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At least 361 records · Page 20

Computational Modeling and Evolutionary Implications of Biochemical Reactions in Bacterial Microcompartments

Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.

bacterial microcompartments↗

Electrolyte-Assisted Hydrogen Cycling in Lithium and Sodium Alanates at Low Pressures and Temperatures

An investigation of electrolyte-assisted hydrogen storage reactions in complex aluminum hydrides (LiAlH4 and NaAlH4) reveals significantly reduced reaction times for hydrogen desorption and uptake in the presence of an electrolyte. LiAlH4 evolves ~7.8 wt% H2 over ~3 h in the presence of a Li-KBH4 eutectic at 130 °C compared to ~25 h for the same material without the electrolyte. Similarly, NaAlH4 exhibits 4.8 wt% H2 evolution over ~4 h in the presence of a diglyme electrolyte at 150 °C compared to 4.4 wt% in ~15 h for the same material without the electrolyte. These reduced reaction times are composed of two effects, an increase in reaction rates and a change in the reaction kinetics. While typical solid state dehydrogenation reactions exhibit kinetics with rates that continuously decrease with the extent of reaction, we find that the addition of an electrolyte results in rates that are relatively constant over the full desorption window. Fitting the kinetics to an Avrami-Erofe’ev model supports these observations. The desorption rate coefficients increase in the presence of an electrolyte, suggesting an increase in the velocities of the reactant-product interfaces. In addition, including an electrolyte increases the growth parameters, primarily for the second desorption steps, resulting in the observed relatively constant reaction rates. Similar effects occur upon hydrogen uptake in NaH/Al where the presence of an electrolyte enables hydrogenation under more practical low temperature (75 °C) and pressure (50 bar H2) conditions.

25 ENERGY STORAGE↗

Sensitivity of two-dimensional model predictions of ozone response to stratospheric aircraft: An update

The Goddard Space Flight Center (GSFC) two-dimensional model of stratospheric photochemistry and dynamics has been used to calculate the O3 response to stratospheric aircraft (high-speed civil transport (HSCT)) emissions. The sensitivity of the model O3 response was examined for systematic variations of five parameters and two reaction rates over a wide range, expanding on calculations by various modeling groups for the NASA High Speed Research Program and the World Meteorological Organization. In all, 448 model runs were required to test the effects of variations in the latitude, altitude, and magnetitude of the aircraft emissions perturbation, the background chlorine levels, the background sulfate aerosol surface area densities, and the rates of two key reactions. No deviation from previous conclusions concerning the response of O3 to HSCTs was found in this more exhaustive exploration of parameter space. Maximum O3 depletions occur for high-altitude, low altitude HSCT perturbations. Small increases in global total O3 can occur for low-altitude, high-altitude injections. Decreasing aerosol surface area densities and background chlorine levels increases the sensitivity of model O3 to the HSCT perturbations. The location of the aircraft emissions is the most important determinant of the model response. Response to the location of the HSCT emissions is not changed qualitatively by changes in background chlorine and aerosol loading. The response is also not very sensitive to changes in the rates of the reactions NO + HO2 yields NO2 + OH and HO2 + O3 yields OH + 2O2 over the limits of their respective uncertainties. Finally, levels of lower stratospheric HO(sub x) generally decrease when the HSCT perturbation is included, even though there are large increases in H2O due to the perturbation.

Considine, David B.↗

Atomic-Level Features for Kinetic Monte Carlo Models of Complex Chemistry from Molecular Dynamics Simulations

The high computational cost of evaluating atomic interactions recently motivated the development of computationally inexpensive kinetic models, which can be parametrized from MD simulations of complex chemistry of thousands of species or other processes and accelerate the prediction of the chemical evolution by up to four order of magnitude. Such models go beyond the commonly employed potential energy surface fitting methods in that they are aimed purely at describing kinetic effects. So far, such kinetic models utilize molecular descriptions of reactions and have been constrained to only reproduce molecules previously observed in MD simulations. Therefore, these descriptions fail to predict the reactivity of unobserved molecules, for example in the case of large molecules or solids. In this work, we propose a new approach for the extraction of reaction mechanisms and reaction rates from MD simulations, namely the use of atomic-level features. Using the complex chemical network of hydrocarbon pyrolysis as example, it is demonstrated that kinetic models built using atomic features are able to explore chemical reaction pathways never observed in the MD simulations used to parametrize them, a critical feature to describe rare events. Atomic-level features are shown to construct reaction mechanisms and estimate reaction rates of unknown molecular species from elementary atomic events. Through comparisons of the model ability to extrapolate to longer simulation timescales and different chemical compositions than the ones used for parameterization, it is demonstrated that kinetic models employing atomic features retain the same level of accuracy and transferability as the use of features based on molecular species, while being more compact and parametrized with less data. We also find that atomic features can better describe the formation of large molecules enabling the simultaneous description of small molecules and condensed phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reaction Pathways and Energy Consumption in NH 3 Decomposition for H 2 Production by Low Temperature, Atmospheric Pressure Plasma

Pathways for NH 3 decomposition to N 2 and N 2 H 4 by atmospheric pressure nonthermal plasma are analyzed using a combination of molecular beam mass spectrometry measurements and zero-dimensional kinetic modeling. Experimental measurements show that NH 3 conversion and selectivity towards N 2 formation scale monotonically with the specific energy input into the plasma with ~ 100% selectivity to N 2 formation achieved at specific energy inputs above 0.12 J cm −3 (3.1 eV (molecule NH 3 ) −1 ). The kinetic model recovers these trends, although it underpredicts N 2 selectivity at low specific energy input. These discrepancies can be explained by the underestimation of reaction rate coefficients for reactions that consume N 2 H x species in collisions with H radicals and/or radial nonuniformities in power deposition, gas temperature, and species concentrations that are not represented by the plug flow approximation used in the model. The kinetic model shows that N 2 formation proceeds through N 2 H x decomposition pathways rather than NH x decomposition pathways in low temperature, atmospheric pressure plasma. Higher selectivity toward N 2 production can be achieved by operating at higher NH 3 conversion and with a higher gas temperature. Furthermore, the high energy cost of NH 3 decomposition by atmospheric pressure nonthermal plasma found in this work (25–50 eV (molecule NH 3 converted) −1 ; 17–33 eV (molecule H 2 formed) −1 ) is a result of the energy requirement for electron-impact dissociation of NH 3 and the significant re-formation of NH 3 by three-body recombination reactions between NH 2 and H.

Nonthermal plasma↗

Cationic Tantalum Hydrides Catalyze Hydrogenolysis and Alkane Metathesis Reactions of Paraffins and Polyethylene

Sulfated aluminum oxide (SAO), a high surface area material containing sulfate anions that behave like weakly coordinating anions, reacts with Ta(=CH t Bu)(CH 2 t Bu) 3 to form [Ta(CH 2 t Bu) 2 (O–) 2 ][SAO] (1). Subsequent treatment with H 2 forms Ta–H + sites supported on SAO that are active in hydrogenolysis and alkane metathesis reactions. In both reactions Ta–H + is more active than related neutral Ta–H sites supported on silica. This reaction chemistry extends to melts of high-density polyethylene (HDPE), where Ta–H + converts 30% of a low molecular weight HDPE (M n = 2.5 kg mol –1 ; D = 3.6) to low molecular weight paraffins under hydrogenolysis conditions. Under alkane metathesis conditions Ta–H + converts this HDPE to a high MW fraction (M n = 6.2 kDa; D = 2.3) and low molecular weight alkane products (C 13 –C 32 ). Furthermore, these results show that incorporating charge as a design element in supported d 0 metal hydrides is a viable strategy to increase the reaction rate in challenging reactions involving reorganization of C–C bonds in alkanes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of ring-enlargement reactions in the formation of aromatic hydrocarbons

Ring-enlargement reactions can provide a fast route towards the formation of six-membered single-ring or polycyclic aromatic hydrocarbons (PAHs). To investigate the participation of the cyclopentadienyl (C 5 H 5 ) radical in ring-enlargement reactions in high-temperature environments, a mass-spectrometric study was conducted. Experimental access to the C 5 H 5 high-temperature chemistry was provided by two counterflow diffusion flames. Cyclopentene was chosen as a primary fuel given the large amount of resonantly stabilized cyclopentadienyl radicals produced by its decomposition and its high tendency to form PAHs. In a second experiment, methane was added to the fuel stream to promote methyl addition pathways and to assess the importance of ring-enlargement reactions for PAH growth. The experimental dataset includes mole fraction profiles of small intermediate hydrocarbons and of several larger species featuring up to four condensed aromatic rings. Results show that, while the addition of methane enhances the production of methylcyclopentadiene and benzene, the concentration of larger polycyclic hydrocarbons is reduced. The increase of benzene is probably attributable to the interaction between the methyl and the cyclopentadienyl radicals. However, the formation of larger aromatics seems to be dominated only by the cyclopentadienyl driven molecular-growth routes which are hampered by the addition of methane. Furthermore, in addition to the experimental work, two chemical mechanisms were tested and newly calculated reaction rates for cyclopentadiene reactions were included. In an attempt to assess the impact of cyclopentadienyl ring-enlargement chemistry on the mechanisms’ predictivity, pathways to form benzene, toluene, and ethylbenzene were investigated. Results show that the updated mechanism provides an improved agreement between the computed and measured aromatics concentrations. Nevertheless, a detailed study of the single reaction steps leading to toluene, styrene, and ethylbenzene would be certainly beneficial.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploration for astromers near 132 Sn with the Canadian Penning Trap

Nuclear isomers can have significant impacts on astrophysical nucleosynthesis processes, with recent efforts demonstrating that the population of isomeric states with different half-lives may require separate treatment in reaction networks to accurately capture the differences in heating or in identifiable electromagnetic signals. Several potential so-called “astromers” in tin and antimony isotopes near doubly magic 132 Sn were identified and direct mass measurements of their ground and isomeric states were performed with the Canadian Penning Trap at Argonne National Laboratory's CARIBU facility, and their impact on astrophysical reaction rates and in reaction networks was calculated. Finally, it was found that 129⁢𝑔,𝑚 Sn , with measured mass excesses of −80593.2⁢(25) and −80557.4⁢(25) keV, respectively, and an excitation energy of 35.8(35) keV, behaves as an astromer during neutron capture in the 𝑖-process and in the 𝑟-process.

isomer decays↗

FLASSH 1.0: Full Law Analysis Scattering System Hub

Nuclear technologies, such as thermal reactors and critical systems, are driven by reaction rates which are directly dependent on thermal neutrons. The ability to calculate reaction rates is directly linked to the capability to predict and understand the cross sections. For atoms bound within a material structure, the available modes of energy exchange are captured in the Thermal Scattering Law (TSL, i.e. S(α,β)). The TSL is fundamentally a material property and can be defined explicitly to account for the excitation and deexcitation of the lattice energy states. This work describes the development of the Full Law Analysis Scattering System Hub (FLASSH) which calculates the TSL and cross sections. FLASSH is a modern code which has been designed to produce accurate TSL evaluations, remove historical approximations, and improve formulations while making advance physics accessible and simple to use.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Enhanced methanol production from photothermal CO 2 reduction via multilevel interface design

Photothermal CO 2 hydrogenation is a promising route to produce methanol as a sustainable liquid solar fuel. However, most existing catalysts require a combination of solar irradiation and additional heat input to achieve a satisfactory reaction rate. For the few that can be driven solely by light, their reaction rates are one order of magnitude lower. We develop a photothermal catalyst with multilevel interfaces that achieves improved methanol production from photothermal CO 2 hydrogenation without external heat. The catalyst features a layered structure comprising Cu/ZnO/Al 2 O 3 (CZA) covered by oxidized carbon black (oCB), where the oCB/CZA interface promotes efficient heat generation and transfer, and the Cu/oxide interface contributes to high catalytic activity. Under a mild pressure of 8 bar, our oCB/CZA catalyst shows a methanol selectivity of 64.7% with a superior production rate of 4.91 mmol·g cza −1 ·h −1 , at least one order of magnitude higher than other photothermal catalysts solely driven by light. This work demonstrates a photothermal catalyst design strategy for liquid solar fuel production.

CO2 hydrogenation↗

Chemical nonequilibrium effects on the flow in the windward plane of symmetry of a blunted delta orbiter

The extent, and some of the consequences, of nonequilibrium effects in the inviscid orbiter flow field are examined. Calculations have been made for the reacting flow along selected streamlines in the windward plane of symmetry of a blunted delta shape representative of a shuttle orbiter. An approximate model of the pressure field in the windward plane of symmetry of a blunted delta wing was constructed from wind tunnel measurements of the body surface pressure distribution and approximate calculations of the shock shape and streamline locations. Numerical solutions for the flow along streamlines were obtained for this pressure distribution, and solutions were obtained for both equilibrium and finite-reaction rate, nonequilibrium chemical reactions. Since the streamtube solutions are much easier to compute than fully three-dimensional, reacting flows, results were obtained for a wide range of conditions. The validity of this approach is based on the assumptions that the pressure field is insensitive to nonequilibrium effects and that the flow along streamlines is quasi-one dimensional. Numerical solutions have been used to verify this approach for other blunted slender shapes such as spherically blunted cones.

Lordi, J. A.↗

Mechanisms and observations for isotope fractionation of molecular species in planetary atmospheres

Chemcial and physical processes which may give rise to isotope fractionation of molecular species in the atmospheres of both earth and other planets are reviewed, along with observations of isotopically substituted molecules in planetary atmospheres. Mechanisms for production of isotope fractionation considered include atmospheric escape and the effect of isotope substitution on equilibrium constants (including those of phase changes), photolysis rates, and chemical reaction rates. The isotopes considered for compounds in the terrestrial atmosphere include D, T, C-13, C-14, N-15, O-18, and S-34. Compounds for which data about isotopic composition in the terrestrial atmosphere are summarized include CO, CO2, O3, N2O, NH3, SO2, H2S, H2O, H, H2, and CH4. Planetary atmospheres discussed include those of Venus, Mars, Jupiter, Saturn, Uranus, and Titan; isotopes reviewed are D, C-13, N-15, and O-18. Suggestions for additional research in the area of isotopically substituted molecules in atmospheres are offered.

Kaye, Jack A.↗

Computed potential energy surfaces for chemical reactions

The objective was to obtain accurate potential energy surfaces (PES's) for a number of reactions which are important in the H/N/O combustion process. The interest in this is centered around the design of the SCRAM jet engine for the National Aerospace Plane (NASP), which was envisioned as an air-breathing hydrogen-burning vehicle capable of reaching velocities as large as Mach 25. Preliminary studies indicated that the supersonic flow in the combustor region of the scram jet engine required accurate reaction rate data for reactions in the H/N/O system, some of which was not readily available from experiment. The most important class of combustion reactions from the standpoint of the NASP project are radical recombinaton reactions, since these reactions result in most of the heat release in the combustion process. Theoretical characterizations of the potential energy surfaces for these reactions are presented and discussed.

Walch, Stephen P.↗

Effect of water on carbon monoxide-oxygen flame velocity

The flame velocities were measured of 20 percent oxygen and 80 percent carbon monoxide mixtures containing either light water or heavy water. The flame velocity increased from 34.5 centimeters per second with no added water to about 104 centimeters per second for a 1.8 percent addition of light water and to 84 centimeters per second for an equal addition of heavy water. The addition of heavy water caused greater increases in flame velocity with equilibrium hydrogen-atom concentration than would be predicted by the Tanford and Pease square-root relation. The ratio of the flame velocity of a mixture containing light water to that of a mixture containing heavy water was found to be 1.4. This value is the same as the ratio of the reaction rate of hydrogen to that of deuterium and oxygen. A ratio of reaction rates of 1.4 would also be required for the square-root law to give the observed ratio of flame-velocity changes.

Mcdonald, Glen E↗

Efficient Parametric Uncertainty Analysis of an Earth Entry Vehicle Concept Using Least Angle Regression

The objective of this work was to outline and apply an efficient and accurate parametric un-certainty propagation approach to the analysis of convective heating on an Earth entry vehicle concept. The described approach was based on Least Angle Regression used to solve a sparse and underdetermined linear system in the point-collocation non-intrusive polynomial chaos surrogate method. This approach involved an iterative process to computing the non-zero terms of the underlying polynomial chaos model using only enough samples to converge uncertainty interval predictions and Sobol index values based global nonlinear sensitivity estimates. The Earth entry vehicle was analyzed at three points along a representative trajectory for a Mars return mission. 329 sources of uncertainty were identified in the computational fluid dynamics model used to predict the forebody convective heating. These included uncertainty in flow field chemical rates, collision integrals, heats of formation, surface finite rate char model reaction rates, wall roughness height, and the turbulent Schmidt number. Results from this study showed that convective heating uncertainty as high as 50% of the nominal was predicted with only about 50 evaluations of the computational model. This was far fewer than would be required for a sampling-based approach or a full basis polynomial chaos model, which would have required over 50,000 samples. Additionally, results showed that over 90% of the total convective heating uncertainty was due to uncertainty in the N2catalytic rate on the surface, while the remainder of the uncertainty was attributed to the turbulent Schmidt number and the wall roughness uncertainties.

Thomas K West IV↗

Algebraic Turbulence-Chemistry Interaction Model

The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

Norris, Andrew T.↗

Fermi-Based Kinetic Model for the Sabatier Reaction: Sabatier Principle and Beyond It

The CO 2 methanation reaction (aka the Sabatier reaction) is one of the important carbon utilization technologies to reduce atmospheric greenhouse gases. In this study, kinetic modeling of the Sabatier reaction proceeding via the CO route has been presented by considering weak and strong chemisorption concepts rooted in electronic theory. Based on the single-route mechanism of the Sabatier reaction, the dependence of the reaction rate on the position of the catalyst Fermi level with respect to the antibonding states of the reagent (CO 2 ) and the product (CH 4 ), is demonstrated with the classic Sabatier volcano-shape. Furthermore, the model was applied to explain experimental results of reaction rates for Ni- and Ru-based catalytic systems and to understand origin of enhancement of turnover frequencies established for dynamic catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantitative analyses of products and rates in polyethylene depolymerization and upcycling

Depolymerization and upcycling are promising approaches to managing plastic waste. However, quantitative measurements of reaction rates and analyses of complex product mixtures arising from depolymerization of polyolefins constitute significant challenges in this emerging field. Here, we detail techniques for recovery and analysis of products arising from batch depolymerization of polyethylene. We also describe quantitative analyses of reaction rates and products selectivity. This protocol can be extended to depolymerization of other plastics and characterization of other product mixtures including long-chain olefins. For complete details on the use and execution of this protocol, please refer to Sun et al.

Lee, Yu-Hsuan↗