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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 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

An improved approach to the analysis of drug-protein binding by distance geometry

The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard C-C distance representations.

NASA Discipline Exobiology↗
DOE OSTI2020

Density functionals combined with van der Waals corrections for graphene adsorbed on layered materials

Standard density functionals like Perdew-Burke-Ernzerhof (PBE) or Strongly Constrained and Appropriately Normed (SCAN) need a correction to account for long-range van der Waals (vdW) interaction. The damped Zaremba-Kohn model (dZK) starts from a formula for the vdW interaction of a distant atom with a solid surface, both with known dielectric properties, damps this formula at short range, and then treats an adsorbed molecule or atomic layer as a collection of renormalized atoms. Here, we extend this model to graphene adsorbed on semiconducting layered materials [bulk graphite and hBN, and multilayer transition metal dichalcogenides (TMD)] by including the C 4 asymptotic term and multiple electrostatic image effects due to the two surfaces of the substrate slabs in the vdW calculations. The resulting SCAN-vdW-dZK and PBE-vdW-dZK give approximately the same results for the systems considered here, in agreement with available reference values. The predicted binding energies are roughly 25% lower than those from SCAN+rVV10 (revised Vydrov and Van Voorhis 2010), and ~15% lower than those from PBE+rVV10. Since SCAN+rVV10 usually overbinds, the predicted binding energies by SCAN-vdW-dZK and PBE-vdW-dZK are expected to be closer to the true values. The predicted equilibrium binding distances from SCAN-vdW-dZK and PBE-vdW-dZK are slightly larger (~ 0.1 Å) than those from SCAN+rVV10, and close to those from SCAN. The binding energy depends upon the number of substrate layers more strongly in vdW-dZK than in rVV10. The C 4 -term contributions can be 40% of the total vdW interactions, and the C 5 term contributes about 10%. The effects of images and the back surfaces of slabs can contribute about 4–10%. The vdW interaction energy power laws from the vdW-dZK model for graphene adsorbed on multilayer MoS 2 show slowly varying decay to the pairwise exponent –4 with increasing separation $\textit{D}$, very similar to those obtained from the random-phase approximation and renormalization group approaches by Ambrosetti et al. Both the PBE-vdW-dZK and SCAN-vdW-dZK give a greater increase in interlayer binding energy when the TMD substrate changes from monolayer to four-layer for the graphene/TMD adsorption systems. This is consistent with the relevant electron-energy-loss spectroscopy experimental results showing increased dielectric response from the substrate with increasing substrate layer number.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Fate of arsenic during the interactions between Mn-substituted goethite and dissolved Fe(II)

Geogenic arsenic has become a globally-distributed groundwater contaminant, liberated from the weathering of arsenic-bearing sulfide minerals and often transported to aquifer sediments adsorbed to iron oxides. Among the iron oxides, goethite (α-FeOOH) is uniquely important for the fate of arsenic because of its widespread abundance, stability, and high affinity for binding arsenic. Goethite is ubiquitous in soils and sediments and often contains substituted elements, including manganese. Structural manganese may affect the surface reactivity and redox capacity of goethite and alter the mechanisms of recrystallization catalyzed by dissolved Fe(II), potentially affecting arsenic adsorption. Here, this study examined the fate of As(V) during the interactions between dissolved Fe(II) and Mn-substituted goethites at pH 4 and 7 as well as associated changes in arsenic speciation. At pH 7, the addition of dissolved Fe(II) initially increases the adsorption of As(V) onto Mn-bearing and Mn-free goethites. For the Mn-substituted goethites, the adsorbed As(V) slowly releases to solution at longer aging times. Fe(II) addition at pH 4 slightly increases As(V) uptake by Mn-substituted goethites, with differences in total sorption correlating with the Mn content in goethite. The addition of Fe(II) releases substantial dissolved manganese but the amount solubilized is higher at pH 4 compared to 7, suggesting that the presence of adsorbed As(V) may substantially promote the Mn release at pH 4. X-ray absorption fine structure spectroscopy shows that arsenic is stabilized as As(V) in all the samples and adsorbed on goethite via a bidentate binuclear mechanism. Fitting results show that the binding distance and coordination numbers are stable in Mn-free goethite and Mn-substituted goethite samples; the effect of substituted Mn on the surface complex structure is minor. High resolution transmission electron microscopy and X-ray diffraction confirm that no secondary ferrous arsenate minerals precipitate under both pH conditions. This study improves our understanding of the Fe(II)-As(V) interactions on iron oxides, and demonstrates that the substituted cations such as manganese may quantitatively alter the geochemical fate of arsenic during the reaction of dissolved Fe(II) with Fe(III) oxides.

58 GEOSCIENCES↗
DOE OSTI2026

pH-Driven Restructuring of Hydration Layers and Cation Adsorption at the Alumina–Water Interface

Oxide−water interfaces underpin ion separations, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. However, the molecular-scale links between pHdependent surface protonation, hydration-layer structure, and counterion adsorption remain poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)−water interface in 10 mM Rb + over pH 3−12. CTR measurements reveal two distinct adsorbed water layers at ∼2.2 and ∼3.5 Å above the surface. Each water layer shifts toward the substrate at transition pHs near 6.5 and 10.6, respectively, reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb + coverage and a decrease in mean adsorption height from ∼3.5 to ∼2.7 Å with increasing pH, indicating enhanced counterion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., the potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥ 3.5. The negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb + coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid−base chemistry to ion binding distances at an oxide−water interface.

Adsorption↗
DOE OSTI2026

pH-Driven Restructuring of Hydration Layers and Cation Ad-sorption at the Alumina-Water Interface

Oxide-water interfaces underpin ion separation, catalysis, and electrochemical energy technologies, where the electrical double layer (EDL) controls adsorption, transport, and reactivity. Yet, the molecular-scale link between pH-dependent surface protonation, hydration-layer structure, and counter-ion adsorption remains poorly defined. Here, we combine in situ crystal truncation rod (CTR) and resonant anomalous X-ray reflectivity (RAXR) with streaming potential measurements and ab initio molecular dynamics (AIMD) simulations to resolve the chemical and structural evolution of the EDL at the single-crystal alumina (012)-water interface in 10 mM Rb+ over pH 3-12. CTR measurements reveal two distinct adsorbed water layers at ~2.2 and ~3.5 Å above the surface that each shift toward the substrate at transition pHs near 6.5 and 10.6, respectively, directly reflecting changes in primary hydration layer structure in response to the deprotonation of bridging and terminal aluminol groups. RAXR shows a 10-fold increase in Rb+ coverage and a decrease in mean adsorption height from ~3.5 to ~2.7 Å with increasing pH, indicating enhanced counter-ion binding accompanied by Stern layer contraction. Streaming potential measurements demonstrate that the zeta potential, i.e., potential at the hydrodynamic shear plane, is positive at pH 3 and becomes negative at pH ≥3.5. This negative charge magnitude increases with increasing pH, consistent with progressive surface deprotonation at higher pH. AIMD identifies inner- and outer-sphere Rb+ complexes whose adsorption heights and coordination geometries depend sensitively on the protonation state of surface oxygens, providing atomistic support for the experimentally inferred trends. These measurements establish two discrete, site-specific pH transitions in hydration-layer structure that track aluminol (de)protonation and quantitatively link them to a pH-driven contraction of the Stern layer (increasing Rb+ coverage and decreasing adsorption height). This provides a direct structural basis for connecting surface acid-base chemistry to ion binding distances at an oxide-water interface.

Electrical double layer (EDL), Surface protonation↗
DOE OSTI2023

Synthesis of Zwitterionic CsPbBr 3 Nanocrystals with Controlled Anisotropy using Surface‐Selective Ligand Pairs

Abstract Mechanistic studies of the morphology of lead halide perovskite nanocrystals (LHP‐NCs) are hampered by a lack of generalizable suitable synthetic strategies and ligand systems. Here, the synthesis of zwitterionic CsPbBr 3 NCs is presented with controlled anisotropy using a proposed “surface‐selective ligand pairs” strategy. Such a strategy provides a platform to systematically study the binding affinity of capping ligand pairs and the resulting LHP morphologies. By using zwitterionic ligands (ZwL) with varying structures, majority ZwL‐capped LHP NCs with controlled morphology are obtained, including anisotropic nanoplatelets and nanorods, for the first time. Combining experiments with density functional theory calculations, factors that govern the ligand binding on the different surface facets of LHP‐NCs are revealed, including the steric bulkiness of the ligand, the number of binding sites, and the charge distance between binding moieties. This study provides guidance for the further exploration of anisotropic LHP‐NCs.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Perspectives on van der Waals Density Functionals: The Case of TiS 2

The van der Waals interaction is of foundational importance for a wide variety of physical systems. In particular, van der Waals forces lie at the heart of potential device technologies that may be realized from the functional organization of layered two-dimensional (2D) nanomaterials. Furthermore, for intermediate to large-scale applications modeling, van der Waals density functionals have become the de facto choice for first-principles calculations. In particular, the vdW-DF family of functionals have provided a systematic approach to this theoretically challenging problem. While much progress has been made, there remains room for improvement in the microscopic description of vdW forces from these density functionals. In this work, we compute benchmark results for the binding energy and the electronic density response to binding in TiS2 via accurate diffusion quantum Monte Carlo calculations. We compare these benchmark data to results obtained from local, semilocal, and van der Waals functionals. In particular, we gauge the quality of the original vdW-DF/vdW-DF2 functionals, as well as updated variants such as vdW-DF-C09, vdW-DF-optB88, vdW-DF-optB86b, and vdW-DF2-B86R. We find a close relationship between the accuracy of predicted interlayer separation distances and binding energies for TiS 2 , with the vdW-DF-optB88 functional performing very well in terms of both quantities. In general, the more recently developed functionals are systematic improvements over older ones. However, when considering the response of the electron density to binding, we find that local-density approximation (LDA) and PBEsol generally outperform the vdW-DF functionals in describing the interlayer charge accumulation with vdW-DF-C09 variants performing the best overall.

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

Kinetic Control via Binding Sites within the Confined Space of Metal Metalloporphyrin‐Frameworks for Enhanced Shape‐Selectivity Catalysis

Abstract One striking feature of enzyme is its controllable ability to trap substrates via synergistic or cooperative binding in the enzymatic pocket, which renders the shape‐selectivity of product by the confined spatial environment. The success of shape‐selective catalysis relies on the ability of enzyme to tune the thermodynamics and kinetics for chemical reactions. In emulation of enzyme's ability, we showcase herein a targeting strategy with the substrate being anchored on the internal pore wall of metal‐organic frameworks (MOFs), taking full advantage of the sterically kinetic control to achieve shape‐selectivity for the reactions. For this purpose, a series of binding site‐accessible metal metalloporphyrin‐frameworks (MMPFs) have been investigated to shed light on the nature of enzyme‐mimic catalysis. They exhibit a different density of binding sites that are well arranged into the nanospace with corresponding distances of opposite binding sites. Such a structural specificity results in a facile switch in selectivity from an exclusive formation of the thermodynamically stable product to the kinetic product. Thus, the proposed targeting strategy, based on the combination of porous materials and binding events, paves a new way to develop highly efficient heterogeneous catalysts for shifting selectivity.

Zhang, Weijie↗
DOE OSTI2023

Kinetic Control via Binding Sites within the Confined Space of Metal Metalloporphyrin-Frameworks for Enhanced Shape-Selectivity Catalysis

One striking feature of enzyme is its controllable ability to trap substrates via synergistic or cooperative binding in the enzymatic pocket, which renders the shape-selectivity of product by the confined spatial environment. The success of shape-selective catalysis relies on the ability of enzyme to tune the thermodynamics and kinetics for chemical reactions. In emulation of enzyme's ability, we showcase herein a targeting strategy with the substrate being anchored on the internal pore wall of metal-organic frameworks (MOFs), taking full advantage of the sterically kinetic control to achieve shape-selectivity for the reactions. For this purpose, a series of binding site-accessible metal metalloporphyrin-frameworks (MMPFs) have been investigated to shed light on the nature of enzyme-mimic catalysis. They exhibit a different density of binding sites that are well arranged into the nanospace with corresponding distances of opposite binding sites. Furthermore, such a structural specificity results in a facile switch in selectivity from an exclusive formation of the thermodynamically stable product to the kinetic product. Thus, the proposed targeting strategy, based on the combination of porous materials and binding events, paves a new way to develop highly efficient heterogeneous catalysts for shifting selectivity.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation

Ligand unbinding is mediated by its free energy change, which has intertwined contributions from both energy and entropy. It is important, but not easy, to quantify their individual contributions to the free energy profile. We model hydrophobic ligand unbinding for two systems, a methane particle and a C 60 fullerene, both unbinding from hydrophobic pockets in all-atom water. Using a modified deep learning framework, we learn a thermodynamically optimized reaction coordinate to describe the hydrophobic ligand dissociation for both systems. Interpretation of these reaction coordinates reveals the roles of entropic and enthalpic forces as the ligand and pocket sizes change. In both cases, we observe that the free-energy barrier to unbinding is dominated by entropy considerations. Furthermore, the process of methane unbinding is driven by methane solvation, while fullerene unbinding is driven first by pocket wetting and then fullerene wetting. For both solutes, the direct importance of the distance from the binding pocket to the learned reaction coordinate is present, but low. Furthermore, our framework and subsequent feature important analysis thus give useful thermodynamic insight into hydrophobic ligand dissociation problems that are otherwise difficult to glean.

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

Nature's Strongest Force

The strongest force in the universe is called, aptly, the strong force. We never get to witness its fearsome power because it works only across subatomic distances, where it binds quarks together inside protons and neutrons and joins those nucleons into atomic nuclei. Of the four basic forces of nature, the strong force is by far the most potent—it’s 100 trillion trillion trillion times stronger than the force of gravity. Additionally, it’s also the most mysterious.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Effect of Ionic Core on the Properties of Non-Isothermal Plasmas

This study investigates the effects of ionic cores on non-isothermal plasmas using a novel ion-ion interaction potential that incorporates screening effects from both ion cores and exchange-correlation interactions. Our findings indicate that with increasing distance, the effective potential approaches a Yukawa-like screening potential, while at shorter distances, strong electron binding weakens screening. The different values of the cutoff radius ' cut and core edge steepness α significantly influence the potential behavior and radial distribution functions (RDFs). Higher coupling parameters (Γ i ) strengthen the electron-ion interactions, leading to deeper potential wells and more pronounced non-ideality corrections. Increasing Θ decreases the absolute values of non-ideality corrections, indicating fewer interactions in the system. A larger cutoff radius r cut due to weaker screening effects. As Γ i at a fixed parameter also reduces corrections increases, non-ideality corrections grow, reflecting stronger coupling. The results show the importance of taking into account the ion core effects in dense non-isothermal plasma research.

dense plasmas↗
NASA NTRS1978

Effective core potentials for the cadmium and mercury atoms

Ab initio effective core potentials have been obtained for the cadmium and mercury atoms by the methods of Kahn et al. (1976). Both two and twelve valence electron representations of Cd and Hg were tested for various atom state-configurations by comparison with all-electron calculations. The generated potentials were used to obtain the equilibrium bond distances and molecular binding energies for the dichloride and dimethyl compounds of both atoms from single and optimum-double configuration self-consistent field calculations.

Basch, H.↗
DOE OSTI2026

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗
DOE OSTI2021

van der Waals corrected density functionals for cylindrical surfaces: Ammonia and nitrogen dioxide adsorbed on a single-walled carbon nanotube

In this work, we extend the damped Zaremba-Kohn model (dZK) for long-range dispersion interaction between a molecule and a planar surface to molecules adsorbed on a curved cylindrical surface, and employ this extended model as an additive correction to the semilocal density functionals PBE (Perdew-Burke-Ernzerhof) and SCAN (strongly constrained and appropriately normed). The resulting PBE+vdW (van der Waals)-dZK and SCAN+vdW-dZK are applied to two systems, NH3 and NO2 molecules adsorbed on a single-wall carbon nanotube (CNT), for calculations of binding energies and equilibrium distances. For comparison, the results from vdW nonlocal functionals, such as SCAN+rVV10 and PBE+rVV10, are also presented. The binding energies from PBE+rVV10 (Vydrov and Van Voorhis), SCAN+rVV10, PBE+vdW-dZK, and SCAN+vdW-dZK are about 70–115 meV for the system of CNT + NH 3 and 300–500 meV for the system of CNT + NO 2 . The results from PBE+vdW-dZK and SCAN+vdW-dZK are closer to each other than those from PBE+rVV10 and SCAN+rVV10 are. The relatively closer results from PBE+vdW-dZK and SCAN+vdW-dZK indicate the consistency of our developed vdW–dZK model for cylindrical surfaces. All methods, including PBE, SCAN, PBE+rVV10, SCAN+rVV10, PBE+vdW-dZK, and SCAN+vdW-dZK, give approximately the same binding energy differences between two adsorption configurations (types I and II) for the two systems. This implies that the two adsorption sites have approximately the same adsorption stability. The exponent of the vdW interaction power law from our vdW-dZK model for the two systems is about 0 at short distance, largely due to the damping factor, and tends slowly to –4 to –4.5 at distances D about 20–50 Å. At even larger distances, the vdW power-law exponent approaches –5. This feature is very similar to the one calculated with random-phase approximation and renormalization group approaches, supporting the applicability of our methods. Our developed vdW-dZK method provides a highly efficient and reliable method for large systems with cylindrical surfaces, such as vdW interactions with nanotubes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1981

Universal binding energy relations in metallic adhesion

Scaling relations which map metallic adhesive binding energy onto a single universal binding energy curve are discussed in relation to adhesion, friction, and wear in metals. The scaling involved normalizing the energy to the maximum binding energy and normalizing distances by a suitable combination of Thomas-Fermi screening lengths. The universal curve was found to be accurately represented by E*(A*)= -(1+beta A) exp (-Beta A*) where E* is the normalized binding energy, A* is the normalized separation, and beta is the normalized decay constant. The calculated cohesive energies of potassium, barium, copper, molybdenum, and samarium were also found to scale by similar relations, suggesting that the universal relation may be more general than for the simple free electron metals.

Ferrante, J.↗
DOE OSTI2025

Understanding the Existence of a Na 2 Dimer in a High-Spin State

The recent observation of a high-spin Na 2 dimer formed on the surface of liquid helium nanodroplets raises some fundamental questions, as the ground state of Na 2 is known to have zero spin. Is it protected against spontaneous dissociation? What is its binding energy and interatomic distance? Is it stable at a higher temperature? Using calculations based on density functional theory (with and without long-range interaction) and coupled cluster methods, CCSD(T), we show that the bonding in the high-spin Na 2 dimer is governed by van der Waals interaction with binding energy (bond length) varying between −0.030 eV (5.108 Å) and −0.192 eV (4.231 Å), depending on the computational method used. Thus, the experimental method used by Kresin and coworkers can be very useful to study larger metastable high-spin clusters such as Li 4 which was predicted in 1985 to have a tetrahedral structure carrying a magnetic moment of 2 μ B , while its ground state is planar and nonmagnetic.

Basis sets↗