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NASA NTRS1978

Wear of single-crystal silicon carbide in contact with various metals in vacuum

Sliding friction experiments were conducted in vacuum with single crystal silicon carbide (0001) surface in contact with transition metals (tungsten, iron, rhodium, nickel, titanium, and cobalt), copper, and aluminum. The hexagon shaped cracking and fracturing of silicon carbide that occurred is believed to be due to cleavages of both the prismatic and basal planes. The silicon carbide wear debris, which was produced by brittle fracture, slides or rolls on both the metal and silicon carbide and produces grooves and indentations on these surfaces. The wear scars of aluminum and titanium, which have much stronger chemical affinity for silicon and carbon, are generally rougher than those of the other metals. Fracturing and cracking along the grain boundary of rhodium and tungsten were observed. These may be primarily due to the greater shear moduli of the metals.

Miyoshi, K.↗

NASA NTRS2002

Influence of Unweighting on Insulin Signal Transduction in Muscle

Unweighting of the juvenile soleus muscle is characterized by an increased binding capacity for insulin relative to muscle mass due to sparing of the receptors during atrophy. Although carbohydrate metabolism and protein degradation in the unweighted muscle develop increased sensitivity to insulin in vivo, protein synthesis in vivo and system A amino acid transport in vitro do not appear to develop such an enhanced response. The long-term goal is to identify the precise nature of this apparent resistance in the insulin signal transduction pathway and to consider how reduced weight-bearing may elicit this effect, by evaluating specific components of the insulin signalling pathway. Because the insulin-signalling pathway has components in common with the signal transduction pathway for insulin-like growth factor (IGF-1) and potentially other growth factors, the study could have important implications in the role of weight-bearing function on muscle growth and development. Since the insulin signalling pathway diverges following activation of insulin receptor tyrosine kinase, the immediate specific aims will be to study the receptor tyrosine kinase (IRTK) and those branches, which lead to phosphorylation of insulin receptor substrate-1 (IRS-1) and of Shc protein. To achieve these broader objectives, we will test in situ, by intramuscular injection, the responses of glucose transport, system A amino acid transport and protein synthesis to insulin analogues for which the receptor has either a weaker or much stronger binding affinity compared to insulin. Studies will include: (1) estimation of the ED(sub 50) for each analogue for these three processes; (2) the effect of duration (one to four days) of unweighting on the response of each process to all analogues tested; (3) the effect of unweighting and the analogues on IRTK activity; and (4) the comparative effects of unweighting and analogue binding on the tyrosine phosphorylation of IRTK, IRS-1, and Shc protein.

Tischler, Marc E.↗

DOE OSTI2025

Cyclic Peptides for Lanthanide Binding

Lanthanide ions are difficult to separate from one another due to their similar chemical properties. The discovery of lanthanide-binding peptides and proteins in nature has led to an increased interest in the possibility of utilizing the strong binding of peptides to lanthanide ions for their separations; as such, there has been an effort to identify or design peptides with improved lanthanide binding and selectivity toward particular lanthanide ions. Here, in this study, we designed and characterized lanthanide-binding cyclic peptides (LBCPs) with molecular dynamics simulations, electronic structure calculations, and emission spectroscopy. Luminescent decay measurements were done to determine the number of water molecules coordinated to the Eu 3+ ion in Eu-LBCP complexes and compare to the predicted number of water molecules by computation to assess the lanthanide-binding affinity of LBCPs. Measured stability constants show binding of the LBCPs to the Eu 3+ ion with stronger than micromolar affinity. We were able to identify multiple peptides that selectively bind to middle lanthanides. We describe the structural basis of the lanthanide-binding selectivity trend with strongest binding to the middle lanthanides, followed by the heavier lanthanides, and finally to the lighter ions.

ions↗

DOE OSTI2026

Rational Design of Lanmodulin Variants for Size-Based Selectivity of Individual Rare Earth Elements

Rare earth elements (REEs) are essential to modern technologies, yet their high physical and chemical similarity makes separation of individual REEs difficult and environmentally taxing. Metalloproteins offer a promising alternative for selective REE binding, as they tend to have high metal ion affinity and specificity. Lanmodulin (LanM), in particular, has arisen as a potential candidate for REE separation as it exhibits picomolar affinity for elements in the REE family. Prior work has shown that the single point mutation D9N can shift LanM’s preference away from lanthanides toward actinides, motivating efforts to tune selectivity of LanM through targeted mutagenesis. Here, we tested the hypothesis that introducing selective aspartic acid to glutamic acid substitutions in the metal coordinating EF hands of LanM would impose steric constraints that would drive LanM affinity away from larger ions, such as La3+, to smaller ions, such as Y3+. To test this hypothesis, a combination of computational and experimental approaches were employed to evaluate the signal mutations LanM D5E and LanM D3E and the double mutants LanM D1ED5E and LanM D3ED9E. Surprisingly, increasing the number of mutations within the metal center did not enhance affinity for smaller REEs, or decrease affinity for larger ions. Only the single point mutation LanM D5E weakened La3+ binding by one order of magnitude relative to LanM wild type (WT), and pairing it with a second mutation to produce LanM D1ED5E drove La3+ affinity to be stronger than that seen for LanM WT. The D3E mutation alone prevented proper expression and folding, but paring it with D9E to produce LanM D3ED9E rescued expression and yielded La3+ affinities comparable to LanM WT. All variants that expressed (LanM D5E, LanM D1ED5E, LanM D3ED9E) displayed Y3+ affinities comparable to LanM WT. Overall, these results highlight the tunability of LanM’s metal-binding environment but also expose current limitations in predicting structural responses to point mutations within a protein sequence. This work establishes a foundation that can be used for refining computational and experimental strategies to engineer metalloproteins with tailored REE selectivity.

Close, Emily [Pacific Northwest National Laborator↗

DOE OSTI2020

Oxygen Affinity: The Missing Link Enabling Prediction of Proton Conductivities in Doped Barium Zirconates

Proton-conducting oxides, specifically doped barium zirconates, have garnered much attention as electrolytes for solid-state electrochemical devices operable at intermediate temperatures (400–600 °C). In chemical terms, hydration energy, E hyd , and proton–dopant association energy, E as , are two key parameters that determine whether an oxide exhibits fast proton conduction, but to date ab initio studies have for the most part studied each parameter separately, with no clear correlation with proton conductivity identified in either case. Here, we demonstrate that the oxygen affinity, E O.dopant , defined as the energy released when an oxide ion enters an oxygen vacancy close to a dopant atom, is the missing link between these two parameters and correlates well with experimental proton conductivities in doped barium zirconates. Ab initio calculations of point defects and their complexes in Sc-, In-, Lu-, Er-, Y-, Gd-, and Eu-doped barium zirconates are used to determine E hyd , E as , E O.dopant , and the hydrogen affinity, E H.host , of each system. These four energy terms are related by E hyd = E O.dopant + 2E H.host + 2E as . Complementary impedance spectroscopy measurements reveal that the stronger the calculated oxygen affinity of a system, the higher the proton conductivity at 350 °C. Although the proton trapping site is also an important factor, the results show that oxygen affinity is an excellent predictor of proton conductivity in these materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Metallic Cu Surface Enables Reversible Na Metal Anodes and Stabilizes Anode-Free Sodium Metal Batteries

Anode free Na metal batteries are promising for future energy storage because they not only provide the highest energy densities but also eliminate the need of handling hazardous Na metals during battery manufacturing. However, they suffer from much faster degradation due to strong sensitivities even to trace levels of side reactions. In view of the crucial roles of surface chemistry on modulating electrochemical plating, this work systematically investigated a series of Cu surfaces for Na plating and stripping in the 1.0 M NaPF 6 diglyme electrolyte. Our results suggest that Na plating and stripping on pure Cu surface without Cu oxide species exhibits much better reversibility and smaller overpotentials across a wide range of current densities, especially for the first plating/stripping cycle. The high performance includes consistently higher than 99.8% Faradaic efficiencies, much more stable interfacial resistance, and negligible formation of mossy Na after 500 cycles. This improved performance can be explained based on the stronger Na-Cu affinity compared with the Na-CuO affinity. Anode-free Na metal batteries equipped with high-capacity sodium vanadium phosphate cathodes and pure Cu current collector exhibited at least 70% capacity retention for 100 cycles.

Electrochemistry↗

DOE OSTI2023

Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin

Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N 2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). Lastly, these data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Intrinsic emittance properties of an Fe-doped β-Ga 2 O 3 (010) photocathode: Ultracold electron emission at 300 K and the polaron self-energy

Measurements of the spectral emission properties of an iron-doped a β-Ga 2 O 3 (010) photocathode at 300 K reveal the presence of an ultracold contribution to the total electron beam emission with a 6 meV mean transverse energy (MTE) in the 3.5–4.4 eV photon energy range (282–354 nm). This extreme sub-thermal photoemission signal is consistent with direct emission of electrons photoexcited from the Fe dopant states into the low effective mass and positive electron affinity primary conduction band, and it is superimposed on a stronger signal with a larger MTE associated with an (optical)phonon-mediated momentum-resonant Franck–Condon (FC) emission process from a thermally populated and negative electron affinity upper conduction band. For photon energies above 4.5 eV, a transition from a long to a short transport regime is forced by an absorption depth reduction to below 100 nm and both MTE signals exhibit spectral trends consistent with phonon-mediated FC emission if the polaron formation self-energy is included in the temperature of the initial thermalized photoexcited electron distribution.

Angeloni, Louis A. [University of Illinois, Chicag↗

DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Binding of noble gas atoms by superhalogens

Because of their closed shells, noble gas (Ng) atoms (Ng = Ne, Ar, Kr, and Xe) seldom take part in chemical reactions, yet finding such mechanisms not only is of scientific interest but also has practical significance. Following a recent work by Mayer et al. [Proc. Natl. Acad. Sci. U. S. A. 116, 8167–8172 (2019)] on the room temperature binding of Ar to a superelectrophilic boron site embedded in a negative ion complex, B 12 (CN) 11 - , we have systematically studied the effect of cluster size and terminal ligands on the interaction of Ng by focusing on B 12 X 11 (Ng) (X = H, CN, and BO) and B 12 X 10 (Ng) 2 (X = CN and BO) whose stabilities are governed by the Wade–Mingos rule and on C 5 BX 5 (Ng) (X = H, F, and CN) and C 4 B 2 (CN) 4 (Ng) 2 whose stabilities are governed by the Huckel’s aromaticity rule. Our conclusion, based on density functional theory, is that both the cluster size and the terminal ligands matter—the interaction between the cluster and the Ng atoms becomes stronger with increasing cluster size and the electron affinity of the terminal ligands. Our studies also led to a counter-intuitive finding—removing multiple terminal ligands can enable electrophilic centers to bind multiple Ng atoms simultaneously without compromising their binding strength.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Threading–Unthreading Transition of Linear-Ring Polymer Blends in Extensional Flow

Adding small amounts of ring polymers to a matrix of their linear counterparts is known to increase the zero-shear-rate viscosity because of linear-ring threading. Uniaxial extensional rheology measurements show that, unlike its pure linear and ring constituents, the blend exhibits an overshoot in the stress growth coefficient. By combining these measurements with ex-situ small-angle neutron scattering and nonequilibrium molecular dynamics simulations, this overshoot is shown here to be driven by a transient threading–unthreading transition of rings embedded within the linear entanglement network. Prior to unthreading, embedded rings deform affinely with the linear entanglement network and produce a measurably stronger elongation of the linear chains in the blend compared to the pure linear melt. Thus, rings uniquely alter the mechanisms of transient elongation in linear polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2002

Modeling of Carbon Nanotube Schottky Barrier Modulation Due to Oxidation

A model is proposed for the experimentally observed lower Schottky barrier for holes in air than in vacuum at a metallic electrode - semiconducting carbon nanotube (CNT) junction. In oxidation occurring in air, the negatively charged oxygen molecules on a material usually enhance the surface dipole and provide stronger electron confinement within the bulk. Thus the CNT electron affinity will increase in air. Then the Schottky barrier for holes will have to increase according to the standard band-alignment theory, but this is against the experiment. In order to overcome this difficulty, we propose a new Schottky barrier model, assuming there is a transition region between the electrode and the CNT and an appreciable potential can drop there. The role of the oxidation is to increase this potential drop with negatively charged oxygen molecules, leading to a lower Schottky barrier for holes. This mechanism prevails for both p- and n-CNTs. The model consistently explains all the reported CNT device experiments.

Yamada, Toshishige↗

DOE OSTI2023

Solvent Acts as the Referee in a Match‐Up Between Charged and Preorganized Receptors

The prevalence of anion-cation contacts in biomolecular recognition under aqueous conditions suggests that ionic interactions should dominate the binding of anions in solvents across both high and low polarities. Investigations of this idea using titrations in low polarity solvents are impaired by interferences from ion pairing that prevent a clear picture of binding. To address this limitation and test the impact of ion-ion interactions across multiple solvents, we quantified chloride binding to a cationic receptor after accounting for ion pairing. In these studies, we created a chelate receptor using aryl-triazole CH donors and a quinolinium unit that directs its cationic methyl inside the binding pocket. In low-polarity dichloromethane, the 1 : 1 complex (log K 1 : 1 ~ 7.3) is more stable than neutral chelates, but fortuitously comparable to a preorganized macrocycle (log K 1 : 1 ~ 6.9). Polar acetonitrile and DMSO diminish stabilities of the charged receptor (log K 1 : 1 ~ 3.7 and 1.9) but surprisingly 100-fold more than the macrocycle. While both receptors lose stability by dielectric screening of electrostatic stability, the cationic receptor also pays additional costs of organization. Thus even though the charged receptor has stronger binding in apolar solvents, the uncharged receptor has more anion affinity in polar solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Formation of a Strong Heterogeneous Aluminum Lewis Acid on Silica

Abstract Al(OC(CF 3 ) 3 )(PhF) reacts with silanols present on partially dehydroxylated silica to form well‐defined ≡SiOAl(OC(CF 3 ) 3 ) 2 (O(Si≡) 2 ) ( 1 ). 27 Al NMR and DFT calculations with a small cluster model to approximate the silica surface show that the aluminum in 1 adopts a distorted trigonal bipyramidal coordination geometry by coordinating to a nearby siloxane bridge and a fluorine from the alkoxide. Fluoride ion affinity (FIA) calculations follow experimental trends and show that 1 is a stronger Lewis acid than B(C 6 F 5 ) 3 and Al(OC(CF 3 ) 3 )(PhF) but is weaker than Al(OC(CF 3 ) 3 ) and i Pr 3 Si + . Cp 2 Zr(CH 3 ) 2 reacts with 1 to form [Cp 2 ZrCH 3 ][≡SiOAl(OC(CF 3 ) 3 ) 2 (CH 3 )] ( 3 ) by methide abstraction. This reactivity pattern is similar to reactions of organometallics with the proposed strong Lewis acid sites present on Al 2 O 3 .

Samudrala, Kavyasripriya K.↗

DOE OSTI2022

Formation of a Strong Heterogeneous Aluminum Lewis Acid on Silica

Samudrala, Kavyasripriya K.↗

DOE OSTI2020

Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing

Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARSCoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. Furthermore, these results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Molecular Recognition at Mineral Interfaces: Implications for the Beneficiation of Rare Earth Ores

Ce-bastnäsite is the single largest mineral source for light rare-earth elements. In view of the growing industrial importance of rare-earth minerals, it is critical to develop more efficient methods for separating the valuable rare-earth-containing minerals from the surrounding gangue. In this work, we employ a combination of periodic density functional theory (DFT) and molecular mechanics (MM) calculations together with the de novo molecular design program HostDesigner to identify bis-phosphinate ligands that preferentially bind to the (100) Ce-bastnäsite surface rather than the (104) calcite surface. DFT calculations for a simple phosphinate ligand were employed to qualitatively understand key behaviors involved in ligand–metal, ligand–solvent, and solvent–metal interactions. These insights were then used to guide the search for flexible, rigid, and semirigid hydrocarbon linkers to identify candidate bis-phosphinate ligands with the potential to bind preferentially to Ce-bastnäsite. Among the five most promising bis-phosphinate ligands suggested by theoretical studies, three ligands were synthesized and their adsorption characteristics to bastnäsite (100) interfaces were characterized using vibrational sum-frequency (vSFG) spectroscopy, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, and isothermal titration calorimetry (ITC). The efficacy of the selective interfacial molecular binding was demonstrated by identifying a bis-phosphinate ligand capable of providing an overall higher surface coverage of alkyl groups relative to a monophosphinate ligand. The results highlight the interplay between adsorption binding strength and maximum surface coverage in determining ligand efficiency to render the mineral surface hydrophobic. DFT calculations further indicate that all tested ligands have higher affinity for Ce-bastnäsite than for calcite. Finally, this is consistent with the ITC data showing stronger adsorption enthalpy to bastnäsite than to calcite, making these ligands promising candidates for selective flotation of Ce-bastnäsite.

58 GEOSCIENCES↗