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Results for “transition state theory”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Geo‐Structurally Based Correction Factor for Apparent Dissolution Rates in Fractured Media

Abstract Field measurements of apparent geochemical weathering reaction rates in subsurface fractured porous media are known to deviate from laboratory measurements by multiple orders of magnitude. To date, there is no geologically based explanation for this discrepancy that can be used to predict reaction rates in field systems. Proposed correction factors are typically based on ad hoc characterizations related to geochemical kinetic models. Through a series of high‐fidelity reactive transport simulations of mineral dissolution within explicit 3D discrete fracture networks, we are able to link the geo‐structural attributes with reactive transport observations. We develop a correction factor to linear transition state theory for the prediction of the apparent dissolution rate based on measurable geological properties. The modified rate law shows excellent agreement with numerical simulations, indicating that geological structure could be a primary reason for the discrepancy between laboratory and field observations of apparent dissolution rates in fractured media.

58 GEOSCIENCES↗
DOE OSTI2025

Anomalous entropy-driven kinetics of dislocation nucleation

The kinetics of dislocation reactions, such as dislocation multiplication, controls the plastic deformation in crystals beyond their elastic limit, therefore critical mechanisms in a number of applications in materials science. We present a series of large-scale molecular dynamics simulations that shows that one such type of reactions, the nucleation of dislocation at free surfaces, exhibit unconventional kinetics, including unexpectedly large nucleation rates under compression, very strong entropic stabilization under tension, as well as strong non-Arrhenius behavior. These unusual kinetics are quantitatively rationalized using a variational transition state theory approach coupled with an efficient numerical scheme for the estimation of vibrational entropy changes. These results highlight the need for a variational treatment of the kinetics to quantitatively capture dislocation reaction kinetics, especially at low-to-moderate strains where large deformations are required to activate reactions. These observations suggest possible explanations to previously observed unconventional deformation kinetics in both molecular dynamics simulations and experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

The Bell-Evans-Polanyi relation for hydrogen evolution reaction from first-principles

The versatile Bell-Evans-Polanyi (BEP) relation stipulates the kinetics of a reaction in terms of thermodynamics. Herein, we establish the BEP relation for the hydrogen evolution reaction (HER) from fundamental electrochemical principles leveraging the Butler-Volmer relation for a one-step, one-electron process and the transition state theory. Based on first-principles investigations of HER mechanisms on fourteen metal electrodes, we firmly justify the BEP relation solely using an easy-to compute hydrogen adsorption free energy and universal electrochemical constants.

42 ENGINEERING↗
DOE OSTI2022

High accuracy barrier heights, enthalpies, and rate coefficients for chemical reactions

Abstract Quantitative chemical reaction data, including activation energies and reaction rates, are crucial for developing detailed kinetic mechanisms and accurately predicting reaction outcomes. However, such data are often difficult to find, and high-quality datasets are especially rare. Here, we use CCSD(T)-F12a/cc-pVDZ-F12// ω B97X-D3/def2-TZVP to obtain high-quality single point calculations for nearly 22,000 unique stable species and transition states. We report the results from these quantum chemistry calculations and extract the barrier heights and reaction enthalpies to create a kinetics dataset of nearly 12,000 gas-phase reactions. These reactions involve H, C, N, and O, contain up to seven heavy atoms, and have cleaned atom-mapped SMILES. Our higher-accuracy coupled-cluster barrier heights differ significantly (RMSE of ∼5 kcal mol −1 ) relative to those calculated at ω B97X-D3/def2-TZVP. We also report accurate transition state theory rate coefficients $${k}_{\infty }(T)$$ k ∞ ( T ) between 300 K and 2000 K and the corresponding Arrhenius parameters for a subset of rigid reactions. We believe this data will accelerate development of automated and reliable methods for quantitative reaction prediction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The atmospheric importance of methylamine additions to Criegee intermediates

We report that Criegee intermediates are important targets for study in atmospheric chemistry because of their capacity to oxidize airborne species. Among these species, ammonia has received critical attention for its presence in polluted agricultural or industrial areas and its role in forming particulate matter and condensation nuclei. Although methylamine has been given less attention than ammonia, both theoretical and experimental studies have demonstrated that the additional methyl substitution on the ammonia derivatives increases the rate constants for some systems. This suggests that the methylamine addition to Criegee intermediates could be more significant to atmospheric processes. In this work, geometries are optimized at the DF-CCSD(T)/ANO1 level for the methylamine addition reactions to the simplest Criegee intermediate and the anti- and syn-methylated Criegee intermediates. Energies for each stationary point were computed at the CCSD(T)/CBS level with corrections from the CCSDT(Q) method. Rate constants are obtained for each reaction using canonical transition state theory. Although methylamine addition proved to be a more favorable reaction relative to ammonia addition, the significantly lower concentration of atmospheric methylamine limits the prevalence of these reactions, even in the most optimal conditions. It is unlikely that the methylamine addition to Criegee intermediates will contribute significantly to the consumption of Criegee intermediates in the atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Theoretical H + O 3 rate coefficients from ring polymer molecular dynamics on an accurate global potential energy surface: assessing experimental uncertainties

Thermal rate coefficients and kinetic isotope effects have been calculated for an important atmospheric reaction H/D + O 3 → OH/OD + O2 based on an accurate permutation invariant polynomial-neural network potential energy surface, using ring polymer molecular dynamics (RPMD), quasi-classical trajectory (QCT) and variational transition-state theory (VTST) with multidimensional tunneling. The RPMD approach yielded results that are generally in better agreement with experimental rate coefficients than the VTST and QCT ones, especially at low temperatures, attributable to its capacity to capture quantum effects such as tunneling and zero-point energy. Additionally, the theoretical results support one group of existing experiments over the other. In addition, rate coefficients for the D + O 3 → OD + O 2 reaction are also reported using the same methods, which will allow a stringent assessment of future experimental measurements, thus helping to reduce the uncertainty in the recommended rate coefficients of this reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The CH(X 2 Π) + H 2 O reaction: two transition state kinetics

he reaction of ground state methylidyne (CH) with water vapor (H 2 O) is theoretically re-investigated using high-level coupled cluster computations in combination with semi-classical transition state theory (SCTST) and two-dimensional master equation simulations. Insertion of CH into a H–O bond of H 2 O over a submerged barrier via a well-skipping mechanism yielding solely H and CH 2 O is characterized. The reaction kinetics is effectively determined by the formation of a pre-reaction van der Waals complex (PRC, HC—OH 2 ) and its subsequent isomerization to activated CH 2 OH in competition with PRC re-dissociation. The tunneling effects are found to be minor, while variational effects in the PRC → CH 2 OH step are negligible. The calculated rate coefficient k ( T ) is nearly pressure-independent, but strongly depends on temperature with pronounced down-up behavior: a high value of 2 x 10 -10 cm 3 s -1 at 50 K, followed by a fairly steep decrease down to 8 × 10 -12 cm 3 s -1 at 900 K, but increasing again to 5 × 10 -11 cm 3 s -1 at 3500 K. Over the T-range of this work, k ( T ) can be expressed as: k ( T , P = 0) = 2.31 × 10 -11 ( T /300 K) -1.615 exp(-38.45/ T ) cm 3 s -1 for T = 50-400 K k ( T , P = 0) = 1.15 × 10 -12 ( T /300 K) 0.8637 exp(892.6/ T ) cm 3 s -1 for T = 400-1000 K k ( T , P = 0) = 4.57 × 10 -15 ( T /300 K) 3.375 exp(3477.4/ T ) cm 3 s -1 for T = 1000–3500 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Predicting third-body collision efficiencies for water and other polyatomic baths

Low-pressure-limit microcanonical (collisional activation) and thermal rate constants are predicted using a combination of automated ab initio potential energy surface construction, classical trajectories, transition state theory, and a detailed energy- and angular-momentum-resolved collision kernel. Several systems are considered, including CH 4 (+M) and HO 2 (+M), with an emphasis on systems where experimental information is available for comparison. The a priori approach involves no adjustable parameters, and we show that the predicted thermal rate constants are in excellent agreement with experiments, with average deviations of less than 25%. Notably, the a priori approach is shown to perform equally well for atomic, diatomic, and polyatomic baths, including M = H 2 O, CO 2 , and “fuel” baths like M = CH 4 and NH 3 . Additionally, the utility of microcanonical rate constants for interpreting trends and inferring mechanistic details in the thermal kinetics is demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A matrix completion algorithm for efficient calculation of quantum and variational effects in chemical reactions

This work examines the viability of matrix completion methods as cost-effective alternatives to full nuclear Hessians for calculating quantum and variational effects in chemical reactions. The harmonic variety-based matrix completion (HVMC) algorithm, developed in a previous study (https://doi.org/10.1063/5.0018326), exploits the low-rank character of the polynomial expansion of potential energy to recover, using a small sample, vibrational frequencies (square roots of nuclear Hessian eigenvalues) constituting the reaction path. Furthermore, these frequencies are essential for calculating rate coefficients using variational transition state theory with multidimensional tunneling (VTST-MT). HVMC performance is examined for four SN2 reactions and five hydrogen transfer reactions, with each H-transfer reaction consisting of at least one vibrational mode strongly coupled to the reaction coordinate. HVMC is robust and captures zero-point energies, vibrational free energies, zero-curvature tunneling, and adiabatic ground state and free energy barriers as well as their positions on the reaction coordinate. For medium to large reactions involving H-transfer, with the exception of the most complex Ir catalysis system, less than 35% of total eigenvalue information is necessary for accurate recovery of key VTST-MT observables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Experimental and computational studies of the kinetics of the reaction of hydrogen peroxide with the amidogen radical

In this work, the pulsed-laser photolysis/laser-induced fluorescence method is used to study the kinetics of the reaction of NH 2 with H 2 O 2 to yield a second-order rate constant of (2.42 ± 0.55) × 10 –14 cm 3 molecule –1 s –1 at 412 K in 10–22 mbar of Ar bath gas. There are no prior measurements for comparison. To check this value and enable reliable extrapolation to other temperatures, we also compute thermal rate constants for this process over the temperature range 298–3000 K via multi-structural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT). The CVT/SCT rate constants are derived using a dual-level direct dynamics approach utilizing single-point CCSD(T)-F12b/cc-pVQZ-F12 energies—corrected for core-valence and scalar relativistic effects—and M06-2X/MG3S geometries, gradients, and Hessians—for all stationary and non-stationary points along the reaction path. The multistructural method with torsional anharmonicity, based on a coupled torsional potential, is then employed to calculate correction factors for the rate constants, accounting for the comprehensive effects of torsional anharmonicity on the kinetics of this reaction system. The final MS-CVT/SCT rate constants are found to be in good agreement with our measurements and can be expressed in modified Arrhenius form as 2.13 × 10 –15 (T/298 K) 4.02 exp(–513 K/T) cm 3 molecule –1 s –1 over the temperature range of 298–3000 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Stress-dependent activation entropy in thermally activated cross-slip of dislocations

Cross-slip of screw dislocations in crystalline solids is a stress-driven thermally activated process essential to many phenomena during plastic deformation, including dislocation pattern formation, strain hardening, and dynamic recovery. Molecular dynamics (MD) simulation has played an important role in determining the microscopic mechanisms of cross-slip. However, due to its limited timescale, MD can only predict cross-slip rates in high-stress or high-temperature conditions. The transition state theory can predict the cross-slip rate over a broad range of stress and temperature conditions, but its predictions have been found to be several orders of magnitude too low in comparison to MD results. This discrepancy can be expressed as an anomalously large activation entropy whose physical origin remains unclear. Here, we resolve this discrepancy by showing that the large activation entropy results from anharmonic effects, including thermal softening, thermal expansion, and soft vibrational modes of the dislocation. We expect these anharmonic effects to be significant in a wide range of stress-driven thermally activated processes in solids.

Science & Technology - Other Topics↗
DOE OSTI2020

Quasi-equilibrium predictions of water desorption kinetics from rapidly-heated metal oxide surfaces

Controlling sub-microsecond desorption of water and other impurities from electrode surfaces at high heating rates is crucial for pulsed power applications. Despite the short time scales involved, quasi-equilibrium ideas based on transition state theory (TST) and Arrhenius temperature dependence have been widely applied to fit desorption activation free energies. Here, we apply molecular dynamics (MD) simulations in conjunction with equilibrium potential-of-mean-force (PMF) techniques to directly compute the activation free energies (ΔG*) associated with desorption of intact water molecules from Fe 2 O 3 and Cr 2 O 3 (0001) surfaces. The desorption free energy profiles are diffuse, without maxima, and have substantial dependences on temperature and surface water coverage. Incorporating the predicted ΔG* into an analytical form gives rate equations that are in reasonable agreement with non-equilibrium molecular dynamics desorption simulations. We also show that different ΔG* analytical functional forms which give similar predictions at a particular heating rate can yield desorption times that differ by up to a factor of four or more when the ramp rate is extrapolated by 8 orders of magnitude. This highlights the importance of constructing a physically-motivated ΔG* functional form to predict fast desorption kinetics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"

This model data package is associated with the publication “Thermodynamic control on the decomposition of organic matter across different electron acceptors” submitted to Soil Biology and Biochemistry (Zheng et al., 2023; https://doi.org/10.1016/j.soilbio.2024.109364).In this research, a thermodynamic modeling framework is built to flexibly incorporate both organic matter (OM) molecules and electron acceptors for estimating potential free energy release from various redox reactions and to further predict reaction rates based on Microbial Transition State Theory. The model package includes scripts for thermodynamic modeling and postprocessing. Input Fourier-transform ion cyclotron resonance (FTICR) data are from a previous experimental study (Boye et al., 2018), and model outputs are free energy predictions and stoichiometric coefficients associated with all possible redox reactions.This data package is associated with the project GitHub repository found at MM_bioenergetic_modeling.This data package contains four folders (Input_FTICR, Model, Output, and Output_processing), a file-level metadata (FLMD) csv, and a data dictionary (dd) csv. Please see Zheng_bioenergetic_modeling_flmd.csv for a list of all files contained in this data package and descriptions for each. The Zheng_bioenergetic_modeling_dd.csv file describes the csv column headers. The “Model” folder contains scripts to run energy balance calculations for each electron acceptor. The “Output” folder contains csv files with stoichiometric information from model simulations. And the "Output_processing" folder contains scripts for reaction rate calculations and to generate plots.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Scaling of Transition State Vibrational Frequencies and Application of d -Band Theory to the Brønsted–Evans–Polanyi Relationship on Surfaces

Semiempirical energy relations provide a means of estimating thermodynamic properties. Specifically, linear scaling relationships (LSRs) and Brønsted–Evans–Polanyi (BEP) relationships correlate adsorption energies between adsorbates across surfaces and reaction energies with activation barriers, respectively. Although vibrational scaling relations (VSRs) exist between adsorbates at identical sites, scaling between vibrational frequencies of adsorbed local minima and transition states is lacking. Here, we present density functional theory calculations for AH X (A = C, N, O) diffusions on transition metal surfaces and reveal linear scaling between frequencies of local minima and the transition state between those minima. Using d-band theory and linear muffin tin orbital theory (LMTO), we derive the slopes of these transition state vibrational scaling relations (TSVSRs) and, in so doing, provide a rigorous theory extending the original BEP relations developed for solution chemistry to surface chemistry. Furthermore, with a single reference DFT calculation, we predict the slopes and quantify uncertainty in the predictions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nucleation Rate Theory for Coordination Number: Elucidating Water-Mediated Formation of a Zigzag Na 2 SO 4 Morphology

Predicting and controlling nanostructure formation during nucleation can pave the way to synthesizing novel energy materials via crystallization. However, such control over nucleation and crystallization remains challenging due to an inadequate understanding of critical factors that govern evolving atomistic structures and dynamics. Here, in this paper, we utilize coordination number as a reaction coordinate and rate theory to investigate how sodium sulfate, commonly known as a phase-change energy material, nucleates in a supersaturated aqueous solution. In conjunction with ab initio and force field-based molecular dynamics simulation, the rate theoretical analysis reveals that sodium sulfate from an initially dissolved metastable state transits to a heterogeneous mixture of prenucleated clusters and finally to a large cylindrical zigzag morphology. Measurements of Raman spectra and their ab initio modeling confirm that this nucleated morphology contains a few waters for every sulfate. Rate processes such as solvent exchange and desolvation exhibit high sensitivity to the evolving prenucleation/nucleation structures, providing a means to distinguish between critical nucleation precursors. Desolvation and forming the first-shell interionic coordination structure via monomer-by-monomer addition around sulfates are found to explain the formation of large nuclei. Thus, a detailed understanding of the step-by-step structure formation across scales has been achieved. This can be leveraged to predict nucleation-related structures and dynamics and potentially control the synthesis of novel phase-change materials for energy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Supervised learning and the finite-temperature string method for computing committor functions and reaction rates

A central object in the computational studies of rare events is the committor function. Though costly to compute, the committor function encodes complete mechanistic information of the processes involving rare events, including reaction rates and transition-state ensembles. Under the framework of transition path theory, Rotskoff et al. [Proceedings of the 2nd Mathematical and Scientific Machine Learning Conference, Proceedings of Machine Learning Research (PLMR, 2022), Vol. 145, pp. 757–780] proposes an algorithm where a feedback loop couples a neural network that models the committor function with importance sampling, mainly umbrella sampling, which collects data needed for adaptive training. Here, in this work, we show additional modifications are needed to improve the accuracy of the algorithm. The first modification adds elements of supervised learning, which allows the neural network to improve its prediction by fitting to sample-mean estimates of committor values obtained from short molecular dynamics trajectories. The second modification replaces the committor-based umbrella sampling with the finite-temperature string (FTS) method, which enables homogeneous sampling in regions where transition pathways are located. We test our modifications on low-dimensional systems with non-convex potential energy where reference solutions can be found via analytical or finite element methods, and show how combining supervised learning and the FTS method yields accurate computation of committor functions and reaction rates. We also provide an error analysis for algorithms that use the FTS method, using which reaction rates can be accurately estimated during training with a small number of samples. The methods are then applied to a molecular system in which no reference solution is known, where accurate computations of committor functions and reaction rates can still be obtained.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

High-Pressure Rate Rules for Ether Alkylperoxy Radical Isomerization

The first isomerization reaction of an alkylperoxy (RO 2 ) radical holds significant importance in low-temperature oxidation, as it governs the branching ratios of the hydroperoxyalkyl (QOOH) radicals, which influence the competition between the chain-propagation and chain-branching reactions. In this study, we systematically calculated high-pressure rate rules for the RO 2 isomerization reaction of monoethers, exploring 5-, 6-, 7-, and 8-membered ring transition states. Primary, secondary, and tertiary carbon sites, where both the abstracting peroxy group and the abstracted hydrogen are located, were considered, with particular emphasis on distinguishing between secondary carbons adjacent (alpha) and nonadjacent to the ether functional group. Using the G4//B3LYP/6-311++G(2df,2pd) level of theory and the transition state theory, we estimated the rate constants and the Arrhenius coefficient for over 120 possible isomerization reactions. We examined the effect of ring size and ring atoms, revealing that 6- and 7-membered ring isomerizations were generally the fastest. The impact of the ether functional group on transition states was investigated by comparing reactions with identical ring size, peroxy, and radical positions, but with the ether functional group positioned either outside (i.e., out) or inside (i.e., in) the transition state ring, leading to differences in the rate constants. When comparing to analogous alkane rate constants, differences of up to an order of magnitude were observed, underscoring the need for caution when assigning rate rules by analogy. We applied our rate constants in the di-iso-butyl ether kinetic model and evaluated their influence on low-temperature chemistry finding that they altered the branching ratios by up to a factor of 9, highlighting the significance of site-specific rate constants for more accurate low-temperature modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗