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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Effects of Al Substitution for Fe in Na₅FeSi₄O₁₂ (5.1.8) Glasses: Structure and Crystallization

In this study, the effects of substituting Al for Fe in 5Na2O∙(Al2O3)x∙(Fe2O3)1-x∙8SiO2 glass, x=0 to 1, and Na5AlxFe1-xSi4O12 (5.1.8) crystal, were investigated using thermal analysis, Fe K-edge X-ray absorption, X-ray diffraction, Raman spectroscopy, and Electron Probe Microanalysis. In both glass and crystallized glass, nearly all the Fe was tetrahedrally coordinated Fe3+, as expected from the high concentration of Na2O. The substitution of Al for Fe in the glasses caused the glass transition temperature to increase as polymerization increased, as evidenced by Raman, likely due to both field strength differences of Al vs Fe and a small amount of Fe2+ network modifier present with Fe. After heat treatment at 700 °C for 24 hours, the glasses had crystallized, forming Na2SiO3 and NaAlSiO4 in compositions with high Al concentrations and the 5.1.8 crystal in compositions with high Fe concentrations. Through electron microprobe, it was determined that <0.04 formula unit Al incorporated into the 5.1.8 crystal, i.e. Na5Fe0.96Al0.04Si4O12. The 5.1.8 crystal only formed when Fe concentration was higher than Al in the starting glass.

Antonio, Raine (ORCID:0009000634297975)↗
NASA NTRS1985

Hibonite: Crystal Chemistry and Origin of Blue Coloration in Meteoritic Assemblages

The blue color and optical spectra of hibonite, a common constituent of refractory inclusions in carbonaceous chondrites, are discussed. Because they may be manifestations of exotic cation species stabilized in unusual coordination sites in the hibonite crystalstructure. Hibonite, ideally CaAl12O19, is conducive to atomic substitution of host Ca2+ and Al3+ ions by a variety of lanthanide and first series transition elements. The latter cations are responsible for the colors of many rock-forming minerals as a result of intraelectronic or intervalence transitions. The visible-region spectra of most oxide and silicate minerals are generally well understood. Assignments of absorption bands in meteoritic hibonite optical spectra due to uncertainties of cation valencies and complexities in the crystal structure are examined. The crystal chemistry of hibonite is reviewed, Mossbauer spectral measurements of iron-bearing hibonite and electronic transitions that may be responsible for the blue coloration of meteoritic hibonites are discussed.

Burns, R. G.↗
NASA NTRS1993

Global expression for representing cohesive-energy curves. II

Schlosser et al. (1991) showed that the R dependence of the cohesive energy of partially ionic solids may be characterized by a two-term energy relationship consisting of a Coulomb term arising from the charge transfer, delta-Z, and a scaled universal energy function, E*(a *), which accounts for the partially covalent character of the bond and for repulsion between the atomic cores for small R; a* is a scaled length. In the paper by Schlosser et al., the normalized cohesive-energy curves of NaCl-structure alkali-halide crystals were generated with this expression. In this paper we generate the cohesive-energy curves of several families of partially ionic solids with different crystal structures and differing degrees of ionicity. These include the CsCl-structure Cs halides, and the Tl and Ag halides, which have weaker ionic bonding than the alkali halides, and which have the CsCl and NaCl structures, respectively. The cohesive-energy-curve parameters are then used to generate theoretical isothermal compression curves for the Li, Na, K, Cs, and Ag halides. We find good agreement with the available experimental compression data.

Schlosser, Herbert↗
NASA NTRS1996

The Influence of Gravity on Nucleation, Growth, Stability and Structure in Crystallizing Colloidal Suspensions

Our goal is to understand the dynamics of particles within colloidal crystals. In particular, we focus on the influence of the cell walls and gravity on the particle dynamics. In this study, we will use a novel light scattering experiment, known as diffusing wave spectroscopy, to probe particle motions in turbid suspensions. This is a noninvasive experimental probe of interparticle dynamics.

Gast, Alice P.↗
NASA NTRSDate not supplied

Analysis of "Stone" Samples from C-Type Asteroid Ryugu

As a part of activities of initial analysis, we analyzed eighteen Ryugu “stone” samples of 1 ~ 8mm in size: seven stones from the 1st touch down site and eleven from the 2nd touch down site. Ryugu stones were analyzed first using X-rays, UV, visible, near-infrared, mid-infrared, and muon probes for surface reflectance spectra, internal 3D structure and element distribution, crystal structures, and bulk composition of light elements such as C, N, and O. Measurements for magnetic, thermal, and physical properties using some stones were also performed. TOF-SIMS analysis of fluid inclusions as being continued. Small particles separated from some stones were analyzed by IR-CT. Based on 3D-CT images of individual stones, objects of interests were identified, separated by pFIB cutting, and exposed by polishing on the surface of epoxy disks. FE-EPMA/FE-SEM analysis was made on ~40 polished epoxy disks for chemical composition and textural observation. FIB sections and small (~15 μm in size) fragments were separated from polished surface and analyzed by TEM, STXM,XRF, and nano-CT.

T. Nakamura↗
DOE OSTI2023

Synthesis and physical properties of a new layered ferromagnet Cr 1.21 Te 2

Single crystals of a new layered compound, Cr 1.21 Te 2 , were synthesized via a vapor transport method. The crystal structure and physical properties were characterized by single crystal and powder x-ray diffraction, temperature- and field-dependent magnetization, zero-field heat capacity, and angle-resolved photoemission spectroscopy. Cr 1.21 Te 2 , containing two Cr sites, crystalizes in a trigonal structure with a space group P-3 (No. 147). The Cr site in the interstitial layer is partially occupied. Physical property characterizations indicate that Cr 1.21 Te 2 is metallic with hole pockets at the Fermi energy and undergoes a ferromagnetic phase transition at ~ 173 K. The magnetic moments align along the c axis in the ferromagnetic state. Based on low-temperature magnetization, the spin stiffness constant, D, and spin excitation gap, Δ , were estimated according to Bloch's law to be D = 94 ± 17 meV Å 2 and Δ = 0.45 ± 0.33 meV, suggesting its possible application as a low dimensional ferromagnet.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Sub-molecular structural relaxation at a physisorbed interface with monolayer organic single-crystal semiconductors

Arranging molecules into highly symmetric, topological crystal structures has been recognized as the best approach to functionalize electronic properties in molecular crystals, where the constituent molecules have been assumed to be rigid in shape. Here, in striking contrast, we demonstrate that the molecules in a monolayer organic crystal can undergo a significant deformation in proximity to the substrate, which is reflected by an asymmetry in the electron density profile. X-ray reflectivity and X-ray absorption spectroscopies in conjunction with density-functional theory calculations reveal that the highly planarized π-core are deformed into a bent shape, while the bulk lattice parameters are maintained. The molecular shape change is found to be perfectly suppressed in a bilayer single crystal, which leads to a 40% increase in mobility in the bilayer crystal. Our finding of a unique, sub-molecular scale shape change in monolayer single crystals can offer possibilities for functionalizing electrical properties via nano-scale physisorption.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural Asymmetry and Chiral-Induced Spin Selectivity in Chiral Palladium-Halide Semiconductors

Chiral Pb-free metal-halide semiconductors (MHSs) have attracted considerable attention in the field of spintronics due to various interesting spin-related properties and chiral-induced spin selectivity (CISS) effect. Despite their excellent chemical and structural tunability, the material scope and crystal structure of Pb-free chiral MHSs exhibiting the CISS effect are still limited; chiral MHSs that have metal-halide structures of octahedra and tetrahedra are only reported. Here, we report a new class of chiral MHSs, of which palladium (Pd)-halides are formed in 1D square-pyramidal structures or 0D square-planar structures, with a general formula of ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x (MBA = methylbenzylammonium; x = 0, 0.25, 0.5, 0.75, and 1) for the first time. The crystals adopt the 1D helical chain of Pd-halide square-pyramid (for x = 0, 0.25, 0.5, and 0.75) and 0D structure of Pd-halide square-plane (for x = 1). All the Pd-halides are distorted by the interaction between the halide and the chiral organic ammonium and arranged in a noncentrosymmetric position. Circular dichroism (CD) for ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x indicates that chirality was transferred from chiral organic ammonium to Pd-halide inorganics. ((R-MBA) 2 PdBr 4 ) 1-x ((R-MBA) 2 PdCl 4 ) x (x = 0, 0.25, 0.5, and 0.75) shows a distortion index of 0.127-0.128, which is the highest value among the previously reported chiral MHSs to the best of our knowledge. We also find that (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 crystals grow along the out-of-plane direction during spin coating and have high c-axis orientation and crystallinity, and (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 (x = 0 and 0.5) crystals exhibit a CISS effect in polycrystalline bulk films. In conclusion, these results demonstrate the possibility of a new metal-halide series with square-planar structures or square-pyramidal structures for future spintronic applications.

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

First-order structural phase transition at low temperature in GaPt 5 P and its rapid enhancement with pressure

Single crystals of X Pt 5 ⁢P (X = Al, Ga, and In), belonging to the 1-5-1 family of compounds, were grown from a Pt-P solution at high temperatures, and measurements of the ambient pressure, temperature-dependent magnetization, resistivity, and x-ray diffraction were made. Additionally, the ambient-pressure Hall resistivity and temperature-dependent resistance under pressure were measured on GaPt 5 ⁢P. All three compounds have a tetragonal P4/mmm crystal structure at room temperature with metallic transport and weak diamagnetism over the 2–300 K temperature range. Surprisingly, at ambient pressure, both the transport and magnetization measurements on GaPt 5 ⁢P show a steplike feature in the 70–90 K region, suggesting a possible structural phase transition. Neither AlPt 5 ⁢P nor InPt 5 ⁢P have any signatures of a phase transition in their temperature-dependent electrical resistance and magnetization data. Both the hysteretic nature and sharpness of the features in the GaPt 5 ⁢P data suggest that the transition is first-order. Further, single-crystal x-ray diffraction measurements provided further details of the structural transition with a possibility of a crystal symmetry different from P⁢4/mmm below the transition temperature. The transition is characterized by anisotropic changes in the lattice parameters and a volume collapse with respect to the high-temperature tetragonal crystal structure. Furthermore, satellite peaks are observed at two distinct and nonequivalent wave vectors (0, 0, 0.5) and (0.5, 0.5, 0.5), and density functional theory calculations present phonon softening, especially at (0.5, 0.5, 0.5), as a possible driving mechanism. Additionally, we find that the structural transition temperature increases rapidly with increasing pressure, reaching room temperature by ~2.2 GPa, highlighting the high degree of pressure sensitivity of GaPt 5 ⁢P and fragile nature of its room-temperature structure. Even though the volume collapse and extreme pressure sensitivity suggest chemical pressure should drive a similar structural change in AlPt 5⁢ P, where both unit-cell dimensions and volume are smaller, its structure is found to be the same as that of the room-temperature GaPt 5 ⁢P. Overall, GaPt 5 ⁢P stands out as a sole member of the 1-5-1 family of compounds for which a temperature-driven structural change has been observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Zintl pnictides Yb10CdSb9 and Yb14CdSb11: New candidate thermoelectric materials

The synthesis of new materials is the lifeline of solid-state science, and it continues to offer us unique opportunities for testing various theoretical formulations and models on a practical material. Such an avenue, therefore, provides a breeding ground for technological innovations and advancements that can completely revolutionize our world. Here, we report the results of our exploratory syntheses in the Yb–Cd–Sb compositional space that lead to the identification of two new Zintl antimonides, namely, Yb10CdSb9 and Yb14CdSb11. Their crystal structures were established via single-crystal X-ray diffraction methods; the basic electronic and transport properties of the new materials were also characterized. Yb10CdSb9 crystallizes in a disordered variant of the tetragonal Ca10LiMgSb9 structure type with unit cell parameters a = 11.8473(8) Å and c = 17.1302(12) Å (space group P42/mnm). Yb14CdSb11 crystallizes in the tetragonal Ca14AlSb11 structure type with unit cell parameters: a = 16.605(3) Å and c = 12.144(7) Å (space group I41/acd). Although the structures of both compounds can be rationalized within the framework of the Zintl formalism, based on the partitioning of the valence electrons in the much disordered Yb10CdSb9 phase, the charge is indicative of a slightly electron-rich composition. Electronic structure calculations in both cases support the notion of intrinsic semiconductor behavior, as expected for a Zintl phase. The temperature dependence of the electrical resistivity of a single crystal of Yb10CdSb9 is in line with that, and the evolution of the Seebeck coefficient indicates an electron-dominated transport mechanism, and a respectable power factor of 0.71 μW/cm K2 at 460 K can be calculated for Yb10CdSb9. The electrical resistivity of Yb14CdSb11, however, evolves in a semimetallic manner, which could suggest an overdoped sample or degenerate semiconducting behavior.

Ogunbunmi, Michael O. (ORCID:0000000253409198)↗
DOE OSTI2023

Synthesis, crystal and electronic structures, linear and nonlinear optical properties, and photocurrent response of oxyhalides CeHaVIO 4 (Ha = Cl, Br; VI = Mo, W)

Four heteroanionic oxyhalides, CeClMoO 4 , CeBrMoO 4 , CeClWO 4 , and CeBrWO 4 , have been studied as multifunctional materials, which show a combination of good second harmonic generation (SHG) response and photocurrent signals. Millimeter-sized CeHaVIO 4 (Ha = Cl, Br; VI = Mo, W) crystals were grown by halide salt flux. The crystal structure of CeHaVIO 4 crystals was accurately determined by single-crystal X-ray diffraction. CeClMoO 4 , CeBrMoO 4 , and CeBrWO 4 are isostructural to each other, and crystallize in the acentric LaBrMoO 4 structure type. CeClWO 4 crystallizes in a new structure type with unit cell parameters of a = 19.6059(2) Å, b = 5.89450(10) Å, c = 7.80090(10) Å, and β = 101.4746(8)°. The bandgaps of CeHaVIO 4 fall into the range of 2.8(1)–3.1(1) eV, which are much smaller than those of isotypic LaHaVIO 4 (Ha = Cl, Br; VI = Mo, W) in the range of 3.9(1)–4.3(1) eV. The narrowing of bandgaps in CeHaVIO 4 originates from the presence of partially filled 4f orbitals of cerium atoms, which was confirmed by density functional theory (DFT) calculations. The moderate bandgaps make CeHaVIO 4 suitable for infrared nonlinear optical (IR NLO) applications. CeBrMoO 4 and CeBrWO 4 exhibit moderate SHG responses of 0.58× AGS and 0.46× AGS, respectively, and are both type-I phase-matching materials. Moderate SHG response, easy growth of crystals, high ambient stability, and type-I phase-matching behavior make CeBrMoO 4 and CeBrWO 4 great materials for IR NLO applications. CeHaVIO 4 films also exhibited good photocurrent response upon light radiation. Furthermore, this work demonstrates the rich structural chemistry of the REHaVIO 4 (RE = Y, La–Lu; Ha = Cl, Br; VI = Mo, W) family and the potential presence of more multifunctional materials.

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

Structure of puromycin-sensitive aminopeptidase and polyglutamine binding

Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Å. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

X-Ray Diffraction Analysis of NLO Crystals: Traditional Applications and More New Opportunities

Single crystal X-ray diffraction analysis is one of the more important methods for the molecular and crystal structure determination of matter and therefore it has a great importance in material science including design and engineering of different compounds with non-linear optical (NLO) properties. It was shown in our previous publications that this method provides unique information about molecular structure of NLO compounds, their crystal symmetry and crystal packing arrays, molecular conformation and geometries and many other structural and electronic characteristics that are important for understanding the nature of NLO properties of solids. A very new application of the X-ray diffraction method is related to analysis of the electron density distribution p(r) in crystals and some of its characteristics (atomic and group charges, dipole and higher multipole moments, etc.), that may be obtained directly form the diffraction measurements. In the present work, we will discuss our preliminary low temperature high-resolution X-ray data for the m-nitroaniline (mNA) single crystal (VI). This is one of the "classical" organic NLO materials and electron density distribution analysis in this simple compound has a great scientific interest.

Antipin, Mikhail Yu.↗
DOE OSTI2024

Pressure‐Dependent “Insulator–Metal–Insulator” Behavior in Sr‐Doped La 3 Ni 2 O 7

Abstract Recently, superconductivity at high temperatures is observed in bulk La 3 Ni 2 O 7−δ under high pressure. However, the attainment of high‐purity La 3 Ni 2 O 7−δ single crystals remains a formidable challenge. Here, the crystal structure and physical properties of single crystals of Sr‐doped La 3 Ni 2 O 7 synthesized at high pressure (20 GPa) and high temperature (1400 °C) are reported. Through single crystal X‐ray diffraction, it is shown that high‐pressure‐synthesized paramagnetic Sr‐doped La 3 Ni 2 O 7 crystallizes in an orthorhombic structure with Ni─O─Ni bond angles of 173.4(2)° out‐of‐plane and 175.0(2)°and 176.7(2)°in plane. The substitution of Sr alters in band filling and the ratio of Ni 2+ /Ni 3+ in Sr‐doped La 3 Ni 2 O 7 , aligning them with those of “La 3 Ni 2 O 7.05” , thereby leading to significant modifications in properties under high pressure relative to the unsubstituted parent phase. At ambient pressure, Sr‐doped La 3 Ni 2 O 7 exhibits insulating properties, and the conductivity increases as pressure goes up to 10 GPa. However, upon further increasing pressure beyond 10.7 GPa, Sr‐doped La 3 Ni 2 O 7 transits back from a metal‐like behavior to an insulator. The insulator–metal–insulator trend under high pressure dramatically differs from the behavior of the parent compound La 3 Ni 2 O 7−δ , despite their similar behavior in the low‐pressure regime. These experimental results underscore the considerable challenge in achieving superconductivity in nickelates.

36 MATERIALS SCIENCE↗