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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ~10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. In conclusion, the findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

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

Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria

The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

X-ray quantification of oxygen groups on diamond surfaces for quantum applications

Abstract Identifying the surface chemistry of diamond materials is increasingly important for device applications, especially quantum sensors. Oxygen-related termination species are widely used because they are naturally abundant, chemically stable, and compatible with stable nitrogen vacancy centres near the diamond surface. Diamond surfaces host a mixture of oxygen-related species, and the precise chemistry and relative coverage of different species can lead to dramatically different electronic properties, with direct consequences for near-surface quantum sensors. However, it is challenging to unambiguously identify the different groups or quantify the relative surface coverage. Here we show that a combination of x-ray absorption and photoelectron spectroscopies can be used to quantitatively identify the coverage of carbonyl functional groups on the { 100 } diamond surface. Using this method we reveal an unexpectedly high fraction of carbonyl groups ( > 9%) on a wide range of sample surfaces. Furthermore, through a combination of ab initio calculations and spectroscopic studies of engineered surfaces, we reveal unexpected complexities in the x-ray spectroscopy of oxygen terminated diamond surfaces. Of particular note, we find the binding energies of carbonyl-related groups on diamond differs significantly from other organic systems, likely resulting in previous misestimation of carbonyl fractions on diamond surfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Kinetically Controlled Linker Binding in Rare Earth-2,5-Dihydroxyterepthalic Acid Metal–Organic Frameworks and Its Predicted Effects on Acid Gas Adsorption

In the pursuit of highly stable and selective metal–organic frameworks (MOFs) for the adsorption of caustic acid gas species, an entire series of rare earth MOFs have been explored. Each of the MOFs in this series (RE-DOBDC; RE = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu; DOBDC = 2,5-dihydroxyterepthalic acid) was synthesized in the tetragonal space group I4/m. Crystallized MOF samples, specifically Eu-DOBDC, were seen to have a combination of monodentate and bidentate binding when synthesized under typical reaction conditions, resulting in a contortion of the structure. However, extended crystallization times determined that this binding is kinetically controlled and that the monodentate binding option was crystallographically eliminated by extended reaction times at higher temperatures. Furthermore, this series allows for the direct study of the effect of the metal center on the structure of the of the MOF; herein, the lanthanide metal ionic radii contraction across the periodic table results in a reduction of the MOF pore size and lattice parameters. Scanning electron microscopy–energy-dispersive spectroscopy was used to investigate the stages of crystal growth for these RE-DOBDC MOFs. All MOFs, except Er-DOBDC had a minimum of two stages of growth. These analogues were demonstrated by analysis of neutron diffraction (PND) to exhibit a cooperative rotational distortion of the secondary building unit, resulting in two crystallographically distinct linker sublattices. Computational modeling efforts were used to show distinct differences on acid gas (NO 2 and SO 2 ) binding energies for RE-DOBDC MOFs when comparing the monodentate/bidentate combined linker with the bidentate-only linker crystal structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Thermodynamics of calcium binding to heparin: Implications of solvation and water structuring for polysaccharide biofunctions

Heparan sulfates are found in all animal tissues and have essential roles in living systems. This family of biomacromolecules modulates binding to calcium ions (Ca 2+ ) in low free energy reactions that influence biochemical processes from cell signaling and anticoagulant efficacy to biomineralization. Despite their ubiquity, the thermodynamic basis for how heparans and similarly functionalized biomolecules regulate Ca 2+ interactions is not yet established. Using heparosan (Control) and heparins with different positions of sulfate groups, we quantify how SO 3 − and COO − content and SO 3 − position modulate Ca 2+ binding by isothermal titration calorimetry. The free energy of all heparin-Ca2+ interactions (ΔG rxn ) is dominated by entropic contributions due to favorable water release from polar, hydrophilic groups. Heparin with both sulfate esters (O-SO 3 − ) and sulfamides (N-SO 3 − ) has the strongest binding to Ca 2+ compared to heparosan and to heparin with only O-SO 3 − groups (~3X). By linking Ca 2+ binding thermodynamics to measurements of the interfacial energy for calcite (CaCO 3 ) crystallization onto polysaccharides, we show molecule-specific differences in nucleation rate can be explained by differences in water structuring during Ca 2+ interactions. A large entropic term (-TΔS rxn ) upon Ca 2+ –polysaccharide binding correlates with high interfacial energy to CaCO 3 nucleation. Combining our measurements with literature values indicates many Ca 2+ –polysaccharide interactions have a shared thermodynamic signature. The resulting enthalpy–entropy compensation relationship suggests these interactions are generally dominated by water restructuring involving few conformational changes, distinct from Ca 2+ –protein binding. Our findings quantify the thermodynamic origins of heparin-specific interactions with Ca 2+ and demonstrate the contributions of solvation and functional group position during biomacromolecule-mediated ion regulation.

15 GEOTHERMAL ENERGY↗
NASA NTRS1993

Analytical and experimental investigation of the feasibility of accelerated lifetime testing of materials exposed to an atomic oxygen beam

The interaction of atomic particles with surfaces is of both scientific and technological interest. Past work emphasizes the measurement of high-energy sputtering yields. Very little work utilized low-energy beams for which chemical and electronic effects can be important. Even less work has been carried out using well-defined low-energy projectiles. The use of low-energy, reactive projectiles permits one to investigate surface processes that have not been well characterized. As the energy of the projectile decreases, the collisional cascades and spikes, that are common for high-energy projectiles, become less important, and chemical and electronic effects can play a significant role. Aspects of particle-surface interactions are of concern in several areas of technology. For example, the erosion, desorption, and glow of surfaces of spacecraft in orbit are important in the arena of space technology. The materials studied under this contract are of possible use on the exterior portions of the power generation system of Space Station Freedom. Under the original designs, Space Station Freedom's power generation system would generate potential differences on the surface as high as 200 volts. Ions in the plasma that often surround orbiting vehicles would be accelerated by these potentials leading to bombardment and erosion of the exposed surfaces. The major constituent of the atmosphere, approximately 90 percent, in the low earth orbit region is atomic oxygen. Since atomic oxygen is extremely reactive with most materials, chemical effects can arise in addition to the physical sputtering caused by the acceleration of the oxygen ions. Furthermore, the incident oxygen ions can remain embedded in the exposed surfaces, altering the chemical composition of the surfaces. Since the effective binding energy of a chemically altered surface can be quite different from that of the pure substrate, the sputtering yield of a chemically altered surface is usually different also. The low-energy O+ sputtering yield measurements, reported here, will help quantify the erosion rates for materials exposed to the low-earth orbit environment. These measurements are of technological importance in another respect. In most surface analysis techniques, a surface is bombarded with ions, electrons or photons. Information concerning the structure of the surface and near-surface bulk, abundance of impurities and defects, as well as other surface properties are obtained either from the desorbed species or from the scattered projectiles. Because of their low penetration depth, low-energy ions provide an advantage over other techniques because they provide information that is more indicative of conditions on the surface rather than integrated effects arising from deeper in the bulk. A better understanding of the microscopic processes involved in these interactions is not only of basic scientific interest, but will also aid the scientific community by increasing the accuracy and usefulness of these surface analysis techniques.

Albridge, Royal↗
DOE OSTI2022

Novel Amorphous Carbons for the Adsorption of Phosphate: Part I. Elucidation of Chemical Structure of N-Metal-Doped Chars

Due to phosphate’s necessity in agriculture and its danger to the environment, the development of adsorbents for its removal has been the subject of intensive research activity. Although the introduction of nitrogen functionality to chars and modification of biochar with metals have proven to change the character of the char structure, making it more active toward nutrients, there is no study regarding the doping of biochar with metals and nitrogen simultaneously for the adsorption of phosphates. This paper is the first of two in which we report the production, characterization, and evaluation of N-metal-doped biochars from cellulose for phosphate removal from liquid effluents. In this part, we describe the production and characterization of N-Ca-, N-Fe-, and N-Mg-doped biochars. The elemental composition and surface area of each of the materials produced is reported. Elemental and surface characterization of the chars are reported with the largest N content appearing at a temperature of 800 °C (12.5 wt %) and a maximum surface area for biochar produced at 900 °C (1314 m2/g). All of the adsorbents were visualized by scanning electron microscope (SEM), confirming that although there are some crystals on the surface of the biochar produced, most of the N, Mg, and Ca are part of the polyaromatic ring structure. Transmission electron microscope (TEM) images clearly show the formation of nanoclusters with the metals in the case of N-Fe and N-Ca biochars. The N-Mg biochars show a uniform distribution of the Mg through the carbon surface. X-ray photoelectron spectroscopy (XPS) studies of the biochars produced with metals and varying nitrogen levels clearly show Mg and Ca peaks shifting their position in the presence of N, suggesting the formation of stable structures between metals and N in the carbon polyaromatic ring system. To elucidate the nature of these structures, we conducted DFT-based calculations on different configurations of the nitrogenated structures. The calculated binding energy shifts were found to closely match the XPS experimental binding energy, confirming the likelihood of these structures in biochar. Finally, based on our experimental and modeling results, we hypothesize that an important fraction of the Mg and Ca is introduced to these biochars at the edges. Another fraction of Mg and Ca is in the form of phthalocyanine-like internal structures. More experimental studies are needed to confirm the formation of these very interesting structures and their potential use as adsorbents or catalysts.

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

Trends and descriptors of heterogeneous hydroformylation activity and selectivity of RhM 3 (M = Fe, Co, Ni, Cu and Zn) catalysts

Here monometallic Rh/MCM-41 and bimetallic RhM 3 /MCM-41 (M = Fe, Co, Ni, Cu, or Zn) catalysts are synthesized and tested for vapor-phase ethylene hydroformylation reaction. Co is found to exhibit a significant promotion effect on the selectivity of hydroformylation to C 3 oxygenates, followed by Fe and Cu, with Ni and Zn showing a negative effect. DFT calculations reveal that the addition of a secondary metal can provide a new type of site, being able to selectively tune the binding energies of reaction intermediates, and thus lead to different catalytic performances.

30 DIRECT ENERGY CONVERSION↗
NASA NTRS1979

Electron Spectroscopy for Chemical Analysis (ESCA) study of atmospheric particles

The results of analyses by ESCA (Electron Spectroscopy for Chemical Analysis) on several Nuclepore filters which were exposed during air pollution studies are presented along with correlative measurements by Neutron Activation Analysis and Scanning Electron Microscopy. Samples were exposed during air pollution studies at Norfolk, Virginia and the NASA Kennedy Space Center (KSC). It was demonstrated that with the ESCA technique it was possible to identify the chemical (bonding) state of elements contained in the atmospheric particulate matter collected on Nuclepore filters. Sulfur, nitrogen, mercury, chlorine, alkali, and alkaline earth metal species were identified in the Norfolk samples. ESCA binding energy data for aluminum indicated that three chemically different types of aluminum are present in the launch and background samples from NASA-KSC.

Dillard, J. G.↗
NASA NTRS2004

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗
DOE OSTI2020

Self-interaction error overbinds water clusters but cancels in structural energy differences

Here, we gauge the importance of self-interaction errors in density functional approximations (DFAs) for the case of water clusters. To this end, we used the Fermi–Löwdin orbital self-interaction correction method (FLOSIC) to calculate the binding energy of clusters of up to eight water molecules. Three representative DFAs of the local, generalized gradient, and metageneralized gradient families [i.e., local density approximation (LDA), Perdew–Burke–Ernzerhof (PBE), and strongly constrained and appropriately normed (SCAN)] were used. We find that the overbinding of the water clusters in these approximations is not a density-driven error. We show that, while removing self-interaction error does not alter the energetic ordering of the different water isomers with respect to the uncorrected DFAs, the resulting binding energies are corrected toward accurate reference values from higher-level calculations. In particular, self-interaction–corrected SCAN not only retains the correct energetic ordering for water hexamers but also reduces the mean error in the hexamer binding energies to less than 14 meV/ H 2 O from about 42 meV/ H 2 O for SCAN. By decomposing the total binding energy into many-body components, we find that large errors in the two-body interaction in SCAN are significantly reduced by self-interaction corrections. Higher-order many-body errors are small in both SCAN and self-interaction–corrected SCAN. These findings suggest that orbital-by-orbital removal of self-interaction combined with a proper DFA can lead to improved descriptions of water complexes.

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

Constraints on Nuclear Symmetry Energy Parameters

A review is made of constraints on the nuclear symmetry energy parameters arising from nuclear binding energy measurements, theoretical chiral effective field predictions of neutron matter properties, the unitary gas conjecture, and measurements of neutron skin thicknesses and dipole polarizabilities. While most studies have been confined to the parameters 𝑆 𝑉 and L, the important roles played by, and constraints on 𝐾 sym , or, equivalently, the neutron matter incompressibility 𝐾 𝑁 , are discussed. Strong correlations among 𝑆 𝑉 ,𝐿, and 𝐾 𝑁 are found from both nuclear binding energies and neutron matter theory. However, these correlations somewhat differ in the two cases, and those from neutron matter theory have smaller uncertainties. To 68% confidence, it is found from neutron matter theory that 𝑆 𝑉 = 32.0 ± 1.1 MeV, 𝐿 = 51.9 ± 7.9 MeV and 𝐾 𝑁 = 152.2 ± 38.1 MeV. Theoretical predictions for neutron skin thickness and dipole polarizability measurements of the neutron-rich nuclei 48 Ca, 120 Sn, and 208 Pb are compared to recent experimental measurements, most notably the CREX and PREX neutron skin experiments from Jefferson Laboratory. By themselves, PREX I+II measurements of 208 Pb and CREX measurement of 48 Ca suggest 𝐿 = 121 ± 47 MeV and 𝐿 = −5 ± 40 MeV, respectively, to 68% confidence. However, we show that nuclear interactions optimally satisfying both measurements imply 𝐿 = 53 ± 13 MeV, nearly the range suggested by either nuclear mass measurements or neutron matter theory, and is also consistent with nuclear dipole polarizability measurements. This small parameter range implies 𝑅 1.4 = 11.6 ± 1.0 km and Λ 1.4 = 228$^{+148}_{−90}$, which are consistent with NICER X-ray and LIGO/Virgo gravitational wave observations of neutron stars.

neutron skins↗
NASA NTRS1992

A comparison of the coupled cluster and internally contracted averaged coupled-pair functional levels of theory for the calculation of the MCH2(+) binding energies for M = Sc to Cu

The correlation contribution to the M-C binding energy for the MCH2(+) systems can exceed 100 kcal/mol. At the self-consistent field (SCF) level, these systems can be more than 50 kcal/mol above the fragment energies. In spite of the poor zeroth-order reference, the coupled cluster single and double excitation method with a perturbational estimate of triple excitations, CCSD(T), method is shown to provide an accurate description of these systems. The maximum difference between the CCSD(T) and internally contracted averaged coupled-pair functional binding energies is 1.5 kcal/mol for CrCH2(+), with the remaining systems agreeing to within 1.0 kcal/mol.

Bauschlicher, Charles W., Jr.↗
DOE OSTI2022

Low Exciton Binding Energies and Localized Exciton–Polaron States in 2D Tin Halide Perovskites

We report aside from band gap reduction, little is understood about the effect of the tin-for-lead substitution on the fundamental optical and optoelectronic properties of metal halide perovskites (MHPs), especially when transitioning from 3D to lower dimensional structures. Herein, we take advantage of the spectro-scopic isolation of excitons in 2D MHPs to study the intrinsic differences between lead and tin MHPs. The exciton’s spectral fine structure indicates a larger polaron binding energy in tin MHPs. Additionally, the electroabsorption responses of the 2D MHPs demonstrates that tin MHPs have exciton binding energies 1.5–2× lower than that of their lead counterparts. Despite the lower binding energy, the excitons in tin MHPs are more Frenkel-like with small radii, small polarizabilities, and large dipole moments. These results are interpreted as consequences of small polaron formation and disorder-induced dipole moments. This work highlights the wide range of intrinsic differences between lead and tin MHPs as well as the complexity of excited states in these systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Quantum Sieving for Isotopic Separations of Gases Using Porous Materials─30 Years of Progress

Here, this paper reviews theoretical and experimental efforts to establish microporous materials that can be used to separate isotopologues of molecular gases such as H 2 and D 2 . Emphasis is placed on use of simplified models to highlight the quantum phenomena that make these separations possible. In equilibrium adsorption, differences in zero point energy in the adsorbed states of molecules favor binding of heaver isotopologues (e.g. D 2 relative to H 2 ). Experimental data showing this effect was reported as early as 1933, but the theoretical work of Beenakkers et al. in 1995 [Chem. Phys. Lett. 232 (1995) 379-382] spurred modern efforts to develop materials with strong so-called quantum sieving. In porous materials where the transition state for molecular diffusion is more strongly confined than the energy minima associated with equilibrium adsorption, differences in zero point energies between these two sites can lead to isotopic differences in molecular diffusivities. This effect favors diffusion of heavier species (e.g. D 2 ) relative to lighter species (e.g. H 2 ). This so-called kinetic quantum sieving has been observed experimentally in porous carbons and in porous organic cage materials. We show that quantum tunneling, which favors hopping of lighter species across energy barriers, diminishes the strength of kinetic quantum sieving but that it appears to make only a small contribution to the net molecular diffusivities in many porous materials of practical interest.

Sholl, David S. [Oak Ridge National Laboratory (OR↗
DOE OSTI2022

A study of in situ reduction of MoO 3 to MoO 2 by X-ray Photoelectron Spectroscopy

Results from X-ray Photoelectron Spectroscopy (XPS) of molybdenum oxide samples are presented to elucidate how Mo (VI) oxide evolves to Mo (IV) oxide upon heating of a MoO 3 sample. XPS data analysis techniques based on manipulation of spectra treated as vectors are shown and allow insights into intermediate phases of Mo oxide which suggest how the original oxide changes under the influence of heat but also supports an interpretation of as-received tetravalent Mo powders as multivalent materials. In particular, several new spectral components were observed and assigned to the Magnéli phase as well as MoO 3 domains that have been modified by the presence of X-rays or temperature. Finally, these assignments comprise a new method of data processing where sample modification is used to inform XPS data interpretation and differ from previous work where the linear relationship of the binding energy of molybdenum oxides has been used.

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

Assessment of DFT functionals for a minimal nitrogenase [Fe(SH) 4 H]- model employing state-of-the-art ab initio methods

We have designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S. We show that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical (QM) methods. For example, different density functional theory (DFT) methods give ΔE estimates that vary by almost 140 kJ/mol, mainly depending on the amount of exact Hartree–Fock included (0%–54%). The model is so small that it can be treated by many high-level QM methods, including coupled-cluster (CC) and multiconfigurational perturbation theory approaches. With extrapolated CC series (up to fully connected coupled-cluster calculations with singles, doubles, and triples) and semistochastic heat-bath configuration interaction methods, we obtain results that seem to be converged to full configuration interaction results within 5 kJ/mol. Our best result for ΔE is 101 kJ/mol. With this reference, we show that M06 and B3LYP-D3 give the best results among 35 DFT methods tested for this system. Brueckner doubles coupled cluster with perturbaitve triples seems to be the most accurate coupled-cluster approach with approximate triples. CCSD(T) with Kohn–Sham orbitals gives results within 4–11 kJ/mol of the extrapolated CC results, depending on the DFT method. Single-reference CC calculations seem to be reasonably accurate (giving an error of ~5 kJ/mol compared to multireference methods), even if the D1 diagnostic is quite high (0.25) for one of the two isomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗