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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Thermodynamic properties of ε -Fe with thermal electronic excitation effects on vibrational spectra

The thermodynamic properties of hexagonal-close-packed iron (ε–Fe) are essential for investigating the internal structure and dynamic properties of planetary cores. Despite their importance to planetary sciences, experimental investigations of ε–Fe at relevant conditions are still challenging. Therefore, ab initio calculations are crucial to elucidating the thermodynamic properties of this system. Here, we use a free energy calculation scheme based on the phonon gas model compatible with temperature-dependent phonon frequencies. We investigate the effects of electronic thermal excitations, which introduces a temperature dependence on phonon frequencies, and the implication for the thermodynamic properties of ε–Fe at extreme pressure (P) and temperature (T) conditions. We disregard phonon-phonon interactions, i.e., anharmonicity and their effect on phonon frequencies. Nevertheless, the current scheme is also applicable to T -dependent anharmonic frequencies. We conclude that the impact of thermal electronic excitations on vibrational properties is not significant up to ~4000 K at 200 GPa but should not be ignored at higher temperatures or pressures. However, the static free energy F st must always include the effect of thermal excitation fully in a continuum of T. Furthermore, our results for isentropic equations of state show good agreement with data from recent ramp compression experiments up to 1400 GPa conducted at the National Ignition Facility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Solving the “Coloring Problem” in InPd 3– x Ag x ( x = 0–0.7) by Phase Diagrams Modeling and Diffraction Experiments

Here, a series of InPd 3–x Ag x (x = 0–1) compositions were synthesized by conventional high-temperature synthesis, and as-synthesized samples were characterized by powder X-ray diffraction experiments. Up to x = 0.7, InPd 3–x Ag x adopts the ternary substitutional variant of the InPd 3 structure (TiAl 3 -type), when x > 0.7, elemental Ag starts to segregate along with the main phase. Accurate structural characterization in InPd 3–x Ag x faces a critical challenge due to the narrow X-ray scattering contrast among constituents In, Pd, and Ag and nearly identical neutron scattering lengths of Pd and Ag. To overcome this “coloring problem”, a combination of calculation of phase diagrams modeling (CALPHAD) and diffraction techniques (X-ray and neutron) was employed. In the compositional range 0 ≤ x ≤ 0.7, InPd 3–x Ag x presents a ternary variant of the TiAl 3 -type structure, where Ag atoms selectively substitute one (the 2b Wyckoff site) of the two Pd sites in InPd 3 . Notably, in contrast to the isologous InPd 3–x Cu x (x = 0–1) system, Ag substitution does not form an ordered VRh 2 Sn-type structure at the limiting composition. The distinct site preference in InPd 3–x Ag x is elucidated by charge population analysis, electronic structure calculations, and orbital-resolved chemical bonding investigations, and the extent of substitution is supported by formation free energy calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Trends in Formic Acid Electro-Oxidation on Transition Metals Alloyed with Platinum and Palladium

Direct formic acid fuel cells (DFAFCs) have emerged as a promising power source to meet increased demands for alternative energy sources in the transportation and portable energy storage sectors. Furthermore, these fuel cells utilize formic acid (FA), a nontoxic and carbon-neutral fuel when produced from biomass or via CO 2 reduction. Despite the promise of DFAFCs, the best monometallic catalysts, platinum and palladium, are poisoned by CO through the indirect oxidation pathway and require large overpotentials. By alloying Pt and Pd with other metals, we aim to improve both the activity and selectivity of these catalysts. Here, we present a systematic density functional theory (GGA-PW91) study of FA electro-oxidation (FAO) on the (111) facet of bimetallic Pt (Pt 3 M) or Pd (Pd 3 M) catalysts (M = Au, Ag, Cu, Pt, Pd, Ir, Rh, Ru, or Re) to evaluate the catalytic performance of these surfaces. For each surface, we calculate free energy diagrams and onset potentials of three key reaction mechanisms: direct oxidation of FA via carboxyl (COOH), direct oxidation of FA via formate (HCOO), and the indirect oxidation of FA that first forms CO en route to full oxidation to CO 2 . We then display the trends in the form of phase diagrams that compare the activity of the calculated surfaces against regions of high activity using the free energies of adsorbed CO and OH as descriptors, enabling high-throughput screening and design of improved catalysts, particularly those alloying Pt or Pd with Ir, Ru, or Re.

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

Reactive force fields for aqueous and interfacial magnesium carbonate formation

Here we develop Mg/C/O/H ReaxFF parameter sets for two environments: an aqueous force field for magnesium ions in solution and an interfacial force field for minerals and mineral–water interfaces. Since magnesium is highly ionic, we choose to fix the magnesium charge and model its interaction with C/O/H through Coulomb, Lennard-Jones, and Buckingham potentials. We parameterize the forcefields against several crystal structures, including brucite, magnesite, magnesia, magnesium hydride, and magnesium carbide, as well as Mg 2+ water binding energies for the aqueous forcefield. Then, we test the forcefield for other magnesium-containing crystals, solvent separated and contact ion-pairs and single-molecule/multilayer water adsorption energies on mineral surfaces. We also apply the forcefield to the forsterite–water and brucite–water interface that contains a bicarbonate ion. We observe that a long-range proton transfer mechanism deprotonates the bicarbonate ion to carbonate at the interface. Free energy calculations show that carbonate can attach to the magnesium surface with an energy barrier of about 0.22 eV, consistent with the free energy required for aqueous Mg–CO 3 ion pairing. Also, the diffusion constant of the hydroxide ions in the water layers formed on the forsterite surface are shown to be anisotropic and heterogeneous. These findings can help explain the experimentally observed fast nucleation and growth of magnesite at low temperature at the mineral–water–CO 2 interface in water-poor conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2022

Configuration Space Integration for Adsorbate Partition Functions: The Effect of Anharmonicity on the Thermophysical Properties of CO–Pt(111) and CH 3 OH–Cu(111)

A method for computing anharmonic thermophysical properties for adsorbates on metal surfaces has been extended to include libration, or frustrated rotation. Classical phase space integration is used with Monte Carlo sampling of the configuration space to obtain the partition function of CO on Pt(111) and CH 3 OH on Cu(111). A minima-preserving neural network potential energy surrogate is used within the integration routines. Direct state counting using discrete variable representation is used to benchmark the results. We find that the phase space integration approach is in excellent agreement with the direct state counting results. Comparison with standard models such as the harmonic oscillator indicates that anharmonicity contributes significantly to the thermodynamic properties of CH 3 OH on Cu(111). We find that there is also a considerable difference between the harmonic oscillator and phase space integration for CO on Pt(111), although the discrepancy can largely be attributed to the presence of multiple binding sites within the unit cell. We demonstrate that a multisite harmonic oscillator model might be sufficient for CO-Pt(111). A more thorough description of the potential energy surface, which can be achieved with phase space integration, is necessary for weakly bound adsorbates such as CH 3 OH. In conclusion, the thermophysical properties were used to calculate free energies of adsorption on the respective metals, and subsequently the equilibrium constants and Langmuir isotherms in relevant temperature ranges. The results show that the choice of model to obtain partition functions greatly affects the resulting surface coverages in kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2000

Apparent Minimum Free Energy Requirements for Methanogenic Archaea and Sulfate-Reducing Bacteria in an Anoxic Marine Sediment

Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5 C) and August (at 27 C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate reducing bacteria exhibited an asymptote of -19.1 +/- 1.7 kj(mol SO4(2-)(sup -1) while methanogenic archaea were apparently supported by energy yields as small as -10.6 +/- 0.7 kj(mol CH4)(sup -1).

Hoehler, Tori M.↗
DOE OSTI2025

Computational discovery of a novel double transition metal nitride MXene and its applications as an anchoring and catalytic material in Li–Se batteries

Double transition metal (DTM) nitride MXenes offer enhanced electrical conductivity and tunable catalytic properties compared to conventional carbide-based MXenes. In this study, we employed first-principles density functional theory (DFT) calculations to discover and computationally validate a novel DTM nitride MXene, Nb 2 TiN 2 , derived from its MAX phase precursor and investigated its potential as an anchoring material (AM) for Li–Se batteries. This newly proposed MXene expands the compositional landscape of DTM nitrides and opens new avenues for functional material design. We performed a comprehensive analysis of the thermodynamic and electronic properties of Nb 2 TiAlN 2 , and the MAX phase precursor to Nb 2 TiN 2 to assess its structural stability and exfoliation potential. Exfoliation energy calculations confirmed the feasibility of synthesizing Nb 2 TiN 2 from Nb 2 TiAlN 2 . We then explored the functionalized form, Nb 2 TiN 2 S 2 , evaluating its capability to serve as an effective anchoring material (AM) in Li–Se batteries by analyzing the reaction mechanisms and kinetics of the selenium reduction reaction (SeRR). Our results indicate that Nb 2 TiN 2 S 2 exhibits a strong binding affinity for lithium polyselenides (Li 2 Se n ), effectively suppressing the shuttle effect. Gibbs free energy calculations for the rate-limiting step of the SeRR reveal favorable kinetics and reduced reaction barriers. Overall, this study provides a detailed evaluation of the structural and electronic properties of a newly proposed DTM nitride MXene and its S-functionalized derivative and the catalyzing effect of Nb 2 TiN 2 S 2 in accelerating the reaction kinetics in Li–Se batteries. These findings underscore the potential importance of the further exploration of MXenes to address current challenges in high-performance Li–Se batteries.

25 ENERGY STORAGE↗
DOE OSTI2024

Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables

In this study, we present a graph neural network-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. Our approach uses simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine from their molten states. Our graph latent variables when biased in well-tempered metadynamics consistently show transitions between states and achieve accurate free energy calculations in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our graph neural net variables for improved sampling. Furthermore, the protocol shown here should be applicable for other systems and with other sampling methods.

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

Polymorphism and phase transitions in Na 2 U 2 O 7 from density functional perturbation theory

Polymorphism and phase transitions in sodium diuranate, Na 2 U 2 O 7 , are investigated with density functional perturbation theory (DFPT). Thermal properties of crystalline α-, β- and γ-Na 2 U 2 O 7 polymorphs are predicted from DFPT phonon calculations, i.e., the first time for the high-temperature γ-Na 2 U 2 O 7 phase (R$\bar{3}$ with combining macron]m symmetry). The standard molar isochoric heat capacities predicted within the quasi-harmonic approximation are C p (298.15K)= 219.4 and 220.9 J K -1 mol -1 mfor P21/a α-Na 2 U 2 O 7 and C2/m β-Na 2 U 2 O 7 , respectively. Gibbs free energy calculations reveal that α-Na 2 U 2 O 7 (P2 1 /a) and β-Na 2 U 2 O 7 (C2/m) are almost energetically degenerate at low temperature, with β-Na 2 U 2 O 7 becoming slightly more stable than α-Na 2 U 2 O 7 as temperature increases. Here these findings are consistent with XRD data showing a mixture of α and β phases after cooling of γ-Na 2 U 2 O 7 to room temperature and the observation of a sluggish α → β phase transition above ca. 600 K. A recently observed α-Na 2 U 2 O 7 structure with P21 symmetry is also shown to be metastable at low temperature. Based on Gibbs free energy, no direct β → γ solid-solid phase transition is predicted at high temperature, although some experiments reported the existence of such phase transition around 1348 K. This, along with recent experiments, suggests the occurrence of a multi-step process consisting of initial β-phase decomposition, followed by recrystallization into γ-phase as temperature increases.

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

Atomistic origins of biomass recalcitrance in organosolv pretreatment

Separation of lignocellulosic biomass components for use in sustainable energy and biomaterials applications remains challenging, since biopolymers such as cellulose and hemicellulose carbohydrates and polyaromatic lignin are found in close proximity within the plant secondary cell wall. Organic solvents have been used to pretreat recalcitrant biomass and separate the interacting polymers, solubilizing the lignin fraction for lignin-first valorization approaches. However, no single organosolv pretreatment approach has proven superior for heterogeneous biomass samples. Here we present a complementary atomic view of interactions between biomass components using molecular simulations, specific to lignin and cellulose, resolving mechanistic hypotheses for how lignin-cellulose composition influences separation processes. Further, using lignin-cellulose binding free energy calculated using molecular simulations, we find polar protic solvents such as methanol and ethanol separate lignin from cellulose, irrespective of the charge on the lignin monomer. Aprotic organic solvents (DMSO, THF, 1,4-dioxane) separate uncharged lignin (phenols and monolignols) from cellulose, while charged lignin (cinnamates) prefer binding to cellulose.

09 BIOMASS FUELS↗
DOE OSTI2022

Machine learning the metastable phase diagram of covalently bonded carbon

Abstract Conventional phase diagram generation involves experimentation to provide an initial estimate of the set of thermodynamically accessible phases and their boundaries, followed by use of phenomenological models to interpolate between the available experimental data points and extrapolate to experimentally inaccessible regions. Such an approach, combined with high throughput first-principles calculations and data-mining techniques, has led to exhaustive thermodynamic databases (e.g. compatible with the CALPHAD method), albeit focused on the reduced set of phases observed at distinct thermodynamic equilibria. In contrast, materials during their synthesis, operation, or processing, may not reach their thermodynamic equilibrium state but, instead, remain trapped in a local (metastable) free energy minimum, which may exhibit desirable properties. Here, we introduce an automated workflow that integrates first-principles physics and atomistic simulations with machine learning (ML), and high-performance computing to allow rapid exploration of the metastable phases to construct “metastable” phase diagrams for materials far-from-equilibrium. Using carbon as a prototypical system, we demonstrate automated metastable phase diagram construction to map hundreds of metastable states ranging from near equilibrium to far-from-equilibrium (400 meV/atom). We incorporate the free energy calculations into a neural-network-based learning of the equations of state that allows for efficient construction of metastable phase diagrams. We use the metastable phase diagram and identify domains of relative stability and synthesizability of metastable materials. High temperature high pressure experiments using a diamond anvil cell on graphite sample coupled with high-resolution transmission electron microscopy (HRTEM) confirm our metastable phase predictions. In particular, we identify the previously ambiguous structure of n -diamond as a cubic-analog of diaphite-like lonsdaelite phase.

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

Water chemistry in flume channel and hyporheic zone (i.e., porewater) associated with: “Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry”

Dissolved oxygen (DO), total organic carbon (TOC), total nitrogen (TN), molecular data for organic matter, and biochemical reactions for surface water and porewater (i.e., hyporheic zone) collected from a water recirculating flume located at the University of Texas, Austin. The flume contained real river water from Lower Colorado River(Austin, TX) and clean sand. Hyporheic exchange in the flume was induced through The study aims to understand relationships between aerobic metabolism of organic matter and molecular characteristics of organic matter, such as thermodynamic signature and nitrogen content, through the extent of the hyporheic zone at 10 cm- resolution, and through time. During the experiment, organic matter (dry leaves) was added to the flume and removed after 24 hours. The water samples were collected before the addition of leaves, at the time of removal of leaves, and at hour 72. The water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and total organic carbon (TOC) and total nitrogen (TN) analysis. Dissolved oxygen content throughout the surface water and the hyporheic zone of the flume was measured with a large planar optode. This data package is associated with the publication ’ Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry’ published in Environmental Science and Technology (Turețcaia et al., 2023 https://doi.org/10.1021/acs.est.3c04765). The dataset is comprised of five folders (1) Diss_O2_pic, (2) input_files (3) output_files; (4) python_code; and (5) R_code . Diss_O2_pic contains siximages of dissolved oxygen distribution in a bedform at hours 0, 24, and 72 of the experiment conducted in a large recirculation flume. Images are in separate R and G channels (i.e., RGB). The input_files contains (1) a csv file with FTICR peaks identified within each sample, (2) a csv file with molecular information pertinent to FTICR data with Gibbs free energy calculations adjusted for environmental temperature, (3) a csv file containing concentrations of non-purgeable organic carbon measured throughout the experiment , (4) a csv file containing concentrations of total nitrogen measured throughout the experiment, (5) a csv file containing total biochemical reactions (i.e., transformations) identified in the dataset, (6) a csv containing transformation profiles, and (7) a csv file containing transformations with formulas, and (8) a jpg file with schematic representation of locations for sample collection. The output_files contains (1) and xlsx file containing percent biochemical reactions containing nitrogen identified across all 39 sample, (2) a csv file of merged FTICR data and molecular information files, (3) a csv files containing average Gibbs free energy within sampling domains and at each sampling location, (4) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 0, (5) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 24, (6) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 72, (7) a csv file with percent chemical classes identified across sampling locations at hour 0, (8) a csv file with percent chemical classes identified across sampling locations at hour 24, (9) a csv file with percent chemical classes identified across sampling locations at hour 72, and (10) a csv file containing percent nitrogen containing biochemical reactions identified across sampling locations at hours 0, 24, and 72. The python_code contains seven ipynb files which are Jupyter Notebooks used for data analysis and figures generation. The R_code contains 3 R files with R code used for data analysis and figures generation. This data package contains the processed data used in the associated manuscript. This data has not been previously published.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Directly Fused Porphyrin‐Tetracyanopentacenequinone Conjugates: Role of the Cross‐Conjugated, Powerful Electron Acceptor in Promoting Highly Efficient Charge Separation

Tetracyanopentacenequinone, a powerful electron acceptor, is fused directly to the porphyrin π-system to create a new class of donor-acceptor conjugates. Owing to the direct fusion and electron-deficient property of tetracyanopentacenequinone, strong intramolecular charge transfer both in the ground and excited states was witnessed. As a control, porphyrin fused with pentacenequinone was also investigated. Upon complete spectral and electrochemical characterization, the excited state properties were initially probed by time-dependent DFT studies, and the occurrence of electron transfer from different excited states was established. Free-energy calculations revealed higher exothermic electron transfer (>600 mV) than the control pentacenequinone-porphyrin systems. Pump-probe studies covering broad spatial and temporal regions revealed efficient excited state charge separation. This was unlike the control pentacenequinone-porphyrin system, where slow charge separation was witnessed only in the case of the zinc derivatives but not the free-base ones, followed by the populating of the triplet excited state. The lifetimes of the charge-separated states ranged between 30–500 ps depending on the solvent and metal ion in the porphyrin cavity. Nanosecond transient absorption studies established the charge recombination path to populate the triplet state of porphyrin or directly to the ground state as a function of solvent polarity and the nature of the conjugate. Furthermore, the significance of cross-conjugated tetracyanopentacenequinone fused directly to the porphyrin π system in promoting highly exothermic and efficient charge separation, irrespective of its cross conjugation, is borne out from this study.

Cross conjugation↗
NASA NTRS1977

The chemical composition of the cores of the terrestrial planets and the moon

Using models of the quasi-chemical theory of solutions, the activity coefficients of silicon are calculated in the melts Fe-Si, Ni-Si, and Fe-Ni-Si. The calculated free energies of solution of liquid nickel and silicon in liquid iron in the interval 0 to 1400 kbar and 1500 to 4000 K, shows that Fe-Ni-Si alloy is stable under the conditions of the outer core of the earth and the cores of the terrestrial planets. The oxidation-reduction conditions are studied, and the fugacity of oxygen in the mantles of the planets and at the core-mantle boundary are calculated. The mechanism of reduction of silicon is analyzed over a broad interval of p and T. The interaction between the matter of the core and mantle is studied, resulting in the extraction of silicon from the mantle and its solution in the material of the core. It is concluded that silicon can enter into the composition of the outer core of the earth and Venus, but probably does not enter into the composition of the cores of Mercury, Mars, and the moon, if in fact the latter possesses one.

Kuskov, O. L.↗
DOE OSTI2025

PSCF+: An Extended and Improved Open-Source Software Package for Polymer Self-Consistent Field Calculations

This work introduces PSCF+, a freely available open‑source software tool for modeling how block copolymers self‑assemble into ordered nanoscale structures. The software allows researchers to study a wide range of polymer models and interaction types, making it possible to directly compare theoretical predictions with molecular and simulation‑based studies in a consistent way. PSCF+ incorporates several recently developed numerical methods that significantly reduce computer memory requirements and speed up calculations, enabling efficient use of modern GPU hardware. Here, it also provides automated tools to calculate free‑energy landscapes and phase boundaries, which are essential for understanding and predicting material behavior. Together, these advances make PSCF+ a powerful and flexible platform for studying polymer self‑assembly and support the design of new polymeric materials for scientific and technological applications.

Chemical calculations↗
DOE OSTI2023

Control of the Structural Charge Distribution and Hydration State upon Intercalation of CO 2 into Expansive Clay Interlayers

Numerous experimental investigations indicated that expansive clays such as montmorillonite can intercalate CO 2 preferentially into their interlayers and therefore potentially act as a material for CO 2 separation, capture, and storage. However, an understanding of the energy–structure relationship during the intercalation of CO 2 into clay interlayers remains elusive. Here, in this study, we use metadynamics molecular dynamics simulations to elucidate the energy landscape associated with CO 2 intercalation. Our free energy calculations indicate that CO 2 favorably partitions into nanoconfined water in clay interlayers from a gas phase, leading to an increase in the CO 2 /H 2 O ratio in clay interlayers as compared to that in bulk water. CO 2 molecules prefer to be located at the centers of charge-neutral hydrophobic siloxane rings, whereas interlayer spaces close to structural charges tend to avoid CO 2 intercalation. The structural charge distribution significantly affects the amount of CO 2 intercalated in the interlayers. These results provide a mechanistic understanding of CO 2 intercalation in clays for CO 2 separation, capture, and storage.

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

Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3 S ,4 S )-3-Amino-4-fluorocyclopentenecarboxylic Acid

Ornithine aminotransferase (OAT) is overexpressed in hepatocellular carcinoma (HCC), and we previously showed that inactivation of OAT inhibits the growth of HCC. Recently, we found that (3S,4S)-3-amino-4-fluorocyclopentenecarboxylic acid (5) was a potent inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), proceeding by an enamine mechanism. Here we describe our investigations into the activity and mechanism of 5 as an inactivator of human OAT. We have found that 5 exhibits 10-fold less inactivation efficiency (k inact /K I ) against hOAT than GABA-AT. A comprehensive mechanistic study was carried out to understand its inactivation mechanism with hOAT. pK a and electrostatic potential calculations were performed to further support the notion that the α,β-unsaturated alkene of 5 is critical for enhancing acidity and nucleophilicity of the corresponding intermediates and ultimately responsible for the improved inactivation efficiency of 5 over the corresponding saturated analogue (4). Intact protein mass spectrometry and the crystal structure complex with hOAT provide evidence to conclude that 5 mainly inactivates hOAT through noncovalent interactions, and that, unlike with GABA-AT, covalent binding with hOAT is a minor component of the total inhibition which is unique relative to other monofluoro-substituted derivatives. Furthermore, based on the results of transient-state measurements and free energy calculations, it is suggested that the α,β-unsaturated carboxylate group of PLP-bound 5 may be directly involved in the inactivation cascade by forming an enolate intermediate. Overall, compound 5 exhibits unusual structural conversions which are catalyzed by specific residues within hOAT, ultimately leading to an enamine mechanism-based inactivation of hOAT through noncovalent interactions and covalent modification.

59 BASIC BIOLOGICAL SCIENCES↗