to calculate rate coefficients for photolytic processes, a value of σ must be specified or estimated. To this end, a group additivity approach was developed that can be used to estimate the values of σ of species that photolyze primarily in the 290–370 nm wavelength region. We demonstrate that this approach can be used to predict accurately unknown values of σ of species for which experimental data are not available. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

Abstract: Grand canonical Monte Carlo simulations have been carried out to investigate the adsorption of water from the vapor phase into the zeolite silicalite. For truly hydrophobic micropores, the simulations predict essentially no adsorption of water at low pressures, followed by rapid pore filling as pressure is increased. The effect of silanol defects in real silicalite samples was explored through simulations using “seeded” water molecules to represent hydrophilic defects. These defects promote adsorption of some water at low pressures, as molecules form hydrogen-bonded clusters around the defects. The defects also shift the pore filling to a lower pressure than in the completely hydrophobic material. [Copyright &y& Elsevier]

The extraframework locations of many metal cations in pentasil zeolites, such as ferrierite, are not known, but new infrared bands in the 800–1000 cm−1 region are experimentally observed upon exchange. To investigate the origin of these bands and to better understand cation siting, density functional theory calculations were performed on ferrierite cluster models for seven divalent metals: magnesium, manganese, iron, cobalt, nickel, copper, and zinc. The calculated properties, such as the metal–zeolite binding energy, follow a U-shaped trend with respect to the number of metal d electrons. The calculated infrared bands are consistent with the occupation of the B and G ferrierite sites by the metal cations. However, a definitive assignment of the published experimental infrared bands to particular extraframework sites was not possible. Despite this limitation, all seven metals were shown to perturb the ferrierite framework similarly. All of the cations coordinate to four framework oxygen atoms and the framework T–O bonds associated with these oxygen atoms are elongated by the metal. This elongation is shown to be proportional to the wavenumber of the infrared bands. [Copyright &y& Elsevier]

A novel MCM-41-supported base catalyst, Ba-MCM-41, was synthesized with a modified impregnation method. Ba2SiO4 was synthesized on the MCM-41 pore wall as confirmed by characterization using X-ray diffraction, X-ray photoelectron spectroscopy, X-ray fluorescence, N2 adsorption, 29Si MAS NMR and transmission electron microscopy. It was also demonstrated that a highly ordered Ba-MCM-41 catalyst with high barium loading (4.1–25.2 wt.%) and dispersion was obtained using this method. The basicity of the catalyst, which was characterized according to the binding energy of O 1s, was increased with increasing amounts of barium in the catalyst. [Copyright &y& Elsevier]

• Linseed oil chemistry in the context of drying of paint is comprehensively reviewed. • The review discusses experimental data similar to outcomes of computational modeling. • Advances in computational modeling related to oils are discussed. This review summarizes computational modeling literature concerning linseed oil autoxidation in the context of oil paint. After discussing the chemical structure and composition of linseed oil, an overview is given of polymer properties of the material and the experimental techniques used to infer these properties. The review proceeds with the survey of existing computational modeling techniques used to investigate the drying process of linseed oil. [ABSTRACT FROM AUTHOR]

Chemical and biological syntheses can both lead to a myriad of compounds. Biology enables us to harness the metabolism of microbial cell factories to produce key target molecules from renewable biomass-derived substrates. Although bio-based feedstocks are sustainably sourced and more benign than the rapidly depleting fossil fuels that chemical processes have historically relied on, limiting pathways solely to biological reactions may not equate to a greener process overall. In fact, bioreactors rely on substantial quantities of water and can be inefficient since organisms typically operate around ambient conditions and are sensitive to perturbations in their environment. Hybridizing biosynthetic pathways with green chemistry can instead be a more potent strategy to reduce our net manufacturing footprint. Emerging chemistries have demonstrated considerable success in performing complex transformations on biological feedstocks without significant solvent use. Many of these transformations would be too slow to perform enzymatically or infeasible altogether. Here, we put forth the concept that by carefully considering the merits and drawbacks of synthetic biology and chemistry as well as one's own use case, there exist many opportunities for coupling the two. Merging these syntheses can unlock a wider suite of functional group transformations, thereby enabling future manufacturing processes to sustainably access a larger space of valuable, platform chemicals. [Display omitted] • Biology can expand the scope of chemical manufacturing, but limitations persist. • Green chemistry offers a sustainable alternative to petrochemical synthesis. • Chemical transformations in biology and chemistry complement one another. • Computational synthesis planning expedites the design of hybrid synthesis routes. [ABSTRACT FROM AUTHOR]

The diversity of the potential arrangements of multiple monomers along the length of polymer chains and their impact on polymer properties spark interest in the design of polymer sequence characteristics for particular applications. Kinetic Monte Carlo (KMC) is a technique that can track the explicit arrangement of monomers in the polymer chains, yet it is difficult to integrate with conventional gradient-based optimization algorithms that are typically invoked to design polymer properties. In this work, we applied and compared derivative-free optimization algorithms to incorporate KMC simulations and find synthesis conditions for achieving property targets and minimizing reaction time, advancing our ability to carry out the design of polymer microstructures and control polymerization processes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The glass transition temperature ( T g ) 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 T g . Fluorescence spectroscopy is used to measure the glass transition temperature ( T g ) of the ultrathin dye-labeled PS layers at specific regions within multilayer films of immiscible polymers. The T g 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 T g 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 T g perturbations in both systems. The magnitude of T g -confinement effects depends not only on the T g 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. [ABSTRACT FROM AUTHOR]

The study of metagenomic samples is crucial for understanding microbial communities in ecosystems. In this study, genomic samples of the “El Coquito” acidic hot spring, located at the Nevados Natural National Park in Colombia, were analysed to evaluate the relationship between its metabolic functionality, and metabolic flows distribution considering the thermodynamic restrictions and the biogeochemical cycles through a flux balance analysis. The metabolic functionality of the metagenome was established by assigning reactions and enzymes to the metabolic routes. On one hand, we found that relevant metabolic groups contribute in a different fashion depending on the objective function of the ecosystem from the amount of metabolic reactions perspective. On the other hand, from the contribution to the total metabolic flow point of view, it seems the metabolic distribution plasticity conserves, as there exists several common groups that significantly contribute to the total metabolic flux of the system. Nevertheless, this plasticity is not maintained for all objective functions due to the differences between the nitrogen and the rest of the cycles, clearly demonstrating that the microbial adaptation capability to the ecosystem is materialized in the distribution of the metabolic flows instead of the frequency of appearance of the same reactions. [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: The microenviroment contributes to directing mammary epithelial cell (MEC) development and the progression of breast cancer. Three-dimensional culture models have been used to support formation of structures that display varying degrees of disorganization that parallel the degree of cancer. Synthetic hydrogels were employed to investigate the mechanisms by which specific adhesion signals in the microenvironment directed development. Polyethylene glycol-based hydrogels supported 3D growth of MECs and directed formation of a range of phenotypes that were functions of genotype, and identity and concentration of adhesion peptides RGD and YIGSR. Non-cancerous and cancerous MECs responded differentially to the same adhesion cues and produced variable structural organizations. An analysis of dynamic signaling pathways revealed differential activities of transcription factors within the MAPK and JAK/STAT pathways in response to genotype and adhesion. These results directly implicate adhesion in cancer development and demonstrate that AP1, CREB, STAT1, and STAT3 all contribute to the genotype dependence of cellular response to adhesion peptides. The tools presented in this work could be applied to other systems and connect extracellular cues with intracellular signaling to molecularly dissect tissue development and further biomaterials development. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

[Display omitted] • Addresses gaps in review literature by proposing a comprehensive mechanistic view for heterogenous nickel-acid catalysts. • Highlights relevant conditions to steer product distributions of ethylene oligomerization towards desirable products. • Focuses on environmentally-friendly and flexlble catalysts to produce a range of products for ever-changing market demands. 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 Brønsted 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. [ABSTRACT FROM AUTHOR]

Abstract: A computational framework has been developed for the construction and evaluation of metabolic pathways given input substrates and knowledge of enzyme-catalyzed reactions. Application of the framework creates new and existing routes to both chemicals known to exist in biological systems and chemicals novel to biological systems. In the present application, we focus on biosynthetic routes to 7-carboxyindole, a specialty chemical currently produced by organic synthesis, using chorismate as a starting compound and the enzyme actions native to the biosynthetic route from chorismate to tryptophyan. Graph theory and its associated algorithms are exploited to represent molecules and perform enzyme-catalyzed reactions. Through repetitive application of the set of operators representing the enzymatic reactions of interest to the reactants and their progeny, reaction pathways are generated automatically. The concept of generalized enzyme function is introduced and defined as the third-level enzyme function (EC i.j.k) according to the four-digit transformations of the enzyme classification system (EC i.j.k.l). This concept maps enzyme-catalyzed reactions to transformations of functional groups and enables the generation of novel species and pathways. Thermodynamic properties are calculated using a group contribution method “on-the-fly” in order to provide one assessment of the relative feasibility of the novel pathways. [Copyright &y& Elsevier]

Metabolism is one of the most complex cellular processes. Connections between biochemical reactions via substrate and product metabolites create complex metabolic networks that may be analyzed using network theory, stoichiometric analysis, and information on protein structure/function and metabolite properties. These frameworks take into consideration different aspects of enzyme chemistry, enzyme structure and metabolite structure, and demonstrate the impact of metabolic biochemistry on the systemic properties of metabolism. The integration of these approaches and the systematic classification of enzyme function and the chemical structure of metabolites will enhance our understanding of metabolism, and could improve our ability to predict enzyme function and novel metabolic pathways. [Copyright &y& Elsevier]