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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme

RNase H enzymes are sequence-nonspecific endonucleases that cleave RNA strands in RNA/DNA hybrid duplexes, an enzymatic process essential in DNA replication and repair in both prokaryotes and eukaryotes. Also, RNase H activity of the reverse transcriptase in human immunodeficiency viruses (HIV-1 and HIV-2) is indispensable for the viral replication cycle. RNase H enzymes play an central role in the development of gene therapies and are targets for novel antivirals. It is therefore of great importance to gain a detailed understanding of the RNase H catalytic mechanism to improve drug design. We utilized Bacillus halodurans RNase H1 (BhRNase H1) to shed light on its function and catalytic mechanism. Room-temperature neutron crystallography of the wild-type and inactive D132N mutant enzymes revealed that E109, belonging to the catalytic DEDD motif, can change its protonation state, allowing us to propose its role in the protonation of the leaving O3′ hydroxyl group of RNA. X-ray crystallography has demonstrated the ability of the RNA/DNA duplex to slide along the protein surface upon metal ion binding at site M A , transforming a product mimic into a Michaelis-like complex, which confirms an essential role of the M A metal ion in catalysis.

Enzyme mechanisms↗
NASA NTRS2011

Stress-Driven Selection of Novel Phenotypes

A process has been developed that can confer novel properties, such as metal resistance, to a host bacterium. This same process can also be used to produce RNAs and peptides that have novel properties, such as the ability to bind particular compounds. It is inherent in the method that the peptide or RNA will behave as expected in the target organism. Plasmid-born mini-gene libraries coding for either a population of combinatorial peptides or stable, artificial RNAs carrying random inserts are produced. These libraries, which have no bias towards any biological function, are used to transform the organism of interest and to serve as an initial source of genetic variation for stress-driven evolution. The transformed bacteria are propagated under selective pressure in order to obtain variants with the desired properties. The process is highly distinct from in vitro methods because the variants are selected in the context of the cell while it is experiencing stress. Hence, the selected peptide or RNA will, by definition, work as expected in the target cell as the cell adapts to its presence during the selection process. Once the novel gene, which produces the sought phenotype, is obtained, it can be transferred to the main genome to increase the genetic stability in the organism. Alternatively, the cell line can be used to produce novel RNAs or peptides with selectable properties in large quantity for separate purposes. The system allows for easy, large-scale purification of the RNAs or peptide products. The process has been reduced to practice by imposing sub-inhibitory concentrations of NiCl2 on cells of the bacterium Escherichia coli that were transformed separately with the peptide library and RNA library. The evolved resistant clones were isolated, and sequences of the selected mini-gene variants were established. Clones resistant to NiCl2 were found to carry identical plasmid variants with a functional mini-gene that specifically conferred significant nickel tolerance on the host cells. Sequencing of the selected mini-gene revealed a propensity of the encoded peptide to bind transient metal ions. Expression of the mini-gene markedly improved growth parameters of the evolved clones at sub-inhibitory concentrations of NiCl2 while being slightly detrimental in the absence of stress. Similar results have been obtained with the RNA libraries. Overall, the results demonstrate a very natural outcome of the selection experiments in which the mini-genes were expected to be either successfully integrated into bacterial genetic networks, or rejected depending upon their effect on host fitness. This described approach can be useful as a laboratory model to study the dynamics of bacterial adaptive evolution on the molecular level. It can also provide a strategy for screening expressed DNA libraries in search of novel genes with desirable properties.

Fox, George E.↗
DOE OSTI2025

Effect of heteroatom incorporation on electronic communication in metal chalcogenide nanoclusters

Metal chalcogenide nanoclusters (NC), specifically of type TM 6 E 8 (L) 6 (TM = transition metal, E = chalcogen, L = ligand) have garnered attention in recent years as promising catalysts and biosensors due to their remarkable electronic and magnetic properties, as well as their ability to undergo supramolecular assembly into 2D materials. Furthermore, the undercoordinated metal chalcogenide NCs have shown distinct surface reactivity, which is strongly dependent on the composition of the TM core. The differences in the reactivity of the undercoordinated species have been attributed to differences in ligand binding energies. Although ligand binding energies in homometallic NCs have been extensively studied, little is known about the effect of heteroatoms in the core on the strength of ligand binding in metal chalcogenide NCs. In this work, we provide new insights into this topic by examining the relative stability of [Co 6−x Fe x S 8 (PEt 3 ) 6 ] + (x = 0–6) NCs towards fragmentation using collision energy-resolved collision-induced dissociation (CID) experiments. We observe that the ligand binding energy gradually decreases until four Fe atoms are incorporated into the cluster core and then gradually increases until all the Co atoms are replaced with Fe. This experimental trend was compared with the results of density functional theory (DFT) calculations, which indicate drastic differences in the electronic communication between Co and Fe atoms in the TM core. By understanding the effect of heteroatom incorporation on ligand binding energy to the NC core, our work provides important insights into the effect of atom-by-atom substitution on the functional properties of tunable nanostructures.

Havenridge, Shana [Argonne National Laboratory (AN↗
DOE OSTI2025

Selectivity of tris complexation for Ni(II), Co(II), and Fe(II) and its effect on carbonate precipitation under alkaline conditions

Simultaneous critical element recovery and ex-situ carbon mineralization of low-grade ultramafic deposits have garnered increasing interest. Understanding the selectivity of metal complexing organic ligands for various divalent metals present in ultramafic rocks during carbonate mineralization is required to optimize this process. Here we evaluate 2-amino-2-(hydroxymethyl)-1,3-propanediol (i.e., Tris) as a model for bidentate ligands that bind divalent metals with both amine and alcohol groups in alkaline conditions (pH 8–10.5) at 25 °C and 80 °C in carbonate-buffered solutions. Protonated Tris forms a stronger complex with metal ions and is selective for trace metals with Ni(II) > Co(II) > Fe(II) during carbonate precipitation, with the rates decreasing but selectivity increasing at lower temperature and lower pH. At 25 °C, metastable amorphous hydrated carbonates form, regardless of the amount of Tris present or pH values. At 80 °C and pH 8, the Co and Fe carbonates that form are a mixture of rosasite-group minerals (Co 2 CO 3 (OH) 2 (H 2 O) and Fe 2 CO 3 (OH) 2 ) and pure carbonates (sphaerocobaltite: CoCO 3 and siderite: FeCO 3 ), with the latter more stabilized with increasing Tris concentration. In mixed metal solutions without Tris at 25 °C where Fe:Ni or Fe:Co is 2:1, Fe increases the rates of Ni or Co carbonate precipitation. However, with increasing Tris concentration the presence of Ni or Co inhibits Fe carbonate precipitation. At 80 °C without Tris, Ni or Co substitute into the iron chukanovite (Fe 2 CO 3 (OH) 2 ) lattice, increasing Ni or Co carbonate precipitation rates. Increasing Tris concentration only slightly inhibits Fe and Co precipitation, but slows Ni precipitation up to 10 times, with Fe progressively partitioning into more pure carbonate phases with distinct crystalline morphologies. These findings suggest bidentate amine-bearing ligands may be effective at Ni and Co recovery during carbon mineralization of Fe-bearing ultramafic deposits at relatively low temperatures and slightly alkaline pH.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo

Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dehydration of Methyl Lactate on Alkali Cation-Exchanged Faujasite: Effects of Metal Cation Identity and Water Pressure

Turnover rates for the catalytic dehydration of methyl lactate (ML) over ion-exchanged faujasite (FAU) catalysts depend on the identity of alkali metal cations (Na + , K + , Cs + ) and local solvation effects. Analysis of rate measurements and in situ infrared spectroscopy gives evidence that the reaction involves kinetically relevant dissociation of adsorbed methyl lactate upon alkali metal cations. This process involves concerted methyl transfer to the surface and dissociation of the alkali metal from the framework, which occurs at cationic active sites that remain predominantly unoccupied under relevant conditions (0.5–10 kPa ML, 0.5–15 kPa H 2 O, 563–583 K). Despite the mechanistic similarities, apparent activation enthalpies (ΔH app ‡ ) decrease linearly (47 kJ mol –1 from Na + to Cs + ) with ionization energy and cationic radius, and apparent activation entropies (ΔS app ‡ ) decrease 74 J mol –1 K –1 . These trends reflect electrostatic interactions that stabilize the cations to the anionic sites on the zeolite: stronger association between these charges leads to increasingly endothermic processes to displace the alkali metal to form a cationic methoxy and an intrapore metal lactate intermediate. Water physisorption measurements suggest alkali metal ions bind superstoichiometric quantities of water within FAU pores, and in situ infrared spectra suggest the concerted adsorption of ML requires reorganization of this water. Consequently, these processes introduce entropic gains that partially offset entropy losses associated with ML adsorption. Hence, turnover rates differ only by a factor of 2 among Na-, K-, and Cs-FAU at 573 K (ΔΔG app ‡ = 5 kJ mol –1 ). These findings demonstrate the interplay of alkali metal ions with zeolite active sites and intrapore water clusters for ML dehydration, indicating that these interactions can be leveraged to deliver optimal performance under different reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2015

Nanopore Device for Reversible Ion and Molecule Sensing or Migration

Disclosed are methods and devices for detection of ion migration and binding, utilizing a nanopipette adapted for use in an electrochemical sensing circuit. The nanopipette may be functionalized on its interior bore with metal chelators for binding and sensing metal ions or other specific binding molecules such as boronic acid for binding and sensing glucose. Such a functionalized nanopipette is comprised in an electrical sensor that detects when the nanopipette selectively and reversibly binds ions or small molecules. Also disclosed is a nanoreactor, comprising a nanopipette, for controlling precipitation in aqueous solutions by voltage-directed ion migration, wherein ions may be directed out of the interior bore by a repulsing charge in the bore.

Pourmand, Nader↗
DOE OSTI2025

Achieving Electrode Smoothing by Controlling the Nucleation Phase of Metal Deposition Through Polymer‐Substrate Binding

Polymer additives [like polyethylene oxide (PEO)] are widely used for smooth electrode deposition in aqueous zinc and many other battery systems. However, the precise mechanism by which they regulate morphology and suppress dendrite formation remains unclear. In this study, the knowledge gap is addressed by using in situ electrochemical atomic force microscopy to directly observe the interfacial evolution during Zn electrodeposition and polymer adsorption on Cu substrates in the presence of varying concentrations of ZnSO 4 and PEO. Contrary to previous literature assumptions, which emphasize the binding to the growing Zn crystal surfaces or Zn 2+ ions, the results demonstrate that PEO smooths Zn films by promoting nucleation of (002)-oriented Zn platelets through interactions with the Cu substrate. Density functional theory simulations support this finding by showing that PEO adsorption on Cu modifies the interfacial energy of Zn/Cu/electrolyte interfaces, favoring the stabilization of Zn (002) on the Cu substrate, as well as confines Zn electrodeposition to a narrow near-surface region. In conclusion, these findings elucidate a novel design principle for electrode smoothing, emphasizing the importance of substrate selection paired with polymer additives that exhibit an attractive interaction with the substrate but minimal interaction with growing crystals, offering a mechanistic perspective for improved battery performance.

Electrodeposition↗
DOE OSTI2025

Biotechnological solutions for critical mineral recovery from unconventional feedstocks

Secure and sustainable metal recovery from unconventional feedstocks is needed to meet the mineral demands of energy, defense, and electronic technologies. Here, we highlight the potential to leverage nature’s ability to extract and differentiate metal ions in biotechnologies that could become the next generation of mining and refining. We describe bulk and trace processes and then discuss the advances and opportunities of two key bioprocesses: microbially mediated solubilization of metal ions from solid matrices (termed ‘bioleaching’) and bio-based separation of solubilized ions via selective adsorption to proteins. Both biotechnologies have advantages such as reduced energy input for leaching low-grade feedstocks and reduced organic solvent demand for separating ions with similar physiochemical properties but require more development for industrial scale recovery from unconventional feedstocks. Innovation in biological science and engineering may bring timely solutions to key challenges toward recovering critical minerals from unconventional feedstocks.

organic↗
DOE OSTI2025

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗
DOE OSTI2025

Influence of Alkyne Precursor Structure on Carbon Nanotube Chiral Distribution: Data-Dense Analysis Across Multiple Catalyst Types

Carbon nanotubes (CNTs) are a desirable material in the field of optoelectronics and semiconductors due to electronic properties (e.g., bandgap) that are dependent upon their chirality, defined by their diameter and lattice angle. Unfortunately, industrial-scale syntheses have yet to realize growth of a single desired chirality and instead rely on postsynthetic separation techniques to refine a chiral mixture, which increases process complexity and cost. Here, we studied the influence of precursor structure on chiral distribution, using a series of terminal alkyne precursors (acetylene, methylacetylene, vinylacetylene, 1-butyne, two enantiomers of 3-butyn-2-ol and a racemic mixture thereof) to grow CNTs across five transition-metal catalysts (Fe, FeMo, and three proportions of CoMo). Multiwavelength Raman spectroscopy on 5,145 spots (5 catalysts, 7 precursors, 3 lasers, and 49 distinct substrate locations on each) determined that acetylene grew the smallest diameter CNTs, while vinylacetylene produced fewer subnanometer CNTs. Though precursor structure did not dictate a uniform chiral shift, it was shown to broaden or narrow chiral distribution, while catalyst structure played a dominant role. In conclusion, this is consistent with metal-precursor binding occurring through unsaturated bonds in the hydrocarbons via the alkyne polymerization mechanism.

Carbon nanotubes↗
DOE OSTI2025

Modular Autonomous Experimentation for Biological Applications (Full Report)

The Modular Autonomous Research System (MARS) was developed to address the pressing need for faster, more reliable, and more adaptable scientific discovery. Traditional experimentation is limited by manual labor, long cycle times, and fragmented data streams, which constrain the ability to explore complex chemical and materials design spaces. To overcome these limitations, we created an integrated, modular platform that combines laboratory robotics, diverse measurement instruments, and a central data infrastructure with artificial intelligence–driven decision-making. The system links liquid handling robots, robotic arms, and optical plate readers into a closed loop where experiments are executed automatically, data is analyzed in real time, and subsequent experimental conditions are adaptively chosen to maximize information gain. Over the course of the project, MARS was validated on two primary test cases—spectroscopic metal–ligand binding assays and peptide-directed mineralization—which highlighted the system’s ability to handle uncertainty and variability in experimental measurements. To further demonstrate modularity and extensibility, we also established additional testbeds in electrochemistry for catalyst discovery and electrolyte formulation for advanced batteries. The results show that MARS can reliably conduct autonomous campaigns with minimal human intervention, adapt to distinct scientific domains, and provide a scalable model for future self-driving laboratories. This work establishes new capabilities for modular, uncertainty-aware automation and directly supports the need for advanced, data-driven research platforms capable of accelerating discovery across a wide range of scientific and national security missions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The safety of magnetic resonance imaging contrast agents

Gadolinium-based contrast agents are increasingly used in clinical practice. While these pharmaceuticals are verified causal agents in nephrogenic systemic fibrosis, there is a growing body of literature supporting their role as causal agents in symptoms associated with gadolinium exposure after intravenous use and encephalopathy following intrathecal administration. Gadolinium-based contrast agents are multidentate organic ligands that strongly bind the metal ion to reduce the toxicity of the metal. The notion that cationic gadolinium dissociates from these chelates and causes the disease is prevalent among patients and providers. We hypothesize that non-ligand-bound (soluble) gadolinium will be exceedingly low in patients. Soluble, ionic gadolinium is not likely to be the initial step in mediating any disease. The Kidney Institute of New Mexico was the first to identify gadolinium-rich nanoparticles in skin and kidney tissues from magnetic resonance imaging contrast agents in rodents. In 2023, they found similar nanoparticles in the kidney cells of humans with normal renal function, likely from contrast agents. We suspect these nanoparticles are the mediators of chronic toxicity from magnetic resonance imaging contrast agents. This article explores associations between gadolinium contrast and adverse health outcomes supported by clinical reports and rodent models.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

The possible role of metal ions and clays in prebiotic chemistry

Eight homoionic bentonites were prepared using alkali, alkaline earth, and transition metal ions as counterions. The interaction of the clays with 5'-AMP was studied and it was found that the alkali metal-substituted clays did not remove any nucleotide from dilute solution, and that zinc-bentonite adsorbed the most (98%). In addition, study of the interaction of seven other nucleotides with zinc-bentonite showed that the purine nucleotides were more strongly absorbed than the pyrimidine nucleotides. Langmuir isotherms were obtained for these systems and the adsorption data were explained by the adsorption coefficient and the accessibility of metal for binding.

Lawless, J. G.↗
NASA NTRS1993

Determination of the structure and bond energies of NiO2 and CuO2

On the basis of extensive ab initio calculations, we estimate the metal-O2 binding energies of NiO2 and CuO2 to be 48 +/- 7 and 18 +/- 4 kcal/mol, respectively. We feel that the experimental estimate of 57 +/- 10 kcal/mol for the binding energy of NiO2 is slightly too large, while we are in complete agreement with the experimental estimate of 15 +10/-5 kcal/mol for CuO2. While the 1A1 ground state of NiO2 definitely has a side-on C(2v) structure, matrix isolation studies suggest that CuO2 has an end-on C(s) structure. Calculations at the coupled-cluster singles plus doubles level with a perturbational estimate of triple excitations, CCSD(T), produce a 2A2 state with C(2v) as a global minimum. However, the entire 2A-double prime ground-state surface is exceedingly flat, precluding a reliable determination of the gas-phase equilibrium structure.

Bauschlicher, Charles W., Jr.↗