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Data and code for reproducing the deep learning framerwork described in CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters
Here, this study revisits the three-point sampling of the simplified Butler-Volmer equation to address the limitations of strong potentiodynamic polarization, which can introduce irreversible damage and uncertainty in corrosion analysis. The method extracts electrochemical kinetic parameters while minimizing polarization effects, evaluates noise sensitivity relative to overpotential, and accounts for errors from signal noise, OCP drift, ohmic resistance, and mass-transfer constraints. Verified against the Tafel extrapolation method for aluminum corrosion across a wide pH range, this low-polarization approach enables accurate evaluations with specific error estimates, offering a robust alternative to linear polarization resistance methods that assume constant Tafel slopes.
Triaminotrinitrobenzene-based high explosives such as LX-17 offer high energy density and exceptional safety, yet their long-term aging behavior at low temperatures remains poorly understood. In this study, several legacy and new production lots of LX-17 were subjected to accelerated aging experiments below 100°C, during which the formation rate of the initial degradation product, monofurazan (F1), was monitored. Kinetic analysis was performed using a sample-age-aware computational approach, yielding activation energy estimates of 82–91 kJ mol −1 for the low-temperature initiation step—markedly lower than the ∼200 kJ mol −1 associated with high-temperature thermal decomposition. Extrapolation from established cookoff models supports the conclusion that the dominant degradation mechanism at low temperatures differs from that at high temperatures. In conclusion, our results provide a unified kinetic framework that bridges the gap between in-service conditions and high-temperature damage.
Here, the goal of the present work was to provide the necessary reaction emulation information to enable detailed process simulation of a chemical looping H 2 production system from fossil fuels using CaFe 2 O 4 . This specifically pertained to the necessary kinetic data, reaction model development, and model rate parameters required for reaction emulation in both reducing and oxidizing environments. A logical methodology was defined, which included discretization of the reaction network, establishing a core model for reaction emulation that could be adapted based on the system phenomena, and development of a rate parameter regression tool designed around the core model. An extensive array of data sets was acquired by which parametric regressions were performed. The work presented and tabulated a comprehensive set of rate parameters for the reduction and oxidation reactions of CaFe 2 O 4 and descendent phases of Ca 2 Fe 2 O 5 , FeO, Fe 3 O 4 , Fe, and CaO to emulate reaction behavior in a looping-based process environment. This included direct reduction using CH 4 , H 2 , and CO, and direct oxidation reactions with steam, CO 2 and O 2 . Dynamic equilibrium was quantified for reactions that could utilize H 2 O and CO 2 as soft oxidants to re-saturate lattice oxygen in the depleted structure/phases. The kinetics associated with the oxidative mechanisms with the soft oxidants were quantified and compared to those of the reducing counterparts. The analysis provided critical insight to emulate reactions for a process that seeks to use natural gas (NG) or other fossil fuels as a direct reductant for the end goal of H 2 production.
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We undertook a detailed rheological investigation to evaluate the kinetic parameters of the forward and reverse Diels–Alder (DA) reactions of a model network cross-linked using a furan prepolymer and a common aromatic bismaleimide. At high temperature where the Winter–Chambon’s criterion of frequency-independence was more applicable, a multiwave technique permitted van’t Hoff analysis and calculation of the reaction thermodynamic parameters, specifically the enthalpy and entropy of the reaction: ΔH° = –38.3 ± 5.2 kJ mol –1 and ΔS° = –94.3 ± 13.4 J mol –1 . At mild temperatures where the G'–G" crossover point is experimentally convenient to measure gelation, isothermal tests were used to obtain reasonable fDA kinetic parameters from Eyring analysis such as the apparent activation enthalpy and entropy of ΔH$^{‡}_{fDA}$ = 76.8 ± 6.9 kJ mol –1 and ΔS$^{‡}_{fDA}$= –82.8 ± 22.2 J mol –1 K –1 . Comparable rheokinetic methods include cross-linking density measurements and stress relaxation tests to calculate effective kinetics, whereas the critical gel conversion was consistently applied here. As a result, rate data are fitted with the Arrhenius equation for comparison purposes and the Eyring equation to demonstrate its broader utility.
The nodal diffusion method is one of the most widely used approaches in modern reactor analysis. In the nodal diffusion method, a coarse multi-group set of “homogenized” parameters is constructed such that the complex geometry of a reactor core along with the energy dependence of neutron and gamma ray cross sections in a nuclear reactor are conserved in the simpler geometry. The homogenization is typically done on a fuel assembly level as is the case in the DIF3D code developed at Argonne National Laboratory. The nodal methodology is used primarily to predict fuel cycle behavior of nuclear systems of which there is a substantial amount of validation in the literature. Another use of the nodal method is to obtain reactivity coefficients and kinetics parameters for use in a safety analysis of a given nuclear reactor. While there are many ways to obtain reactivity worth and kinetics parameters, the work presented in this manuscript is unique as it provides the user with the ability to compute reactivity worths, kinetics parameters, and cross section sensitivities with a Cartesian and hexagonal geometry-based transport code.
The nodal diffusion method is one of the most widely used approaches in modern reactor analysis. In the nodal diffusion method, a coarse multi-group set of “homogenized” parameters is constructed such that the complex geometry of a reactor core along with the energy dependence of neutron and gamma ray cross sections in a nuclear reactor are conserved in the simpler geometry. The homogenization is typically done on a fuel assembly level as is the case in the DIF3D code developed at Argonne National Laboratory. The nodal methodology is used primarily to predict fuel cycle behavior of nuclear systems of which there is a substantial amount of validation in the literature. Another use of the nodal method is to obtain reactivity coefficients and kinetics parameters for use in a safety analysis of a given nuclear reactor. While there are many ways to obtain reactivity worth and kinetics parameters, the work presented in this manuscript is unique as it provides the user with the ability to compute reactivity worths, kinetics parameters, and cross section sensitivities with a Cartesian and hexagonal geometry based transport code. This manuscript serves as a single manual for two separate codes: VARI3D and PERSENT. The VARI3D code (VARIational 3D) is based upon the classic finite difference diffusion theory solver available in DIF3D. The PERSENT code (PERturbation and SENitivity for Transport) is based upon the variational nodal method employed in DIF3D termed VARIANT. The VARIANT solver was added to DIF3D in 1995 and has seen continued development and use for the last 18 years. Because VARI3D primarily uses deprecated coding practices, rather than incorporating the perturbation and sensitivity treatments for transport within VARI3D, a new coding development was built using modern Fortran coding. The primary purpose of this manual is to describe the theory behind PERSENT (and by convenience, that of VARI3D) and discuss the input and output of PERSENT along with giving potential users an idea of how to use it. While this manuscript does describe the input and output of VARI3D, the PERSENT code is intended to be the replacement capability of VARI3D as PERSENT can generate nearly identical (if not superior) diffusion theory results. In this manuscript, the relevant aspects of generalized perturbation theory and exact perturbation theory that apply to both VARI3D and PERSENT are covered. The input and output of VARI3D is displayed by excerpting several of the example problems. Similarly, the input and output of PERSENT is displayed along with tips on how best to use the code. Note that the input and output of the inhomogeneous solver wrapped around DIF3D (DIF3D_IFS) is also discussed as it is needed to carry out some of the sensitivities in PERSENT such as reaction rate ratios. This manuscript describes several perturbation and sensitivity problems, and the results computed using PERSENT. From these sections, potential users should find that PERSENT provides not only the typical tables of numbers desired in perturbation and sensitivity analysis work, but also can visually plot the result for a more thorough understanding of the space and energy distribution (Section 5). Overall, PERSENT is observed to produce accurate reactivity worths and sensitivities for the displayed set of test problems and clearly demonstrates the need to have a transport-based sensitivity capability as evident from the thousands of percent errors observed in the 21-group hexagonal fast reactor problem (covered in Section 7). The uncertainty calculation capability is described in Section 3 and demonstrated in Section 7.
Visible photon fluxes can influence the rate and selectivity of heterogeneously catalyzed reactions on metal nanoparticle surfaces. Models describing the influence of photon fluxes have typically introduced photon flux dependent apparent thermal kinetic parameters (reaction orders, activation energies, binding energies, etc.). This has relied on empirical fitting of reaction rate data, making mechanistic interpretations of how photon fluxes influence elementary step rates challenging and inconsistent with fundamental descriptions of photochemistry on metal surfaces developed from surface science studies. Using the CO adsorption–desorption quasi-equilibrium reaction on Pt/Al 2 O 3 catalysts as a model system, we measured steady state adsorbed CO (CO*) coverages under isothermal and isobaric (1 mbar CO) conditions as a function of temperature (473–573 K) and of 440 nm photon flux ((0.1–5.2) × 10 3 # hv Pt site –1 s –1 ) using in situ IR spectroscopy. Steady state CO* coverage on Pt was photon flux dependent with increasing photon flux causing decreasing coverage, consistent with photons driving CO* desorption rates faster than thermal CO* desorption rates. However, photon flux dependent CO* coverages were essentially temperature independent, inconsistent with models that describe photon effects using perturbations to apparent thermal kinetic parameters. Instead, 120 steady state CO* coverages as a function of temperature and photon flux are quantitatively described by a kinetic model in which the overall desorption rate is a summation of independent thermal and photon induced CO* desorption rates. Site-resolved analysis reveals distinct kinetic parameters for photon driven desorption of CO* from well-coordinated, under-coordinated, and highly under-coordinated Pt sites, with temperature-dependent apparent quantum efficiencies (AQE) consistent with temperature dependence of vibrational quanta distribution of adsorbed CO. The rigorous kinetic rate laws for independent photon and thermal driven pathways allow for predictive modeling of the influence of photon fluxes on the rates of CO* desorption under catalytic conditions. Further, the analysis provides evidence that steady state continuous wave photon fluxes can drive desorption/adsorption reactions on metal surfaces out of thermal equilibrium, reconciling surface science observations of molecular photodesorption with applied catalysis. The work establishes a general kinetic framework to be considered for photon driven processes on metals, and defines catalyst, reaction, and photon flux characteristic design principles for breaking Sabatier limitations.
Mean-field microkinetic models (MKMs) are appealing for their relatively facile construction, computational tractability, and high-throughput catalyst screening capabilities. As such, they will continue to be a valuable tool for materials design in heterogeneous catalysis even as the field aims to describe more complex systems. Numerous prior reports have provided the groundwork for constructing first-principles-based MKMs, including the analysis of strategies for incorporating lateral interactions into thermodynamic parameters (e.g., adsorption energies). Yet, there remains a need for concerted dialogue on methods for calculating and incorporating coverage-dependent kinetic parameters into MKMs. In this Perspective, we assess strategies for doing so, including the corresponding key physical implications and computational challenges. Here, we emphasize that decoupling thermodynamic and kinetic parameters within MKMs can violate thermodynamic consistency and risk unphysical solutions. For some reactions and catalyst materials, scaling relationships can predict coverage-dependent activation energies, but there are several exceptions evident in the literature, indicating that this approach is not universally applicable and that the field could benefit from research aimed at elucidating the limitations. Conducting high-coverage transition state searches is a rigorous but computationally costly strategy, and the effects of various methods for mitigating this cost on resulting energetics have yet to be broadly explored and validated. The goal of this Perspective is to generate discussion on and inspire focused research into the physical relevance of approaches for describing coverage-dependent reaction barriers in MKMs, including the development of computationally tractable methodologies, to advance the applicability of MKMs across diverse reaction chemistries and conditions.
Temperature-controlled, time-resolved picosecond electron pulse radiolysis was utilized to measure the rate of reaction between the solvated electron (eS–) and dissolved oxygen in n-dodecane solutions from 2.5 to 40 °C for the first time. At 20.0 °C, the reaction rate was determined to be k(eS– + O2) = (4.54 ± 0.21) × 1010 M-1 s-1, with an activation energy of Ea = 14.4 ± 1.3 kJ mol-1. These newly determined kinetic parameters are important for predicting and managing the effects of aerated environments on the degradation of organic solvents used in nuclear fuel reprocessing technologies.
Microkinetic models for catalytic systems require estimation of many thermodynamic and kinetic parameters that can be calculated for isolated species and transition states using ab initio methods. However, the presence of nearby coadsorbates on the surface can dramatically alter these thermodynamic and kinetic parameters causing them to be dependent on species coverage fractions. As there are combinatorially many coadsorbed configurations on the surface, computing the coverage dependence of these parameters is far less straightforward. We present a framework for generating and applying machine learning models to predict coverage-dependent parameters for microkinetic models. Our toolkit enables automatic calculation and evaluation of coadsorbed configurations allowing us to sample 2,000 coadsorbed adsorbates and transition states (TSs) for a diverse set of 9 reactions on Cu(111), a challenging surface, with four possible coadsorbates. This dataset was then used to train subgraph isomorphic decision trees (SIDTs) to predict the stability and association energy of configurations. We were able to achieve mean absolute errors (MAEs) of 0.106 eV on adsorbates, 0.172 eV on TSs, and due to natural error cancellation in SIDTs for relative properties, 0.130 eV on reaction energies and 0.180 eV on activation barriers. In conclusion, we describe how to use these models to predict coverage-dependent corrections for adsorbates and TSs and demonstrate on H*, HO*, and O* comparing the generated SIDT model with an iteratively refined version.
Ongoing commercial design activities require a thorough verification of the Argonne Reactor Computation codes be performed. DIF3D is central to this system and substantial work has been done to verify its accuracy on several identified commercial needs. This manuscript details the verification work done on PERSENT which relies upon the DIF3D code for its forward and adjoint flux solution. Previous work identified the PERSENT features required to be verified to support commercial design activities, features of which are generally applicable to hexagonal-Z fast reactor designs. The scope of this verification effort includes verifying PERSENT’s ability to correctly calculate four key quantities: perturbation worth distributions, kinetics parameters, sensitivity coefficients, and cross section uncertainty quantification. This manuscript provides the verification tasks and their results with respect to these quantities needed for commercial design activities. For the perturbation worth distributions, hand calculations are deployed to verify the PERSENT calculated results. Similarly, hand calculation of the PERSENT computed kinetics parameters is also used to verify the PERSENT results. In both of these, the input to PERSENT is manipulated to ensure the hand calculation exactly matches the equations PERSENT is calculating. The sensitivity coefficients involve calculating the derivatives of a parameter (such as reactivity worth), with respect to the cross section data. Direct finite difference calculations with DIF3D are used to verify the PERSENT calculated results. For the uncertainty quantification, manufactured input to PERSENT is used to allow an exact hand calculation to reproduce the PERSENT calculated results. The work detailed in this report verified that significant issues were identified for earlier versions of PERSENT for sensitivity coefficients which were corrected in this work and thus version 12.1.0 of PERSENT must be used to reproduce all of the verified work in this report.
A phase field model is used to investigate how the corrosion rate and morphology of a dealloying metal is controlled by the kinetic rates of bulk solid diffusion, interfacial diffusivity, and interface dissolution. A specific focus is investigating the manner by which variations in these kinetic parameters synergistically influence the onset of a morphological instability at the solid-liquid interface, which is known to precede rapid dealloying corrosion towards highly topologically complex structures such as bicontinuous porous solids. This work demonstrates that this instability can be suppressed by either an increase of interdiffusion in the solid alloy, or by a decreasing rate of dissolution at the solid-liquid interface. When the instability is suppressed, the result is a relatively planar, passivated dealloying front. Importantly, however, coupled changes in kinetic parameters can also promote the morphological instability and sustain fine-scale ligament and pore formation. Finally, the relevance of the solid-liquid interfacial diffusion for determining the rate of dealloying and ligament formation is highlighted. By elucidating the mechanistic influence of bulk and interfacial kinetic factors on the dealloyed morphology, this work helps to rationalize the contrasting morphologies observed in various dealloying systems.
Here, this study develops intrinsic methane oxidation kinetics for ultra-lean methane conditions in the presence of water over a highly active and stable PtPd–Mg/θ-Al 2 O 3 catalyst. Comprehensive laboratory experiments were conducted over a wide range of methane concentrations (150–1200 ppm CH 4 ), water contents (1–5% H 2 O), and industrially relevant space velocities (80,000 ≤ GHSV ≤ 160,000 h -1 ). These systematic experiments informed a two-dimensional, axisymmetric, multiscale reactor model that was used to develop and validate methane oxidation kinetics under practically relevant conditions, including non-isothermal operation and high conversion regimes. Combined experimental and modeling results revealed significant intraparticle diffusion resistance and transport-induced reaction exotherm at elevated temperatures, which limited catalyst utilization despite high intrinsic activity. These transport effects were explicitly incorporated into the reactor model, enabling accurate estimation of intrinsic kinetic parameters without reliance on conventional effectiveness-factor corrections. The resulting kinetic model successfully captured both kinetically controlled and mass-transfer-limited regimes and reliably predicted CH 4 conversion across broad ranges of temperature, methane concentration, and water content
The chemical pulping of biomass involves the recycling of calcium through the calcination of lime mud, which is mostly comprised of calcium carbonate (CaCO 3 ). Lime mud decomposes under elevated temperatures to generate calcium oxide (CaO) and carbon dioxide (CO 2 ), the kinetics of which are strongly influenced by the CO 2 partial pressure and temperature. Oxy-fuel combustion and electrified lime kilns for lime mud calcination are intriguing methods to decarbonize this highly polluting operation within the biomass pulping industry. However, the high CO 2 concentration in oxy-fuel and electrified calcination processes alters the kinetics and overall reactivity of lime mud. For the first time, a model-fitting method is used to determine the kinetic parameters for lime mud calcination under a wide range of temperatures (550 °C–1250 °C) and under different concentrations of CO2 (0 %, 15 %, 50 %, and 90 %). A kinetic model is developed that accurately predicts the reaction rates as a function of temperature and CO 2 concentration. The apparent activation of energy for lime mud calcination is elevated under a high CO 2 environment. Relative to inert gas (N 2 , Ar), the temperature window for calcination is much smaller under high CO 2 environments. The presence of Na in lime mud does not seem to affect calcination under a high CO 2 environment. Finally, particle size variation does not have a significant effect on calcination under a high CO 2 environment.
An alkyne-terminated cobalt complex, [Co(Cp)(dppe ≡H )(Cl)] + (Cp = cyclopentadienyl; dppe ≡H = 1,2-bis-(di-(4-ethynyl-phenyl)phosphino)ethane), (Co ≡H ) was immobilized onto a glassy carbon electrode using two attachment strategies: Cu(I) catalyzed azide–alkyne click chemistry and reductive electropolymerization. The modified electrodes prepared through reductive electropolymerization exhibit current densities and peak resolutions for the electrochemical reduction of the cobalt species, which are amenable to electroanalytical quantification of coupled chemical reactions. Through peak shift analysis of cyclic voltammograms recorded in the presence of 4-chloroanilinium tetrafluoroborate, we quantified the proton transfer rate constant for the stepwise proton-coupled electron transfer reaction that reduces the electrode-immobilized [Co(Cp)(dppe ≡H )(Cl)] + to [H–Co(Cp)(dppe ≡H )] + (k PT app = (9.3 ± 1.8) × 10 5 M –1 s –1 ). In conclusion, the extraction of kinetic parameters for an elementary proton-coupled electron transfer reaction of an electrode-immobilized complex represents the first experimental measurement of its type and lays crucial groundwork for kinetic analyses of hybrid catalyst–electrode architectures.
The kinetics and thermodynamics of elementary reaction steps involved in the catalytic reduction of protons to hydrogen define the reaction landscape for catalysis. The mechanisms can differ in the order of the elementary proton transfer, electron transfer, and bond-forming steps and can be further differentiated by the sites at which protons and electrons localize. Access to fully elucidated mechanistic, kinetic, and thermochemical details of molecular catalysts is crucial to facilitate the development of new catalysts that operate with optimal efficiency, selectivity, and durability. The mechanism by which a catalyst operates, as well as the kinetics and thermodynamics associated with the individual steps, can often be accessed through electroanalytical studies. Here, this Account details the application of cyclic voltammetry to interrogate reaction mechanisms and quantify the kinetics and thermodynamics of elementary reaction steps for a series of molecular catalysts that mediate electrochemical proton reduction. I distinguish the limiting scenarios wherein a catalyst operates under kinetic control vs thermodynamic control, with a focus on detecting how cyclic voltammetry features shift with proton source strength and concentration, as well as scan rate. For systems that operate under kinetic control, catalytic currents are observed at, or slightly positive toward, the formal potential for the redox process that triggers catalysis. Under thermodynamic control, catalytic responses shift as a function of the proton source pKa and effective pH of the solution. After drawing this distinction, we introduce the appropriate voltammetry experiments and accompanying analytical expressions for extracting key metrics from the data. To illustrate analytical strategies to quantify elementary reaction steps of catalysts operating under kinetic control, I describe our studies of proton reduction catalysts Co(dmgBF 2 ) 2 (CH 3 CN) 2 (dmgBF 2 = difluoroboryl-dimethylglyoxime) and [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ (P 2 Ph N 2 Ph = 1,5-phenyl-3,7-phenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, peak shift analysis, foot-of-the-wave analysis, and plateau current analysis are applied to data sets wherein voltammetric response are recorded as a function of catalyst concentration, proton source concentration, proton source strength, and scan rate to quantify rate constants for elementary proton transfer and bond-forming steps in a catalytic cycle. Further, the case study of [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ illustrates how complementary spectroscopic methods can bolster the mechanistic assignment. Collectively, these two studies showcase how detailed mechanistic studies inform on rate-limiting elementary steps in catalysis and other key processes underpinning catalysis. Second, I present analytical strategies to interrogate catalysts operating under thermodynamic control, centered on the case study of [Ni II (P 2 Ph N 2 Bn ) 2 ] 2+ (P 2 Ph N 2 Bn = 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, the application of nonaqueous Pourbaix theory to extract thermodynamic information is introduced, and the construction of a coupled Pourbaix diagram is detailed. This study identifies ligand-based protonation as the key process that places catalysis under thermodynamic control and influences the reaction mechanism. Together, the work detailed in this Account showcases the utility of electroanalytical methods to disentangle complex reaction mechanisms and extract key thermochemical and kinetic parameters for elementary steps of catalysis. Through detailed presentation of the key analytical expressions that underpin these analyses, this Account seeks to facilitate the adoption of cyclic voltammetry by the community to fully extract kinetic, thermochemical, and mechanistic information on electrochemical small-molecule activation.