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All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

Chance and necessity in the selection of nucleic acid catalysts

In Tom Stoppard's famous play [Rosencrantz and Guildenstern are Dead], the ill-fated heroes toss a coin 101 times. The first 100 times they do so the coin lands heads up. The chance of this happening is approximately 1 in 10(30), a sequence of events so rare that one might argue that it could only happen in such a delightful fiction. Similarly rare events, however, may underlie the origins of biological catalysis. What is the probability that an RNA, DNA, or protein molecule of a given random sequence will display a particular catalytic activity? The answer to this question determines whether a collection of such sequences, such as might result from prebiotic chemistry on the early earth, is extremely likely or unlikely to contain catalytically active molecules, and hence whether the origin of life itself is a virtually inevitable consequence of chemical laws or merely a bizarre fluke. The fact that a priori estimates of this probability, given by otherwise informed chemists and biologists, ranged from 10(-5) to 10(-50), inspired us to begin to address the question experimentally. As it turns out, the chance that a given random sequence RNA molecule will be able to catalyze an RNA polymerase-like phosphoryl transfer reaction is close to 1 in 10(13), rare enough, to be sure, but nevertheless in a range that is comfortably accessible by experiment. It is the purpose of this Account to describe the recent advances in combinatorial biochemistry that have made it possible for us to explore the abundance and diversity of catalysts existing in nucleic acid sequence space.

Review, Tutorial↗
DOE OSTI2021

A refined design concept for sulfur-tolerant Pd catalyst supported on zeolite by shape-selective exclusion and hydrogen spillover for hydrogenation of aromatics

Sulfur poisoning of noble metal catalysts has been a major challenge for decades. This work demonstrates the superior sulfur tolerance of a hybrid zeolite-supported Pd catalyst for hydrogenation of tetralin containing benzothiophene. The hybrid catalyst consists of Pd supported on a large-pore acidic zeolite Y (Pd/HY) and a small-pore zeolite A without (Pd/HA) or with surface metal passivation by chemical vapor deposition of SiO 2 (SiO 2 -Pd/HA) and with potassium ion exchange (SiO 2 -Pd/KA). Pd/HY is very active for tetralin hydrogenation but quickly deactivates after exposure to benzothiophene at high concentration of 100 ppm sulfur. The SiO 2 -coated Pd/HA shows no activity for tetralin hydrogenation, but continues to activate H 2 and serve as a source of hydrogen spillover from Pd/HA since these metal sites are protected from thiophenic sulfur due to size-selective exclusion. Adding K ion-exchanged and SiO 2 -coated catalyst SiO 2 -Pd/KA to Pd/HY is even more effective for enhancing sulfur tolerance, both for tetralin hydrogenation and for isomerization of cis-decalin to trans-decalin in the presence of benzothiophene. The turnover frequencies (TOF) of all the catalysts are similar at the exposed sulfur/Pd atomic ratio of around 0.5. With further increase in sulfur/Pd ratio, rapid decline in TOF was observed on Pd/HY, but SiO 2 -Pd/KA + Pd/HY hybrid catalyst shows a significantly higher TOF than that over Pd/HY, even though SiO 2 -Pd/KA or SiO 2 -Pd/HA alone shows no TOF for tetralin hydrogenation. Even after high-dose poisoning at 400 ppm sulfur, the SiO 2 -Pd/KA + Pd/HY hybrid recovered activity more quickly than SiO 2 -Pd/HA + Pd/HY, while the latter in turn is much better than Pd/HY alone. These results point to the higher activity for hydrogen spillover from SiO 2 -Pd/KA where Pd metal sites are protected from not only thiophenic sulfur but also inorganic sulfur H 2 S by shape-selective exclusion. The present work further establishes the validity of shape-selective exclusion and hydrogen spillover in the design concept proposed for a sulfur-tolerant bimodal acidic zeolite-supported metal catalyst for hydrogenation of naphthalene [C.S. Song, Chemtech, 29 (1999) 26–30], and refines the design concept further for limiting the size of small pore in hybrid catalysts to~3 Å for restricting access of H 2 S but allowing entrance of H 2 . Further, this refined design concept is applicable to other supported monometallic and bimetallic catalysts.

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

Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation

Abstract Tuberculosis, caused by Mycobacterium tuberculosis, responsible for ∼1.5 million fatalities in 2018, is the deadliest infectious disease. Global spread of multidrug resistant strains is a public health threat, requiring new treatments. Aminoacyl-tRNA synthetases are plausible candidates as potential drug targets, because they play an essential role in translating the DNA code into protein sequence by attaching a specific amino acid to their cognate tRNAs. We report structures of M. tuberculosis Phe-tRNA synthetase complexed with an unmodified tRNAPhe transcript and either L-Phe or a nonhydrolyzable phenylalanine adenylate analog. High-resolution models reveal details of two modes of tRNA interaction with the enzyme: an initial recognition via indirect readout of anticodon stem-loop and aminoacylation ready state involving interactions of the 3′ end of tRNAPhe with the adenylate site. For the first time, we observe the protein gate controlling access to the active site and detailed geometry of the acyl donor and tRNA acceptor consistent with accepted mechanism. We biochemically validated the inhibitory potency of the adenylate analog and provide the most complete view of the Phe-tRNA synthetase/tRNAPhe system to date. The presented topography of amino adenylate-binding and editing sites at different stages of tRNA binding to the enzyme provide insights for the rational design of anti-tuberculosis drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

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

Synthetically Reversible, Proton-Mediated Nitrite N–O Bond Cleavage at a Dicopper Site

A monocationic dicopper(I,I) nitrite complex [Cu 2 (μ-κ 1 :κ 1 -O 2 N)DPFN][NTf 2 ] (2) (DPFN = 2,7-bis(fluoro-di(2-pyridyl)methyl)-1,8-naphthyridine, NTf 2 – = N(SO 2 CF 3 ) 2 – ), was synthesized by treatment of a dicopper acetonitrile complex, [Cu 2 (μ-MeCN)DPFN][NTf 2 ] 2 (1), with tetrabutylammonium nitrite ([nBu 4 N][NO 2 ]). DFT calculations indicate that 2 is one of three linkage isomers that are close in energy and presumably accessible in solution. Reaction of the μ-κ 1 :κ 1 -O 2 N complex with p-TolSH produces nitrous acid (HONO) and the corresponding dicopper thiolate species via an acid–base exchange reaction. Notably, treatment of 2 with HNTf 2 results in N–O bond cleavage in the putative, HONO-ligated complex to form the more thermodynamically favorable nitrosyl-bridged dicopper complex [Cu 2 (μ-NO)(μ-OH)DPFN][NTf 2 ] 2 (4). This scission can be reversed via deprotonation of the hydroxy ligand with KO t Bu. X-ray diffraction studies confirmed the solid-state molecular structures of 2 and 4. DFT calculations were used to construct a reaction coordinate diagram detailing formation of the μ-NO complex and to describe its electronic structure. The nitrosyl ligand in 4 is chemically labile, as demonstrated by its ready displacement in reactions with CO or NO 2 – .

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

Highly efficient libraries design for saturation mutagenesis

Abstract Saturation mutagenesis is a semi-rational approach for protein engineering where sites are saturated either entirely or partially to include amino acids of interest. We previously reported on a codon compression algorithm, where a set of minimal degenerate codons are selected according to user-defined parameters such as the target organism, type of saturation and usage levels. Here, we communicate an addition to our web tool that considers the distance between the wild-type codon and the library, depending on its purpose. These forms of restricted collections further reduce library size, lowering downstream screening efforts or, in turn, allowing more comprehensive saturation of multiple sites. The library design tool can be accessed via http://www.dynamcc.com/dynamcc_d/. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗
NASA NTRS1999

The use of multiple indices of physiological activity to access viability in chlorine disinfected Escherichia coli O157:H7

A suite of fluorescent intracellular stains and probes was used, in conjunction with viable plate counts, to assess the effect of chlorine disinfection on membrane potential (rhodamine 123; Rh123 and bis-(1,3-dibutylbarbituric acid) trimethine oxonol; DiBAC4(3)), membrane integrity (LIVE/DEAD BacLight kit), respiratory activity (5-cyano-2,3-ditolyl tetrazolium chloride; CTC) and substrate responsiveness (direct viable counts; DVC) in the commensal pathogen Escherichia coli O157:H7. After a 5 min exposure to the disinfectant, physiological indices were affected in the following order: viable plate counts > substrate responsiveness > membrane potential > respiratory activity > membrane integrity. In situ assessment of physiological activity by examining multiple targets, as demonstrated in this study, permits a more comprehensive determination of the site and extent of injury in bacterial cells following sublethal disinfection with chlorine. This approach to assessing altered bacterial physiology has application in various fields where detection of stressed bacteria is of interest.

NASA Discipline Environmental Health↗
DOE OSTI2022

Leveraging Nitrogen Linkages in the Formation of a Porous Thorium–Organic Nanotube Suitable for Iodine Capture

We report the synthesis, characterization, and iodine capture application of a novel thorium–organic nanotube, TSN-626, [Th 6 O 4 (OH) 4 (C 6 H 4 NO 2 ) 7 (CHO 2 ) 5 (H 2 O) 3 ]·3H 2 O. The classification as a metal–organic nanotube (MONT) distinguishes it as a rare and reduced dimensionality subset of metal–organic frameworks (MOFs); the structure is additionally hallmarked by low node connectivity. TSN-626 is composed of hexameric thorium secondary building units and mixed O/N-donor isonicotinate ligands that demonstrate selective ditopicity, yielding both terminating and bridging moieties. Because hard Lewis acid tetravalent metals have a propensity to bind with electron donors of rival hardness (e.g., carboxylate groups), such Th–N coordination in a MOF is uncommon. However, the formation of key structural Th–N bonds in TSN-626 cap some of the square antiprismatic metal centers, a position usually occupied by terminal water ligands. TSN-626 was characterized by using complementary analytical and computational techniques: X-ray diffraction, vibrational spectroscopy, N 2 physisorption isotherms, and density functional theory. TSN-626 satisfies design aspects for the chemisorption of iodine. The synergy between accessibility through pores, vacancies at the metal–oxo nodes, and pendent N-donor sites allowed a saturated iodine loading of 955 mg g –1 by vapor methods. Furthermore, the crystallization of TSN-626 diversifies actinide–MOF linker selection to include soft electron donors, and these Th–N linkages can be leveraged for the investigation of metal-to-ligand bonding and unconventional topological expressions.

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

The Dependence of Olefin Hydrogenation and Isomerization Rates on Zirconium Metal–Organic Framework Structure

Zirconium metal–organic frameworks (Zr-MOFs) are a structurally diverse and well-defined class of materials studied in heterogeneous catalysis. Previously, we showed that partial dehydration of the Zr 6 O 8 node in NU-1000 results in heterolytic H 2 cleavage over adjacent Lewis acid and base sites, leading to catalytic conversion of 1-butene. In this work, given the ubiquity of the Zr 6 O 8 node as a secondary building unit (SBU) in Zr-MOFs, with many different potential MOF topologies and capping ligands surrounding the cluster, we study the influence of thermal pretreatments and MOF topology (MOF-808, NU-1000, UiO-66, and NU-1000-NDC) on the activity of the Zr 6 O 8 cluster for H 2 activation and 1-butene hydrogenation and isomerization. Diffuse reflectance IR in the presence of H 2 and pyridine shows that both thermal pretreatment and MOF topology affect the Brønsted acidity of protons generated from H 2 activation and their resulting activity for olefin conversion. High isomerization activity of dehydrated NU-1000 is correlated with the formation of μ 3 OH species after H 2 activation. Additionally, catalytic studies show that the geometry of open coordination sites on individual Zr 6 O 8 nodes influences butene hydrogenation. For this reason, MOF-808 gives anomalously low hydrogenation activity, despite its relatively high total number of open coordination sites, as calculated either from its crystal structure or from NH 3 adsorption. Furthermore, these results reiterate the importance of pretreatment in defining MOF catalytic activity and demonstrate that MOF topology, outside of simply affecting node accessibility, influences reactivity at individual nodes.

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

Clean Energy Technology Applications on US Mine Land: Technical Analysis

As the United States transitions toward a clean energy economy, an opportunity exists for redeveloping the more than 17,000 mine land sites located across the nation with clean energy technologies, which have a combined potential for generating more than 85 GW of clean electricity. This report provides an overview of the potential of demonstrating and deploying clean energy projects on current and former mine land. Clean energy project refers to a project that demonstrates one or more of the following technologies: solar; microgrids; geothermal; direct air capture; fossil-fueled electricity generation with carbon capture, utilization, and sequestration; energy storage, including pumped storage hydropower and compressed air energy storage; and advanced nuclear technologies. The report discusses the following technologies and their potential for creating jobs and generating tax revenue that would result in direct and indirect benefits to the local economy: Solar photovoltaics (PV) is being developed on current and former mine land in various parts of the world, including the United States. This approach is attractive because it requires limited infrastructure investment and would utilize the bare surfaces of mines and tailing ponds. Solar resource availability may be greater in the southern regions, including the Interior and Appalachian Basins and the southwestern United States. However, since some mine land sites include areas of significant change in elevation, the deployment of PV on mine land may require sophisticated planning to account for shading and irradiance, or may require regrading of the areas. PV does not create significant environmental risks and generally does not face public resistance; Geothermal systems are often spatially and genetically associated with ore deposits, and in some cases, they have been discovered while in search for epithermal mineral resources. Numerous diverse geothermal applications have been employed at mine land around the world, including power generation, mineral extraction from geothermal brines, process heating, direct use for other mining operations, and direct use for non-mining operations and subsurface energy storage, including geothermal heat pumps. Case studies highlighting these applications provide key lessons relating to identifying drivers and barriers to geothermal resource deployment and can be used to create screening tools for identifying the types and locations of mine land most amenable to utilizing geothermal resources; Carbon capture, utilization, and sequestration technologies include direct air capture (DAC) and enhanced weathering. DAC technologies include air contactors, regeneration systems, and CO 2 compression systems. Captured CO 2 can be converted to valuable feedstocks or possibly injected into abandoned subsurface mines where it would be absorbed by alkaline rock waste and mine tailings or by the porous minerals along the walls of the mine. DAC systems can be coupled with energy sources such as wind, solar, grid, or geothermal. Many DAC systems require a source of water or steam; however, some are expected to be net producers of water. Local impacts of DAC systems are expected to be low, and are related to land footprint, material disposal, and upstream impacts of energy and material production; Compressed air energy storage is an established energy storage technology in salt caverns. It has the potential for implementation in underground mines by pressurizing and storing a large amount of air using electrical compressors when excess electricity is available. When a need for discharge emerges, the air is used to spin turbines and produce the necessary volume of electricity. Abandoned or unused mine openings, including shafts, adits, access tunnels, and mined workings of any orientation, offer potential for vast amounts of compressed air energy storage if the site characteristics meet operational requirements; Pumped hydropower storage can be implemented in surface and subsurface mines. In surface mine applications, both reservoirs may be located in a mine pit or artificial reservoirs made of excavated materials. In subsurface mines, the lower reservoir may be implemented by waterproofing and flooding mine shafts and tunnels. The water is then pumped from the lower reservoir to the upper reservoir during periods of low load and high production, and it is discharged through the turbines during periods of peak demand. The potential environmental damages associated with acidity of mine water or the presence of toxic chemicals incentivizes the development of closed-loop technologies, in which water circulates inside the pumped hydropower facility without being discharged into the external water basins; Advanced nuclear energy technologies include small modular reactors, which can be deployed locally to produce electricity and heat. Such units require seismic stability and a supply of cooling water, but population constraints may exist in some areas. Therefore, remote mine land could represent an optimal location for siting advanced nuclear energy technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here. In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry. Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2022

Panchromatic Absorbers Tethered for Bioconjugation or Surface Attachment

The syntheses of two triads are reported. Each triad is composed of two perylene-monoimides linked to a porphyrin via an ethyne unit, which bridges the perylene 9-position and a porphyrin 5- or 15-position. Each triad also contains a single tether composed of an alkynoic acid or an isophthalate unit. Each triad provides panchromatic absorption (350–700 nm) with fluorescence emission in the near-infrared region (733 or 743 nm; fluorescence quantum yield ~0.2). The syntheses rely on the preparation of trans-AB-porphyrins bearing one site for tether attachment (A), an aryl group (B), and two open meso-positions. The AB-porphyrins were prepared by the condensation of a 1,9-diformyldipyrromethane and a dipyrromethane. The installation of the two perylene-monoimide groups was achieved upon the 5,15-dibromination of the porphyrin and the subsequent copper-free Sonogashira coupling, which was accomplished before or after the attachment of the tether. The syntheses provide relatively straightforward access to a panchromatic absorber for use in bioconjugation or surface-attachment processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Formation of Unusual Deprotomers of Citric Acid and Sodium Citrate Aggregates: A Photoelectron Spectroscopy and Computational Study

Given multiple distinct deprotonation sites and flexible structural conformation in citric acid (CA), the intrinsic interaction between protons, sodium cations and citrate anions deems complicated. In this work, we address this issue by combining photoelectron spectroscopy and theoretical modeling on a series of gaseous sodium citrate anion clusters with progressive substitution of protons with sodium cations [(CA-nH)·(n-1)Na]- (n = 1-3). Despite markedly different pKa values for the central (C, 3.28), terminal carboxylic (T, 5.98) and hydroxyl group (O, 18.44), our study reveals experimental observation of all three distinct deprotomers in [CA-1H]- with deprotonation from hydroxyl energetically competitive. Upon Na+ binding to the doubly or triply deprotonated CA, only one kind of deprotonation tautomer, respectively TC or TTC, is experimentally accessible. Moreover, a dianionic dimer [(CA-3H)·2Na]22- is observed. This work displays a diverse binding landscape among protons, sodium and citrate species in the gas phase, advancing our understanding of sodium citrate chemistry.

Yuan, Qinqin↗
DOE OSTI2024

Direct Conversion of CO 2 to Olefins over a Cr 2 O 3 /ZSM-5@CaO Cooperative and Bifunctional Material Under Isothermal Conditions

Direct conversion of point-source CO 2 into fine chemicals over cooperative and bifunctional materials (BFMs) – composed of adsorbents and catalysts – has emerged as a promising approach to improve the energy efficiency of the carbon capture and conversion processes. In this study, a bifunctional material consisting of Cr 2 O 3 /ZSM-5 catalyst and CaO adsorbent was developed and tested in the CO 2 -oxidative dehydrogenation of propane (CO 2 –ODHP) for reactive capture of CO 2 in a fixed bed reactor. First, CaO was prepared using two distinct methods: solid-state and citrate sol–gel. The citrate sol–gel method resulted in small and finely-distributed CaO particles, allowing more accessible sites for CO 2 adsorption. Consequently, a high CO 2 adsorption capacity of ~14 mmol/g was achieved with fast adsorption kinetics compared to CaO prepared by the solid-state method. The CaO adsorbent was then combined with the Cr 2 O 3 /ZSM-5 catalyst for BFM synthesis and tested in the CO 2 –ODHP process, targeting propylene production. The BFM was extensively characterized to provide insights into the BFM’s surface chemistry, morphology, and reaction mechanism in the reactive capture process of CO 2 –ODHP. The results revealed that under isothermal adsorption–reaction conditions at 600 °C, a propane conversion of 22.5%, a propylene selectivity of 55.3%, and an olefin selectivity of 67.3% were achieved. The excellent propylene selectivity was attributed to the catalyst acidity and redox property of the Cr 2 O 3 /ZSM-5 catalyst, which facilitated the reaction pathway of propane dehydrogenation in the process of CO 2 –ODHP. Overall, this study renders Cr 2 O 3 /ZSM-5@CaO as promising BFMs with high CO 2 capture capacity and catalytic activity for integrated CO 2 capture and conversion in the ODHP reaction.

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

Understanding Adsorption and Reactions at Aqueous Oxide Interfaces with Neural Network Potential Molecular Dynamics

Chemical processes at metal oxide−water interfaces are of central importance in geochemistry, biology, and energy technologies. A better understanding of these processes would allow us to make a significant step toward optimizing and controlling them, which could in turn lead to broader impacts. Computational modeling is indispensable to accomplishing this task because complexity and disorder often make it difficult to extract atomistic information from experiments. Balancing computational cost and accuracy, simulation schemes based on efficient machine learning representations of the potential energy surface (PES) predicted by ab initio calculations have become increasingly popular over the past decade. In particular, several studies have demonstrated the ability of machine learning models to accurately reproduce the complex ab initio PESs of aqueous oxide interfaces, allowing simulations of systems and processes that are not accessible with ab initio methods. In this Account, we review our recent efforts to understand adsorption processes and reactions at aqueous oxide interfaces using deep potential molecular dynamics (DPMD), a simulation scheme employing deep neural networks (DNNs), which has proven to be quite successful in accurately describing many different systems in the condensed phase. After summarizing the DPMD methodology, we first review our work on the acid−base chemistry of oxide surfaces in contact with water, a fundamental characteristic that controls proton transfer and surface charge at the interface. We focus on the aqueous interface of rutile IrO 2 , an oxide material thus far considered the best catalyst for the oxygen evolution reaction (OER). We show that this interface is characterized by a large fraction of dissociated water and a strong Brønsted acidity of the surface sites, in good agreement with the experimentally measured value of the point of zero proton charge. In our second example, we investigate how the adsorption of organic species from ambient air or water affects the structure and wettability of the aqueous interfaces of TiO 2 , a prototypical photocatalytic material. This is a question that is relevant to understanding the UV-induced hydrophilicity of TiO 2 surfaces, a property at the basis of self-cleaning windows and related applications. Specifically focusing on formic and acetic acids, the two most common atmospheric organic acids, our simulations reveal that these acids control the wettability of TiO 2 largely through acid−base chemistry at the interface rather than chemisorption on the oxide surface, a finding that could help improve the design of self-cleaning surfaces and photocatalytic devices. Finally, we review our recent study of methanol at TiO 2 −water interfaces, a system whose interest is largely motivated by the role of methanol in enhancing photocatalytic hydrogen evolution on TiO 2 . Our simulations provide mechanistic insights into the coupled roles of the organic adsorbate and water at the TiO 2 interface, with implications for how methanol enhances the activity of H 2 evolution.

adsorption↗
DOE OSTI2023

Electrochemical Acid Sequestration to Ease Ocean Acidification (EASE-OA) - CRADA 600 (Abstract)

The PNNL team will coordinate logistics involved with setting up the field trial on the PNNL Sequim campus in collaboration with Ebb Carbon. Facilities on the PNNL Sequim campus are capable of pumping raw or filtered seawater from Sequim Bay at a rate ~45,000 L hr -1 , which can accommodate the 4000 L hr -1 requirement of the 200 ton CO2 yr-1 Ebb Carbon marine carbon dioxide removal (mCDR) system. The primary tasks for the PNNL team are 1) laying out appropriate indoor and outdoor spaces for installing the Ebb Carbon’s mCDR system, 2) facilitating Ebb Carbon’s access to the PNNL’s seawater intake on the PNNL Sequim campus, 3) conducting mesocosm experiments within the PNNL Sequim campus laboratories to test how the brine and base discharged from the Ebb Carbon system affect marine life, and 4) facilitating Ebb Carbon access to the PNNL Sequim installation site and aiding in maintenance as needed. In addition to these tasks, the PNNL team will provide surface water quality data (e.g., salinity, temperature, pH, dissolved O2) from a monitoring station located on the pier to contextualize starting conditions of the seawater used in the mCDR process. Finally, the PNNL team will also consult with Ebb Carbon on strategies for improving overall system performance and next steps for further scaling and/or monitoring the effectiveness of the mCDR system.

54 ENVIRONMENTAL SCIENCES↗