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At least 505 records · Page 28

A chemical kinetics theory for interpreting the non-monotonic temperature dependence of enzymatic reactions

Abstract. One notable observation of enzymatic chemical reactions is that, for a given abundance of enzymes and substrates, temperature increases cause reaction rates to first increase consistent with the Arrhenius relationship, then plateau, and finally fall off quickly to zero at high temperatures. While many mathematical functions have been used to describe this pattern, we here propose a chemical kinetics theory which successfully replicates this observation and provides insights into the processes responsible for these dynamics. The chemical kinetics theory combines the law of mass action, von Smoluchowski's diffusion-limited chemical reaction theory, and Eyring's transition state theory. This new theory reveals that the thermally reversible enzyme denaturation ensured by the ceaseless thermal motion of molecules and ions in an enzyme solution explains the plateau and subsequent decrease in chemical reaction rates with increasing temperature. The temperature-dependent affinity parameter (K) that relates enzymes and substrates through their binding also affects the shape of the emergent temperature response. We demonstrate that with an increase in substrate availability, K shifts the optimal temperature, where reaction rates plateau, towards higher values. Further, we show that the chemical kinetics theory accurately represents 12 sets of published enzyme assay data and includes the popular mechanistic model by Ratkowsky et al. (2005) as a special case. Given its good performance and solid theoretical underpinning, we believe this new theory will facilitate the construction of more mechanistic-based environmental biogeochemical models.

Tang, Jinyun↗

Determining the Role of Synthesis and Reaction Conditions on the Exposed Surface and Shape of ..beta..-Mo2C Catalysts

The production of drop-in quality biofuels typically can be achieved through catalytic fast pyrolysis (CFP) of biomass, followed by hydrodeoxygenation (HDO) of the vapor-phase product to reduce the oxygen content and stabilize the bio-oil product. To favor selectivity toward desired deoxygenation products, bifunctional catalysts with both acidic and hydrogenation sites are often employed. Due to both its oxophilicity and its ability to promote hydrogenation reactions, molybdenum carbide catalysts have shown promise for promoting the HDO of CFP vapors. However, the surface structure and composition of carbide catalyst particles are not well understood, precluding the establishment of fundamental structure-function relationships needed for the rational development of molybdedum carbide for HDO, as well as other reactions. For orthorhombic ..beta..-Mo2C, the (100) facet is largely studied for computational surface-reaction analyses, possibly due to its similarities with the close-packed (111) facet of noble-metal catalysts. However, it has previously been postulated through ab initio thermodynamic studies that the (111), (110), and (011) facets are most stable, though there is no consensus. Furthermore, while a majority of previous surface stability analyses of ..beta..-Mo2C focus on bulk terminations, the highly carburizing synthesis conditions and the use of ..beta..-Mo2C in carbon-containing reaction applications could introduce non-stoichiometric coverages of surface carbon. As such, this study uses ab initio thermodynamics calculations to assess the relative surface stability of the low-index facets of ..beta..-Mo2C, including consideration of varying the coverage of surface carbon. From this information, Wulff constructions are utilized to predict the synthesis and reaction condition-dependent shape and surface carbon composition of ..beta..-Mo2C catalyst particles.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

Learning heterogeneous reaction kinetics from X-ray movies pixel-by-pixel

Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries 1 and electrocatalysts 2. Experimental characterizations of such materials by operando microscopy produce rich image datasets 3–6, but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation 7. Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces.

Chueh, William↗

Simultaneous reaction and separation of chemicals

The reaction rate of hydrocarbon pyrolysis can be increased to produce solid carbon and hydrogen by the use of molten materials which have catalytic functionality to increase the rate of reaction and physical properties that facilitate the formation and contamination-free separation of the solid carbon. Processes, materials, reactor configurations, and conditions are disclosed whereby methane and other hydrocarbons can be decomposed at high reaction rates into hydrogen gas and carbon products without any carbon oxides in a single reaction step. The process also makes use of specific properties of selected materials with unique solubilities and/or wettability of products into (and/or by) the molten phase to facilitate generation of purified products and increased conversion in more general reactions.

McFarland, Eric W.↗

Methods for isothermal molecular amplification with nanoparticle-based reactions

The present method of detection involves increasing an amount of analyte molecules by an isothermal molecular amplification approach. In the present approach a starting molecule of interest may be amplified through a reaction it induces with specifically engineered and functionalized particles, namely protected particles A and storage particles B. This reaction may result in a set of output DNA molecules that is larger in number than the input DNA molecules. Thus the reaction between nanoparticles for amplification of a certain DNA sequence (input DNA molecules) may occur when there is a match with a targeted molecule (stored molecules on storage particles B) and if the DNA sequence of the input DNA molecules does not match (partially or completely) the targeted molecule the reaction may not occur. Without a certain molecular input of the input DNA molecule the reaction may not occur.

Gang, Oleg↗

Understanding the Active Site Structures and Achieving Catalytic Activity Tuning of Atomically Dispersed FeN 4 Sites for Oxygen Reduction Reaction

Atomically dispersed Fe–—N—C catalysts with high oxygen reduction reaction (ORR) activity have attracted great attention since the last decade. Due to comparable ORR activity and low material cost, they are promising platinum group metal (PGM)-free catalysts that can replace the commercialized Pt/C materials; furthermore, it can facilitate the efficiency of the fuel cell technologies and mitigate dependence on fossil fuels. Great advancements have been made to experimentally optimize the synthesis approach of the Fe–—N—C catalysts, enhance the ORR activity, and improve the catalyst stability. Similarly, recent theoretical studies also provide enriched understanding of the active site structures, properties, and reaction mechanisms. In this review, discussions are made upon utilizing combined experimental and computational spectroscopy to reveal the active site structures, employing mechanistic studies to investigate reaction thermodynamics and kinetics, as well as developing scaling relationships to assist the design and development of future PGM-free catalyst materials. Furthermore, recent advances in studying Fe–—N—C catalysts utilizing electrified surface models and explicit solvation models are also discussed. Not only can these aspects improve the accuracy of theoretical simulation and predictions but also deepen the understanding of the catalyst properties and reaction mechanisms under the effect of surface charges and solvent molecules.

Fe single-atom catalysts↗

Analysis and prediction of reaction kinetics using the degree of rate control

“Degree of rate control” (DRC) analysis provides a quantitative approach for analysing the kinetics of multi-step reaction mechanisms that has been widely applied to both heterogeneous and homogeneous catalysis research, as well as electrocatalysis. The DRC of any given transition state or intermediate is defined as a partial derivative such that it approximately equals the fractional increase in net rate to the product of interest per differential decrease in its standard-state free energy for that species (÷RT), holding constant the standard-state free energies of all other transition states and intermediates. Even very complex mechanisms usually have only a few species with non-zero DRCs and are thus the species whose interactions with the catalyst most strongly affect the net rate. These key DRC values thus offer a simple and intuitive route to optimize catalyst materials, especially with the assistance of computational methods like density functional theory (DFT). These high-DRC species are also the species whose energetics must be most accurately measured or calculated to achieve an accurate kinetic model for any reaction mechanism. In simple cases with a single “rate-determining step”, the DRC for its transition state (TS) is + 1. Catalyst-bound intermediates, on the other hand, often have negative DRCs equal to a small integer times their fractional occupancy of catalyst sites. The apparent activation energy equals a weighted average of the standard-state enthalpies (relative to reactants) of all the species (intermediates, transition states and products) in the reaction mechanism, each weighted by its DRC (+RT). It has been shown that the apparent transfer coefficient in electrocatalysis, an inverted form of the Tafel slope, is a weighted average of the number of electrons transferred to generate each intermediate or product species in the mechanism, weighted again by the DRC. Quantitative analysis of kinetic isotope effects (KIEs, or the ratio of net rates for different reactant isotopes) in complex mechanisms has shown that the logarithm of the KIE equals the weighted average over all species in the mechanism of the difference between the two isotopes in their standard-state free energies (÷RT), again weighted by the DRC. The reaction orders with respect to fluid-phase concentrations of reactants, products and intermediates have also been proven to be directly related to DRCs. Thus, there are numerous experimental observables which equate to short linear combinations of DRCs, so that combinations of experimental measurements might provide access to DRC values. Since its invention for transition states in 1994 and its generalization to include intermediates in 2009, the DRC has thus far mainly been calculated for microkinetic models based either entirely on DFT or on DFT with the key energies (i.e., those for high-DRC species) being fine-tuned to match experiments. The relationships summarized in this work provide new opportunities for using experiments earlier in the development and optimization of microkinetic models that require input from computational catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Degrees of Rate Control in Interconnected Reaction Networks

Overall reactions in interconnected networks exhibit net, forward, and reverse rates that are governed by both constitutive elementary steps in the pathway of interest and branching elementary steps that lead to alternative products. Accordingly, steps in branching pathways exhibit negative net, forward, and reverse degrees of rate control, as they reduce reaction flux to the desired product. We here contextualize the forward and reverse degrees of rate control in terms of kinetic resistances (inverse of rates) and leverage the additive nature of kinetic resistance to decouple kinetic driving forces contributed by constitutive elementary steps and branching points (nodal species) in interconnected networks. Regardless of the network connectivity, forward and reverse degrees of rate control are shown to converge at equilibrium. Away from equilibrium, we identify two critical features of interconnected networks: stoichiometric regularity─condition where all stoichiometric numbers are unity─and pathway symmetry around nodal species─condition where branching pathways share the same rate constants, stoichiometry, and species concentrations/activities─that result in (i) equal forward, reverse, and consequently net degrees of rate control and (ii) forward and reverse degrees of rate control that exhibit constant offsets, respectively, across all extents of reaction. Furthermore, our discourse further provides a mathematical description for the influence of stoichiometric irregularity and pathway asymmetry on forward and reverse degrees of rate control. Altogether, the presented work details the effects of network (inter)connectivity and stoichiometry on reaction kinetics and, in doing so, establishes general protocols for capturing these effects as additive terms in the formulation of forward and reverse degrees of rate control.

10 SYNTHETIC FUELS↗

Trace Key Mechanistic Features of the Arsenite Sequestration Reaction with Nanoscale Zerovalent Iron

Nanoscale zerovalent iron (nZVI) is considered as a highly efficient material for sequestrating arsenite, but the origin of its high efficacy as well as the chemical transformations of arsenite during reaction is not well understood. Here, in this study, we report an in situ X-ray absorption spectroscopy (XAS) study to investigate the complex mechanism of nZVI reaction with arsenite under anaerobic conditions at the time scale from seconds to days. The time-resolved XAS analysis revealed a gradual oxidation of As III to As V in the course of minutes to hours in both the solid and liquid phase for the high (above 0.5 g/L) nZVI dose system. When the reaction time increased up to 60 days, As V became the dominant species. The quick-scanning extended X-ray absorption fine structure (QEAXFS) was introduced to discover the transient intermediate at the highly reactive stage, and a small red-shift in As K-edge absorption edge was observed. The QEAXFS combined with density functional theory (DFT) calculation suggested that the red-shift is likely due to the electron donation in a Fe-O-As complex and possible active sites of As sequestrations include Fe(OH) 4 and 4-Fe cluster. This is the first time that the transient reaction intermediate was identified in the As-nZVI sequestration system at the fast-reacting early stage. This study also demonstrated usefulness of in situ monitoring techniques in environmental water research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unconventional excited-state dynamics in the concerted benzyl (C7H7) radical self-reaction to anthracene (C14H10)

Abstract Polycyclic aromatic hydrocarbons (PAHs) are prevalent in deep space and on Earth as products in combustion processes bearing direct relevance to energy efficiency and environmental remediation. Reactions between hydrocarbon radicals in particular have been invoked as critical molecular mass growth processes toward cyclization leading to these PAHs. However, the mechanism of the formation of PAHs through radical – radical reactions are largely elusive. Here, we report on a combined computational and experimental study of the benzyl (C 7 H 7 ) radical self-reaction to phenanthrene and anthracene (C 14 H 10 ) through unconventional, isomer-selective excited state dynamics. Whereas phenanthrene formation is initiated via a barrierless recombination of two benzyl radicals on the singlet ground state surface, formation of anthracene commences through an exotic transition state on the excited state triplet surface through cycloaddition. Our findings challenge conventional wisdom that PAH formation via radical-radical reactions solely operates on electronic ground state surfaces and open up a previously overlooked avenue for a more “rapid” synthesis of aromatic, multi-ringed structures via excited state dynamics in the gas phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Femtosecond dynamics and coherence of ionic retro-Diels–Alder reactions

Ultrafast tunnel ionization enables femtosecond time-resolved dynamic measurements of the retro-Diels–Alder reactions of positively charged cyclohexene, norbornene, and dicyclopentadiene. Unlike the reaction times of 500–600 ps that are observed following UV excitation of neutral species, on the ionic potential energy surfaces, these reactions occur on a single picosecond timescale and, in some cases, exhibit vibrational coherence. In the case of norbornene, a 270 cm –1 vibrational mode is found to modulate the retro-Diels–Alder reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the use of stereodynamical effects to control cold chemical reactions: The H + D 2 ↔ D + HD case study

Here, quantum calculations are reported for the stereodynamic control of the H + D 2 ↔ D + HD chemical reaction in the energy range of 1–50 K. Stereodynamic control is achieved by a formalism similar to that reported by Perreault et al. [Nat. Chem. 10, 561 (2018)] in recent experimental works in which the alignment of the molecular bond axis relative to the incident relative velocity is controlled by selective preparations of the molecule in a specific or superposition of magnetic projection quantum numbers of the initial molecular rotational level. The approach presented here generalizes the experimental scheme of Perreault et al. and offers additional degree of control through various experimental preparations of the molecular alignment angle. Illustrative results presented for the H + D 2 and D + HD reactions show significant control with the possibility of turning the reaction completely on or off with the appropriate stereodynamic preparation of the molecular state. Various scenarios for maximizing and minimizing the reaction outcomes are identified with the selective preparation of molecular rotational states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First measurement of the 10B(α,n)13N reaction in an inertial confinement fusion implosion at the National Ignition Facility: Initial steps toward the development of a radiochemistry mix diagnostic

We report the first measurement of the 10B(α,n)13N reaction in a polar-direct-drive exploding pusher (PDXP) at the National Ignition Facility (NIF). This work is motivated by the need to develop alternative mix diagnostics, radiochemistry being the focus here. The target is composed of a 65/35 at. % deuterium–tritium (DT) fill surrounded by a roughly 30 μm thick beryllium ablator. The inner portion of the beryllium ablator is doped with 10 at. % of 10B. Radiation-hydrodynamics calculations were performed in 1D to optimize both the remaining boron rho-R and the DT neutron yield. A charged-particle transport post-processor has been developed to study α-induced reactions on the ablator material. Results indicate a large 13N production from α-induced reactions on 10B, measurable by the radiochemical analysis of a gaseous samples system at the NIF. The PDXP target N201115-001 was successfully fielded on the NIF, and nitrogen from the 10B(α,n)13N reaction was measured. The 13N production yield, as well as the DT neutron yield, was, however, lower than expected. Some of the reduced yields can be explained by the oblate shape, but the ratios of the various radiochemical signals are not commensurate with expectations based on a simple reduction of the 1D results. Preliminary 2D radiation-hydrodynamics computations are consistent with the experimental measurements, and work is ongoing to extend the radiochemistry analysis into higher dimensions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Low-energy 17 O(𝑛,𝛾)⁢ 18 O reaction within the microscopic potential model and its role for the weak 𝑟 process

The neutron radiative capture reaction 17 O ⁡(𝑛,𝛾) ⁢18 O plays a pivotal role in both nuclear structure studies and astrophysical nucleosynthesis, particularly in the formation of elements during hydrostatic and explosive stellar environments. We calculated the 17 O ⁡(𝑛,𝛾) ⁢18 O cross section within the Skyrme Hartree-Fock potential model and analyzed electric dipole 𝐸⁢1 transitions to both positive- and negative-parity states below the α-decay threshold in 18 O. Our cross sections are significantly different from the data available in commonly used libraries. We further investigate the impact of the new calculated cross section on weak 𝑟-process nucleosynthesis using large-scale reaction network calculations across a wide range of electron fractions and entropies. Our results show that the 17 O ⁡(𝑛,𝛾) ⁢18 O reaction rate significantly influences the production of first 𝑟-process peak elements, such as strontium, under specific astrophysical conditions. This study highlights the importance of accurate nuclear data for light isotopes in modeling heavy-element synthesis and provides updated reaction rates for future nucleosynthesis simulations.

6 ≤ A ≤ 19↗

γ-ray measurements in fast-neutron-induced reactions on 203 Tl

Fast-neutron-induced reactions can be used to characterize reaction mechanisms, investigate nuclear structure, and impose constraints on nuclear models. Because of the difficulty in predicting such effects, experimental data are important to constrain models. Thallium isotopes located close to the doubly magic Pb 208 nucleus are important for comparison with shell-model calculations. Study the population of excited states in Tl 203 and lighter isotopes in such reactions. Our methods are as follows. γ -ray cross sections were measured. The data were taken by using the Germanium Array for Neutron-Induced Excitations spectrometer. The pulsed neutron source of the Los Alamos Neutron Science Center's Weapons Neutron Research facility provided neutrons in the energy range from 1 to 300 MeV. The time-of-flight technique was used to determine the incident neutron energies. Cross sections for emission of several γ rays in 20 reaction channels were determined. Candidates for the intruder 9 / 2 - state in Tl 203 , from the odd proton in the h 9 / 2 orbital, and the first 5 + states in Tl 202 , 204 , from admixture of configurations, were identified. The excitation energy of the candidate 9 / 2 - , π h 9 / 2 state is in good agreement with the theoretical prediction from a semi-empirical weak-coupling model and its half-life is in the range of tens of nanoseconds. The feeding of a previously known isomer in Tl 202 exhibits similarities with the feeding of other isomers in this mass region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

New constraints on the Al 25 ( p , γ ) reaction and its influence on the flux of cosmic γ rays from classical nova explosions

The astrophysical 25 Al(p,γ) 26 Si reaction represents one of the key remaining uncertainties in accurately modeling the abundance of radiogenic 26 Al ejected from classical novae. Specifically, the strengths of key proton-unbound resonances in 26 Si, that govern the rate of the 25 Al(p,γ) reaction under explosive astrophysical conditions, remain unsettled. Here, we present a detailed spectroscopy study of the 26 Si mirror nucleus 26 Mg. We have measured the lifetime of the 3 + , 6.125-MeV state in 26 Mg to be 19(3) fs and provide compelling evidence for the existence of a 1 – state in the T = 1, A = 26 system, indicating a previously unaccounted for ℓ = 1 resonance in the 25 Al(p,γ) reaction. Using the presently measured lifetime, together with the assumption that the likely 1 – state corresponds to a resonance in the 25 Al + p system at 435.7(53) keV, we find considerable differences in the 25 Al(p,γ) reaction rate compared to previous works. Furthermore, based on current nova models, we estimate that classical novae may be responsible for up to ≈ 15% of the observed galactic abundance of 26 Al.

20 ≤ A ≤ 38↗

Neutron transfer reactions on the ground state and isomeric state of a 130 Sn beam

The structure of nuclei around the neutron-rich nucleus 132 Sn is of particular interest due to the vicinity of the Z = 50 and N = 82 shell closures and the r-process nucleosynthetic path. Four states in 131 Sn with a strong single-particle-like component have previously been studied via the (d,p) reaction, with limited excitation energy resolution. Here, the 130 Sn( 9 Be, 8 Be) 131 Sn and 130 Sn( 13 C, 12 C) 131 Sn single-neutron transfer reactions were performed in inverse kinematics at the Holifield Radioactive Ion Beam Facility using particle-γ coincidence spectroscopy. The uncertainties in the energies of the single-particle-like states have been reduced by more than an order of magnitude using the energies of γ rays. The previous tentative J π values have been confirmed. Decays from high-spin states in 131 Sn have been observed following transfer on the isomeric component of the 130 Sn beam. The improved energies and confirmed spin-parities of the p-wave states important to the r-process lead to direct-semidirect cross-sections for neutron capture on the ground state of 130 Sn at 30 keV that are in agreement with previous analyses. A similar assessment of the impact of neutron-transfer on the isomer would require significant nuclear structure and reaction theory input. There are few measurements of transfer reaction on isomers, and this is the first on an isomer in the 132 Sn region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Uncertainty quantification in breakup reactions

Breakup reactions are one of the favored probes to study loosely bound nuclei, particularly those in the limit of stability forming a halo. In order to interpret such breakup experiments, the continuum discretized coupled channel method is typically used. In this study, the first Bayesian analysis of a breakup reaction model is performed. Herein we use a combination of statistical methods together with a three-body reaction model (the continuum discretized coupled channel method) to quantify the uncertainties on the breakup observables due to the parameters in the effective potential describing the loosely bound projectile of interest. The combination of tools we develop opens the path for a Bayesian analysis of not only breakup processes, but also a wide array of complex processes that require computationally intensive reaction models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗