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DOE OSTI2024

Newton-Okounkov bodies of chemical reaction systems

Despite their noted potential in polynomial-system solving, there are few concrete examples of Newton-Okounkov bodies arising from applications. Accordingly, in this paper, we introduce a new application of Newton-Okounkov body theory to the study of chemical reaction networks and compute several examples. An important invariant of a chemical reaction network is its maximum number of positive steady states Here, we introduce a new upper bound on this number, namely the ‘Newton-Okounkov body bound’ of a chemical reaction network. Further, through explicit examples, we show that the Newton-Okounkov body bound of a network gives a good upper bound on its maximum number of positive steady states. We also compare this Newton-Okounkov body bound to a related upper bound, namely the mixed volume of a chemical reaction network, and find that it often achieves better bounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Networks of electrochemical oxidation of common lithium-ion Battery solvents revealed by NMR spectroscopy

Raising the upper cutoff voltage of lithium-ion batteries (LIBs) to increase energy density often exceeds the electrolyte’s anodic stability limit, accelerating degradation and creating a major durability tradeoff. Designing electrolytes that can sustain long-term high-voltage cycling requires a clearer understanding of the fundamental mechanisms occurring when commercial carbonate solvents oxidize. Here, to this end, simplified single-salt, single-solvent formulations of LiClO 4 and LiPF 6 in dimethyl carbonate (DMC), ethylene carbonate (EC), or ethyl methyl carbonate (EMC) were anodically electrolyzed on inert electrodes and monitored for extended periods of time using 1 H, 13 C, 19 F, and 35 Cl nuclear magnetic resonance (NMR) spectroscopy. The controlled environment of the experiments, coupled to the unique sensitivity of NMR, unveiled novel metastable intermediates and the formation of branching networks of products with temporal evolution. Oxidation of the pristine solvent primarily proceeds through a radical pathway that also produces highly reactive protons but faces competition from a second pathway involving a radical carbocation intermediate. In all cases, the intermediates follow a variety of downstream pathways that can intersect with each other. The concomitant network of reactions represents a significant increase in complexity compared to common descriptions in the literature, yet, critically, it helps explain the wide range of products typically identified in electrolyte oxidation in complete cells. The results highlight the need for refocusing fundamental research on anodic stability to analysis of the hierarchy of reaction networks to better inform efforts to mitigate the detrimental effects on battery performance, including prevention and harvesting of proton and radical products.

Electrolytes↗

DOE OSTI2024

Dataset for scientific paper "Simulated plant‑mediated oxygen input has strong impacts on fine‑scale porewater biogeochemistry and weak impacts on integrated methane fluxes in coastal wetlands", a modeling study based on field observation at the tidal salt marshes of the Parker River Estuary, Massachusetts, United States

This dataset is the raw and processed data for the paper "Simulated plant ‑ mediated oxygen input has strong impacts on fine ‑ scale porewater biogeochemistry and weak impacts on integrated methane fluxes in coastal wetlands". This study investigated how plant-mediated oxygen input affects subsurface biogeochemical reactions of organic carbon degradation and the resulting methane emissions of coastal wetlands by model simulation. We used the subsurface geochemical simulator PFLOTRAN for the modeling, which produced the simulated changes in porewater chemical substances and methane emissions over 10 days under different scenarios of plant-mediated oxygen input.Specifically, this dataset contains: 1) the input files for PFLOTRAN of all simulation runs conducted in this study. Those files are with an extension of ".in", containing information of the biogeochemical reaction network (stoichiometry, reaction rate, Monod constants, etc), fluid flow rate and oxygen concentration in the fluid which together simulated the plant-mediated oxygen input, the configuration of artificial reactions that simulated the methane fluxes, etc. The PFLOTRAN input files are text files, which can be opened by NotePad, but running these input files will require proper installation of PFLOTRAN (instruction: https://documentation.pflotran.org/user_guide/how_to/installation/installation.html). 2) the raw and processed model output from PFLOTRAN of all simulation runs, and 3) the python scripts used to process the raw model output, including random allocation of root cells, converting raw data into organized formats, calculating the methane fluxes based on the model output, data visualization, etc. The raw and processed model output from PFLOTRAN are in .spydata format, which can be viewed with Python. and 3) the python scripts for data processing and analysis are programming scripts, which can be opened with Python.This modeling work, in particular the model parameterization of root density and initial conditions of porewater concentrations of biogeochemical substances, was based on field measurements at the salt marsh of the Upper Parker River Estuary, Massachusetts, United States.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Discovering CO Adsorption and Desorption Pathways from Chemical Reaction Neural Network Modeling of Transient Kinetics Spectroscopy

Here, we demonstrate a data-driven approach to interpreting surface reactions by combining time-resolved gas pulsing infrared spectroscopy with chemical reaction neural networks (CRNNs). Using CO adsorption and desorption on Pd(111) at 460–490 K as a model system, we show how transient kinetic data can reveal detailed reaction mechanisms. Starting with a simple one-species model, we systematically evaluate increasingly complex mechanisms involving hollow and bridge site adsorption. Despite the similar goodness of fit to the same experimental absorbance data, our models predict distinct coverage dynamics for different adsorption sites. Through analysis of spectral peak stability and predicted dynamics, we identify a mechanism in which CO primarily adsorbs on bridge sites followed by rapid conversion to hollow sites as being the most physically consistent with experimental observations. This work provides a framework for extracting mechanistic insights from limited experimental data, demonstrating how machine learning can bridge the gap between transient kinetic measurements and a molecular-level understanding of surface reactions.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Flexible and Modular Simultaneous Modeling of Flow and Reactive Transport in Rivers and Hyporheic Zones

Investigations of coupled multiphysics processes in rivers and hyporheic zones have extensively used numerical models. Most existing models use a sequential, one-way coupling between the surface and subsurface domains. Such one-way coupling potentially introduces error. To overcome this, a fully coupled model, hyporheicFoam, was developed using the open-source computational platform OpenFOAM. It captures the coupled flow and multicomponent reactive transport processes within both surface and subsurface domains and across their interface. The coupling between two domains is implemented by mapping conservative flux boundary conditions at the interface through an iterative algorithm. Reactive transport is enabled by specifying a reaction network. To start, we have implemented reaction kinetics following the double Monod-type model with inhibition. The model capability is illustrated through modeling of both conservative and reactive hyporheic flow and transport through dune bedforms. With the novel coupled model, it is now possible to quantify reactions wherein the reactants and products are constantly exchanging between domains and have feedbacks. hyporheicFoam can simulate large, three-dimensional cases owing to the computational flexibility and power offered by the code structure and parallel design of OpenFOAM.

58 GEOSCIENCES↗

DOE OSTI2024

Catalytic Resonance Theory: The Catalytic Mechanics of Programmable Ratchets

Catalytic reaction networks of multiple elementary steps operating under dynamic conditions via a programmed input oscillation are difficult to interpret and optimize due to reaction system complexity. To understand these dynamic systems, individual elementary catalytic reactions oscillating between catalyst states were evaluated to identify their three fundamental characteristics that define their ability to promote reactions away from equilibrium. First, elementary catalytic reactions exhibit directionality to promote reactions forward or backward from equilibrium as determined by a ratchet directionality metric comprised of the input oscillation duty cycle and the reaction rate constants. Second, catalytic ratchets are defined by the catalyst state of strong or weak binding that permit reactants to proceed through the transition state. Third, elementary catalytic ratchets exhibit a cutoff frequency which defines the transition in applied frequency for which the catalytic ratchet functions to promote chemistry away from equilibrium. All three ratchet characteristics are calculated from chemical reaction parameters including rate constants derived from linear scaling parameters, reaction conditions, and catalyst state. The characteristics of the reaction network’s constituent elementary catalytic reactions provided an interpretation of complex reaction networks and a method of predicting the behavior of dynamic surface chemistry on oscillating catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Butene-Rich Alkene Formation from 2,3-Butanediol through Dioxolane Intermediates

The cost-effective production of sustainable aviation fuels (SAF) remains a major challenge within the energy sector. One approach to address this is the fermentation of biomass feedstocks into oxygenates followed by catalytic conversion to alkenes or other oligomerization precursors. 2,3-Butanediol (BDO) is a promising fermentation product due to its four-carbon nature, its decreased microorganism toxicity and associated higher maximum fermentation titers relative to other alcohols and oxygenates, and its capacity to be readily converted into butene isomers and longer chain alkenes. BDO conversion is currently constrained by separation challenges for BDO isolation due to its high boiling point and hydrophilicity. Here, this work expands upon previous BDO reactive separation via dioxolane formation over a solid acid catalyst by investigating the conversion of dioxolanes into alkene mixtures. Dioxolanes were formed from a range of aldehydes and subsequently converted over a Cu/ZSM-5 catalyst (448–523 K) via an ether cleavage, hydrogenation, and dehydration reaction network to form alkene-rich product mixtures (96% C 3+ alkene yield, 523 K). This selectivity is greater than that of direct BDO conversion to alkenes over an identical catalyst (89%, 523 K). C 3+ alkene selectivity is maximized between 498 and 523 K at complete dioxolane conversion without significant alkene hydrogenation to alkanes. The alkene product distributions can be tailored via both aldehyde selection during dioxolane formation and the dioxolane conversion reaction temperature. Alkene mixtures from dioxolane conversion predominantly reflect the carbon chain length and stereochemistry of BDO and the initial aldehyde at or below 498 K, yet higher reaction temperatures yield alkene mixtures of similar carbon chain distributions, regardless of initial aldehyde selection. Deactivation of the Cu/ZSM-5 catalyst is observed for multiple steps of the overall reaction network but can be minimized by facilitating the complete dioxolane-to-alkene reaction network at temperatures of at least 498 K.

2,3-butanediol↗

DOE OSTI2024

Machine Learning Accelerated First-Principles Study of the Hydrodeoxygenation of Propanoic Acid

The complex reaction network of catalytic biomass conversions often involves hundreds of surface intermediates and thousands of reaction steps, greatly hindering the rational design of metal catalysts for these conversions. Here, we present a framework of machine learning (ML)-accelerated first-principles studies for the hydrodeoxygenation (HDO) of propanoic acid over transition metal surfaces. The microkinetic model (MKM) is initially parametrized by ML-predicted energies and iteratively improved by identifying the rate-determining species and steps (RDS), computing their energies by density functional theory (DFT), and reparameterizing the MKM until all the RDS are computed by DFT. The Gaussian process (GP) model performs significantly better than the linear ridge regression model for predicting both the adsorption free energies and transition state free energies. Parameterized with energies from the GP model, only 5–20% of the full reaction network has to be computed by DFT for the MKM to possess DFT-level accuracy for the TOF and dominant reaction pathway. While the linear ridge regression model performs worse than the GP model, its performance is greatly improved when only transition states are predicted by the regression model and adsorption energies are computed by DFT. Overall, we find that a high accuracy in adsorption free energies is more important for a reliable MKM than a high accuracy in TS free energies. Lastly, based on the GP model with GOH and GCHCHCO as catalyst descriptors, we build two-dimensional volcano plots in activity and selectivity that can help design promising alloy catalysts for HDO reactions of organic acids.

adsorption↗

DOE OSTI2020

Structural conserved moiety splitting of a stoichiometric matrix

Characterising biochemical reaction network structure in mathematical terms enables the inference of functional biochemical consequences from network structure with existing mathematical techniques and spurs the development of new mathematics that exploits the peculiarities of biochemical network structure. The structure of a biochemical network may be specified by reaction stoichiometry, that is, the relative quantities of each molecule produced and consumed in each reaction of the network. A biochemical network may also be specified at a higher level of resolution in terms of the internal structure of each molecule and how molecular structures are transformed by each reaction in a network. The stoichiometry for a set of reactions can be compiled into a stoichiometric matrix N ϵ Z mxn where each row corresponds to a molecule and each column corresponds to a reaction. We demonstrate that a stoichiometric matrix may be split into the sum of m - rank(N) moiety transition matrices, each of which corresponds to a subnetwork accessible to a structurally identifiable conserved moiety. The existence of this moiety matrix splitting is a property that distinguishes a stoichiometric matrix from an arbitrary rectangular matrix.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Degree of rate control and De Donder relations – An interpretation based on transition state theory

We describe sensitivities of elementary steps as salient parameters in determining the rate determining character of elementary steps within a reaction network and develop a formalism wherein the overall composite reaction is described by an apparent rate-determining step that is a sensitivity-weighted average of the elementary steps that comprise the reaction. Reaction parameters—apparent reaction orders, apparent enthalpy and entropy of activation—of the composite reaction network are determined within the framework we develop by application of transition state theory to the apparent rate-determining step. From this formalism we develop methods for determination of surface coverages by measuring only reaction orders, novel methods for discrimination between proposed mechanisms, a proof that the kinetic degrees of rate control sum to unity, and a proof for the relationship between fractional coverages and thermodynamic degrees of rate control. Two complementary formalisms for identifying rate-limiting transition states are broadly employed in chemical kinetics—De Donder relations based on measuring the thermodynamic driving forces of elementary steps during reaction and degrees of rate control based on knowledge of the kinetics of elementary reaction steps. Here, the formalism developed herein unifies these two strategies to elucidate in the most general case a relationship between the thermodynamic driving forces of elementary steps captured by the reversibilities and the kinetic and thermodynamic degrees of rate control.

42 ENGINEERING↗

DOE OSTI2024

The role of stereochemistry in combustion processes

Stereochemical effects significantly influence chemical processes, yet it is not well understood if they are a leading source of uncertainty in combustion modeling. Stereochemistry influences a combustion model (i) at the earliest stage of its construction when mapping the reaction network, (ii) in the computation of individual thermochemical and rate parameters, and (iii) in the prediction of combustion observables. The present work reviews the importance of enumerating stereochemical species and reactions at each of these steps. Further, it analyzes the separate influence of several types of stereochemistry, including geometric, optical, and fleeting transition state diastereomers. Three reaction networks serve to examine which stages of low-temperature oxidation are most affected by stereochemistry, including the first and second oxidation of n-butane, the third oxidation of n-pentane, and the early stages of pyrolysis of 1- and 2-pentene. The 149 reactions in the n-butane mechanism are expanded to 183 reactions when accounting for diastereomerism. Each of these 183 reactions is parameterized with ab initio kinetics computations to determine that, for the n-butane mechanism, the median factor of diastereomeric deviation is 3.5 at 360 K for rate constants and as high as 1.6 for mechanism reactivity, in terms of ignition delay times, as opposed to a mechanism without stereochemical expansion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Resonant amplification of enzymatic chemical oscillations by oscillating flow

Using theory and simulation, we analyzed the resonant amplification of chemical oscillations that occur due to externally imposed oscillatory fluid flows. The chemical reactions are promoted by two enzyme-coated patches located sequentially on the inner surface of a pipe that transports the enclosed chemical solution. In the case of diffusion-limited systems, the period of oscillations in chemical reaction networks is determined by the rate of the chemical transport, which is diffusive in nature and, therefore, can be effectively accelerated by the imposed fluid flows. In this work, we first identify the natural frequencies of the chemical oscillations in the unperturbed reaction–diffusion system and, then, use the frequencies as a forcing input to drive the system to resonance. We demonstrate that flow-induced resonance can be used to amplify the amplitude of the chemical oscillations and to synchronize their frequency to the external forcing. In particular, we show that even 10% perturbations in the flow velocities can double the amplitude of the resulting chemical oscillations. Particularly, effective control can be achieved for the two-step chemical reactions where during the first half-period, the fluid flow accelerates the chemical flux toward the second catalytic patch, while during the second half-period, the flow amplifies the flux to the first patch. The results can provide design rules for regulating the dynamics of coupled reaction–diffusion processes and can facilitate the development of chemical reaction networks that act as chemical clocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Catalytic Conversion of Model Compounds of Plastic Pyrolysis Oil over ZSM-5

Mechanistic investigation of the catalytic conversion of model compounds for plastic pyrolysis oil (1-octene, octadiene, octane, and toluene) over ZSM-5 in a fixed-bed reactor was studied. 1-Octene breaks down into smaller olefins, which undergo further cracking, oligomerization, cyclization, and hydrogen transfer to eventually produce benzene, toluene, xylene (BTX), coke, and hydrogen. The effect of contact time on 1-octene conversion was further investigated and compared with thermodynamics analyses to elucidate the reaction network. Under the reaction conditions (500 oC, 1 atm), octadiene undergoes thermal coking, significantly contributing to reactor fouling. The products from octane cracking are similar to the products from 1-octene conversion whereas toluene undergoes disproportionation, dealkylation and coking. The analysis of spent catalyst showed long-chain hydrocarbons created by oligomerization reactions filled the pores and covered the surface of the catalyst. As a result, when mesoporous ZSM-5 is used instead of conventional, product selectivity is maintained for 70 hours in time-on-stream experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2019

Synthesis of Meteoritic Reaction Intermediates

The organic compounds of carbo- naceous chondrites are structurally diverse products of the prolonged abiotic chemistry that occurred before and during the early stages of the solar system [1]. They also represent the types of prebiotic compounds that may have participated in chemical evolutionary processes that gave rise to life [2]. Pyruvic acid is a key component of primary metabolism that has recently been found in carbonaceous chondrites [3]. Its prominence in biology has inspired us to explore its chemistry and possible role in the origin of metabolism. Our laboratory investigations have found that pyruvate (the ionized form of pyruvic acid) can serve as a single-source reactant to generate what we term a pyruvate reaction network (PRN). The core of the PRN is driven by pyruvate aldol polymerization and decay reactions. These decay reactions lead to the production of stable and unstable compounds which include mono, di, and tricarboxylic acids and a variety of keto acids. Finding evidence of this reaction network in meteorites would establish that the chemistry of pyruvate did occur in a prebiotic environment. Many of the known compounds found in pyruvate reaction mixtures were originally detected in meteorite samples by Cooper et al in 2011. However, multiple synthetic origins not tied to pyruvate chemistry might also explain their meteoritic presence. Thus, a search to find compounds unique to the PRN, such as reaction intermediates, would provide stronger evidence to demonstrate its prebiotic relevance. The identity of these intermediates can only be confirmed by acquiring chemical standards, however, as most are not available commercially, they need to be accessed through chemical synthesis.

Rios, Andro C.↗

NASA NTRS1980

The chemical abundances of the Cassiopeia A fast-moving knots - Explosive nucleosynthesis on a minicomputer

A simplified nuclear reaction network for explosive nucleosynthesis calculations is described in which only the most abundant nuclear species and the most important reactions linking these species are considered. This scheme permits the exploration of many cases without excessive computational effort. Good agreement with previous calculations employing more complex reaction networks is obtained. This scheme is applied to the observed chemical abundances of the fast-moving knots in the supernova remnant Cassiopeia A and it is found that a wide range of initial conditions could yield the observed abundances. The abundances of four of the knots with significant and different amounts of elements heavier than oxygen are consistent with an origin in material of the same initial composition but processed at different peak temperatures and densities. Despite the observed high oxygen abundances and low abundances of light elements in the knots, they did not necessarily undergo incomplete oxygen burning; in fact, it is not even necessary that oxygen have been present in the initial composition. The agreement between the calculated and observed chemical abundances in Cas A and similar supernova remnants depends primarily upon the relevant nuclear physics and does not provide strong evidence in favor of any particular model of the supernova event.

Johnston, M. D.↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

Abstract The sequence‐specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson–Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi‐step DNA reactions. Here we show how an ATP‐dependent helicase, Rep‐X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep‐X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.

Moerman, Pepijn G.↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Consequences of adsorbate-adsorbate interactions for apparent kinetics of surface catalytic reactions

Lateral adsorbate interactions at catalyst surfaces are known to influence adsorption energies and reaction rates. Lattice-based kinetic Monte Carlo (kMC) simulations are able to capture these influences, but such models are typically parameterized for a specific reaction network and catalyst surface. Here we report kMC simulations to probe the influence of lateral interactions on simulated rates, rate orders, apparent activation energies, and Sabatier plots. We construct a simple, two-step reaction network involving a single adsorbate and rate- limiting diatomic dissociation, employ a generic repulsive lateral interaction model consistent with known adsorbate-adsorbate interactions on metal surfaces, and a rate model consistent with known Brønsted-Evans-Polyani relationships for diatomic dissocations. Furthermore, we juxtapose reaction kinetics over a wide range of reaction conditions and catalyst binding energies, as a function of interaction strength. We find that at a given zero-coverage binding energy and external conditions, adsorbate coverage decreases monotonically with increasing interaction strength, but absolute rates can vary linearly or nonlinearly. Interactions flatten the Sabatier volcano and shift the maximum towards stronger binding. Influences on apparent rate orders and activation energies are modest and are sensitive to interaction-induced adsorbate ordering. Model predictions are sensitive to lattice size effects at high coverages. The results, modelled for a simple reaction system, highlight the generic consequences of lateral interactions and guidance for identifying their signatures in observed kinetics.

kinetic Monte Carlo↗