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At least 127 records · Page 7

Physics-based, neural network force fields for reactive molecular dynamics: Investigation of carbene formation from [EMIM + ][OAc - ]

Reactive molecular dynamics simulations enable detailed understanding of solvent effects on chemical reaction mechanisms and reaction rates. While classical molecular dynamics using reactive force fields allows significantly longer simulation time scales and larger system sizes compared with ab initio molecular dynamics, constructing reactive force fields is a difficult and complex task. In this work, we describe a general approach following the Empirical Valence Bond (EVB) framework for constructing ab initio reactive force fields for condensed phase simulations by combining physics-based methods with neural networks (PB/NN). The physics-based terms ensure correct asymptotic behavior of electrostatic, polarization, and dispersion interactions, and are compatible with existing solvent force fields. Neural networks are utilized for versatile description of short-range orbital interactions within the transition state region, and accurate rendering of vibrational motion of the reacting complex. Herein, we demonstrate our methodology for a simple deprotonation reaction of the 1-ethyl-3-methylimidazolium (EMIM+) cation with acetate to form 1-ethyl- 3-methylimidazol-2-ylidene and acetic acid. Our PB/NN force field exhibits ~ 1 kJ/mol MAE accuracy within the transition state region for the gas-phase complex. To characterize solvent modulation of the reaction profile, we compute potentials of mean force (PMFs) for the gas-phase reaction as well as the reaction within a four ion cluster, and benchmark against ab initio molecular dynamics simulations. We find that the surrounding ionic environment significantly destabilizes formation of the carbene product, and we show that this effect is accurately captured by the reactive force field. By construction, the PB/NN potential may be directly employed for simulations of other solvents/chemical environments without additional parameterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oxidation and pyrolysis of methyl propyl ether

The ignition, oxidation, and pyrolysis chemistry of methyl propyl ether (MPE) was probed experimentally at several different conditions, and a comprehensive chemical kinetic model was constructed to help understand the observations, with many of the key parameters computed using quantum chemistry and transition state theory. Experiments were carried out in a shock tube measuring time variation of CO concentrations, in a flow tube measuring product concentrations, and in a rapid compression machine (RCM) measuring ignition delay times. The detailed reaction mechanism was constructed using the Reaction Mechanism Generator software. Sensitivity and flux analyses were used to identify key rate and thermochemical parameters, which were then computed using quantum chemistry to improve the mechanism. Validation of the final model against the 1-20 bar 600-1500 K experimental data is presented with a discussion of the kinetics. The model is in excellent agreement with most of the shock tube and RCM data. Strong non-monotonic variation in conversion and product distribution is observed in the flow-tube experiments as the temperature is increased, and unusually strong pressure dependence and significant heat release during the compression stroke is observed in the RCM experiments. These observations are largely explained by a close competition between radical decomposition and addition to O2 at different sites in MPE; this causes small shifts in conditions to lead to big shifts in the dominant reaction pathways. The validated mechanism was used to study the chemistry occurring during ignition in a diesel engine, simulated using Ignition Quality Test (IQT) conditions. At the IQT conditions, where the MPE concentration is higher, bimolecular reactions of peroxy radicals are much more important than in the RCM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kinetics-Informed Neural Networks

Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize feed-forward artificial neural networks as basis functions to solve ordinary differential equations (ODEs) constrained by differential algebraic equations (DAEs) that describe microkinetic models (MKMs). We present an algebraic framework for the mathematical description and classification of reaction networks, types of elementary reaction, and chemical species. Under this framework, we demonstrate that the simultaneous training of neural nets and kinetic model parameters in a regularized multi-objective optimization setting leads to the solution of the inverse problem through the estimation of kinetic parameters from synthetic experimental data. We analyze a set of scenarios to establish the extent to which kinetic parameters can be retrieved from transient kinetic data, and assess the robustness of the methodology with respect to statistical noise. Furthermore, this approach to inverse kinetic ODEs can assist in the elucidation of reaction mechanisms based on transient data.

36 MATERIALS SCIENCE↗

Exploring the Unusual Reactivity of the Hydrated Electron with CO 2

Many questions remain about the reactions of the hydrated electron despite decades of study. Of particular note is the fact that they do not appear to follow the Marcus theory of electron transfer reactions, a feature that has yet to be explained. To investigate these issues, we use ab initio molecular dynamics (AIMD) simulations to investigate a one of the better studied reactions, the hydrated electron reduction of CO 2 . The rate constant for the hydrated electron-CO 2 reaction complex to react to form CO 2 - is, for the first time, estimated from AIMD simulations. Results at 298 and 373 K show the rate constant is insensitive to temperature, consistent with the low measured activation energy for the reaction, and the implications of this behavior are examined. The sampling provided by the simulations yields insight into the reaction mechanism. The reaction is found to involve both solvent reorganization and changes in the carbon dioxide structure. The latter lead to significant vibrational excitation of the bending and symmetric stretch vibrations in the CO 2 - product, indicating the reaction is vibrationally nonadiabatic. The former is estimated from calculation of an approximate collective solvent coordinate and the free energy in this coordinate is determined. Furthermore, these results indicate that AIMD simulations can reasonably estimate hydrated electron reaction activation energies and provide new insight into the mechanism that can help illuminate the features of this unusual chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Autonomous hybrid optimization of a SiO 2 plasma etching mechanism

Computational modeling of plasma etching processes at the feature scale relevant to the fabrication of nanometer semiconductor devices is critically dependent on the reaction mechanism representing the physical processes occurring between plasma produced reactant fluxes and the surface, reaction probabilities, yields, rate coefficients, and threshold energies that characterize these processes. The increasing complexity of the structures being fabricated, new materials, and novel gas mixtures increase the complexity of the reaction mechanism used in feature scale models and increase the difficulty in developing the fundamental data required for the mechanism. This challenge is further exacerbated by the fact that acquiring these fundamental data through more complex computational models or experiments is often limited by cost, technical complexity, or inadequate models. In this paper, we discuss a method to automate the selection of fundamental data in a reduced reaction mechanism for feature scale plasma etching of SiO 2 using a fluorocarbon gas mixture by matching predictions of etch profiles to experimental data using a gradient descent (GD)/Nelder–Mead (NM) method hybrid optimization scheme. These methods produce a reaction mechanism that replicates the experimental training data as well as experimental data using related but different etch processes.

36 MATERIALS SCIENCE↗

Te(IV) immobilization by siderite: Reaction kinetics, mechanism, and Te isotopic fractionation

Mining and industrial use over recent decades have released tellurium (Te) into the environment where it potentially contaminates soils, water supplies and food sources. Therefore, it is important to find ways of removing mobile and bioavailable Te from aqueous environments. Here, we report aqueous Te(IV) removal by siderite at varying Te concentrations (2, 6 and 10 mg mL –1 Te(IV)) and pH values (7, 7.9 and 9), together with associated isotope fractionation (ε 130 Te/ 125 Te). Our results show effective immobilization of Te(IV) that follows pseudo-first order rate kinetics. Formation of magnetite indicates reduction of Te(IV) on siderite surfaces and the formation of Te(0). The overall isotope fractionation (ε) is small (–0.23 ± 0.06‰) providing evidence that it is primarily controlled by adsorption of Te(IV) occurring simultaneously with reduction of Te(IV). Therefore, Te(IV) removal by siderite under mildly reducing ferruginous conditions may be identifiable by the characteristically small isotopic fractionation during both natural attenuation and active remediation. To our knowledge, this is the first study reporting reaction mechanisms of Te(IV) immobilization by an environmentally relevant Fe(II) mineral.

58 GEOSCIENCES↗

Early-stage oxidation and subsequent damage of the used nuclear fuel extractant TODGA; electron pulse radiolysis and theoretical insights

Radiation induced damage of extractant molecules is a well-known phenomenon responsible for reducing efficiency and increasing the waste and cost of reprocessing used nuclear fuel (UNF). As such, understanding early-stage (pico- to nanoseconds) radiation-induced reaction mechanisms is essential for informing the design of next generation extractants with enhanced radiation robustness. Here, in this work, we utilized picosecond and nanosecond electron pulse radiolysis experiments to probe the early-stage radioactive environment experienced by the organic phase extractant N,N,N',N'-tetraoctyldiglycolamide (TODGA), proposed for separating highly radioactive trivalent minor actinides (specifically americium and curium) from the trivalent lanthanides. Using comparisons to the similar ionization potential (IP) solute p-xylene, this work determined the mechanism of reaction with the ionized diluent (i.e., n-dodecane radical cation, DD˙ + ) is hole transfer to produce TODGA˙ + . At high TODGA concentrations (>100 mM), the majority of this transfer occurs faster than 10 ps via the capture of DD˙ + holes prior to their solvation with a C 37 = 300 mM. The surviving solvated holes were captured with k = (2.38 ± 0.15) × 10 10 M -1 s -1 . Attempts at subsequent hole transfer to lower IP solutes found that only 10% of holes were transferred, indicating bond rupture of TODGA˙ + occurs within 2.6 ns at 200 mM TODGA. Possible reaction pathways for the rapid decomposition of TODGA˙ + were explored using a combination of experiments and density functional theory (DFT) calculations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Microwave-Assisted Reforming of Tar Model Compound Using the Ni/La-CeO2 Catalyst

Gasification of solid feedstocks like coal, biomass and waste plastic produces syngas as a desired product. However, this process also produces an unwanted byproduct known as tar, which is a sticky compound consisting of a mixture of complex aromatic and polyaromatic hydrocarbons. The tar formed during the gasification process lowers the syngas yields and reduces the gasification efficiency by damaging the reactor. Therefore, it is essential to reduce the amount of tar formed during the gasification process. Catalytic reforming of tars is one way to mitigate tars. The goal of this research is to explore the possibility of microwave-assisted catalytic tar conversion to syngas. However, due to the complexity of the tar, toluene has been used as a model tar compound as it is stable and easy to handle. Ni-La/CeO2 was used as a catalyst for this study, which was synthesized by wet impregnation method. Fresh and spent catalysts were analyzed using various techniques to understand the reaction mechanism. The reaction was performed both under microwave (MW) and conventional (CV) reactor for comparison.

catalysis↗

Kinetic Isotope Effects: Interpretation and Prediction Using Degrees of Rate Control

Kinetic isotope effects (KIEs) have been used for decades in catalysis research as a tool for clarifying reaction mechanisms. Significant primary kinetic isotope effects have usually been interpreted as being a result of isotope substitution at a site of bond breaking (or forming) in the rate-determining step in the reaction mechanism. However, quantitative analysis of the magnitude of the KIE in complex multistep reaction mechanisms is seldom reported. We prove here that the logarithm of the rate ratio for two isotopes is the weighted average over all species in the mechanism of their standard-state free energy difference between the two isotopes, divided by RT. The weighting factor is the degree of rate control (DRC) for that species (e.g., transition state, intermediate, reactant) when the rate is measured separately for each isotope. It is instead the degree of selectivity ratio control (DSRC) when the KIE is measured as the product selectivity in a parallel competition between two isotopes within the same reactant molecule. Since only a few species have non-zero DRCs (or DSRCs) for most reactions, only these few contribute to this weighted average and the KIE. We show that this provides a simple way to interpret and quantitatively predict kinetic isotope effects that is powerful in the insights it provides, allowing one to evaluate directly which species contribute most to the KIE. By applying it to H/D KIEs in several example mechanisms, we further show that the traditional way of interpreting KIEs that focuses only on the rate-determining step can easily lead to misunderstanding of KIE and the reaction mechanism. Finally, this highlights the importance to consider the effect of isotope substitution on the energies of all species with large DRCs (i.e, those whose energies are kinetically relevant). This method also offers opportunities for quantitative validation of mechanism-based microkinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of the D1-Val185Asn mutated photosystem II complex with slow O–O bond formation reveals changes in the Cl1 water channel

During photosynthesis, the photosystem II (PSII) enzyme catalyzes the light-driven oxidation of water, fueling life on Earth by storing light energy and releasing O 2 as a byproduct. Determining the molecular mechanism for this water oxidation reaction has been of significant interest for the development of synthetic catalysts, but many details remain elusive. One of the open questions is how protons are strategically removed from the active site, a Mn 4 CaO 5 cluster called the oxygen-evolving complex (OEC), during the reaction cycle via conserved water channels, and how proton transfer contributes to O–O bond formation energetics. Site-directed mutagenesis studies have investigated the role of conserved amino acid side chains in facilitating proton transfer. One of the most influential mutations is the Val185Asn substitution on the D1 subunit, which substantially slows O 2 release kinetics without abolishing catalytic activity. Forming a molecular understanding of how this mutation affects the active site will provide insight into the water oxidation reaction mechanism. Here, we investigated the structural basis of the Val185Asn substitution by determining a 1.99 Å-resolution cryo-EM structure. We observed that Asn185 orients away from the OEC and donates a H-bond to Cl1, a conserved chloride ion. We furthermore observed an alternative D2-Glu312-facing conformation of the D2-Lys317 side chain in the Cl1 water channel, a conformation that is consistent with recent models for proton transfer. These changes also produce perturbations to the hydrogen-bonding network. Overall, these finding provide insight into proton transfer in the Cl1 channel and its effect on the water oxidation reaction mechanism.

cryo-EM↗

Kinetics and Mechanism of the Singlet Oxygen Atom Reaction with Dimethyl Ether

Here, we combine in situ laser spectroscopy, quantum chemistry, and kinetic calculations to study the reaction of a singlet oxygen atom with dimethyl ether. Infrared laser absorption spectroscopy and Faraday rotation spectroscopy are used for the detection and quantification of the reaction products OH, H 2 O, HO 2 , and CH 2 O on submillisecond time scales. Fitting temporal profiles of products with simulations using an in-house reaction mechanism allows product branching to be quantified at 30, 60, and 150 Torr. The experimentally determined product branching agrees well with master equation calculations based on electronic structure data and transition state theory. The calculations demonstrate that the dimethyl peroxide (CH 3 OOCH 3 ) generated via O-insertion into the C–O bond undergoes subsequent dissociation to CH 3 O + CH 3 O through energetically favored reactions without an intrinsic barrier. This O-insertion mechanism can be important for understanding the fate of biofuels leaking into the atmosphere and for plasma-based biofuel processing technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evidence of Zintl Intermediate Phase and Its Impacts on Li and Na Storage Performance of Pb-Based Alloying Anodes

Anode materials based on conversion and alloying reactions are promising to achieve high energy density of advanced sodium-ion batteries (SIBs). While the chemical similarities between sodium and lithium as alkali elements make the benchmarking strategy practical in developing new high-performance anodes, simply borrowing the anode material from one system to the other does not always guarantee success unless it is based on sound understanding of both Li- and Na-reaction mechanisms. In this work, we report the Na storage performance of a Pb-based anode and its fundamental reaction dynamics. In contrast to its excellent electrochemical performances in Li cells (reversible ~600 mAh/g), the newly developed Pb@PbO–C nanocomposite anode has limited electrochemical Na reaction properties showing moderate capacity and rate performances (~300 mAh/g at 20 mA/g). Synchrotron-based X-ray diffraction and absorption spectroscopy studies reveal the fundamental differences in the Na and Li reaction mechanism of the Pb-based anode. Further, unlike Li reaction, the unique Na reaction mechanism involves the formation of a highly ionic NaPb Zintl phase, which comprises tetrahedral Pb 4 clusters, as an intermediate phase. The strong covalent character of the Pb 4 Zintl clusters adversely affects the electronic conductivity and thus limits the electrochemical performance of the Pb-based anode in Na cells. These findings provide new insights applicable to developing high-performance alloying anode materials.

25 ENERGY STORAGE↗

Insights into the Mechanism of Methanol Steam Reforming Tandem Reaction over CeO 2 Supported Single-Site Catalysts

We demonstrated how the special synergy between a noble metal single site and neighboring oxygen vacancies provides an "ensemble reaction pool" for high hydrogen generation efficiency and carbon dioxide (CO 2 ) selectivity of a tandem reaction: methanol steam reforming. Specifically, the hydrogen generation rate over single site Ru 1 /CeO 2 catalyst is up to 9360 mol H 2 per mol Ru per hour (579 mL H2 g Ru -1 s -1 ) with 99.5% CO 2 selectivity. Reaction mechanism study showed that the integration of metal single site and O vacancies facilitated the tandem reaction, which consisted of methanol dehydrogenation, water dissociation, and the subsequent water gas shift (WGS) reaction. In addition, the strength of CO adsorption and the reaction activation energy difference between methanol dehydrogenation and WGS reaction play an important role in determining the activity and CO 2 selectivity. Our study paves the way for the further rational design of single site catalysts at the atomic scale. Furthermore, the development of such highly efficient and selective hydrogen evolution systems promises to deliver highly desirable economic and ecological benefits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallo­graphy provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. Here, to characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

Neurospora crassa↗

Revealing the coupled oxygen and hypochlorite chemistry in saltwater batteries through operando pH and oxygen monitoring

Saltwater batteries (SWBs) that utilize Na⁺ ions from seawater have emerged as promising candidates for low-cost and sustainable grid-scale energy storage. To date, the cathode reaction mechanism of SWBs has been predominantly described by oxygen evolution and reduction reactions (OER/ORR). However, this assumption is valid only under idealized ocean-like conditions with constant pH and continuous oxygen replenishment. In practical systems, SWBs operate in finite volumes of saltwater, where saltwater composition dynamically evolves during cycling. Here, in this work, we systematically investigate the cathode reaction mechanisms of SWBs under finite saltwater conditions using galvanostatic cycling combined with electrochemical diagnostics and operando monitoring of dissolved oxygen and pH. Our results reveal that the cathode chemistry during SWB operation is considerably more complex than previously assumed. In addition to OER and ORR, hypochlorite formation and consumption reactions, along with pH-dependent switching of dominant reaction pathways, play critical roles. We further identify the sequence and relative contributions of these reactions throughout charge–discharge cycling. These findings provide a comprehensive and mechanistically grounded understanding of SWB cathode processes under relatively realistic cell design and operation condition. The insights presented here establish a new framework for interpreting SWB electrochemistry and offer directions for future strategies aimed at improving performance, stability, and practical viability.

Hypochlorite redox reaction↗

Shock tube investigation of high-temperature, extremely-rich oxidation of several co-optima biofuels for spark-ignition engines

To reduce the reliance on fossil fuels in the transportation sector and increase combustion efficiency, the Co-Optima initiative from US Department of Energy identified the top 10 biofuels for downsized, boosted, spark-ignition engines. Most of these biofuels have detailed reaction mechanisms available in literature developed based on studies at temperatures lower than 1700 K and an equivalence ratio of less than five. As such, the performance of these detailed mechanisms at high temperature and extremely rich conditions are unknown. It is important to validate kinetic mechanisms at these conditions because they are conducive to soot formation. Prediction of soot by chemical kinetic models relies on the prediction of underlying benchmark species like carbon monoxide and ethylene. In this work, we conduct high temperature (1700–2050 K) and high equivalence ratio(Φ=8.6) oxidation of these biofuels, namely 2,4,4-trimethyl-1-pentene (α-diisobutylene), ethanol, cyclopentanone, methyl acetate, and 2-methylfuran, blended in ethylene behind reflected shock waves at 4–4.7 atm pressure. Carbon monoxide and ethylene time histories are measured simultaneously using a continuous feedback quantum cascade laser near 4.9 µm and a tunable CO 2 gas laser at 10.532 nm, respectively. Results show that ethanol blend forms more carbon monoxide than other biofuels and consumes ethylene faster than the biofuel blends in the temperature range considered. Overall, the performance of different mechanisms in literature are evaluated against the experimental results. The novel reaction mechanism ‘the Co-Optima model’, which includes the sub mechanisms for all the biofuels in this study, was found to be the best mechanism for the experimental conditions studied.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure

The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. Here, to clarify the mechanism, we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ~18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme–substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanoscale Li, Na, and K ion-conducting polyphosphazenes by atomic layer deposition

A key trailblazer in the development of thin-film solid-state electrolytes has been lithium phosphorous oxynitride (LiPON), the success of which has led to recent progress in thin-film ion conductors. Here we compare the structural, electrochemical, and processing parameters between previously published LiPON and NaPON ALD processes with a novel ALD process for the K analogue potassium phosphorous oxynitride (KPON). In each ALD process, alkali tert-butoxides and diethylphosphoramidate are used as precursors. To understand the ALD surface reactions, this work proposes a reaction mechanism determined by in-operando mass spectrometry for the LiPON process as key to understanding the characteristics of the APON (A = Li, Na, K) family. As expected, NaPON and LiPON share similar reaction mechanisms as their structures are strikingly similar. KPON, however, exhibits similar ALD process parameters but the resulting film composition is quite different, showing little nitrogen incorporation and more closely resembling a phosphate glass. Due to the profound difference in structure, KPON likely undergoes an entirely different reaction mechanism. Furthermore, this paper presents a comprehensive summary of ALD ion conducting APON films as well as a perspective that highlights the versatility of ALD chemistries as a tool for the development of novel thin film ion-conductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗