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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

Morphology and the Strength of Intermolecular Contact in Protein Crystals

The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.

Matsuura, Yoshiki↗
DOE OSTI2024

New examples of ferroelectric nematic materials showing evidence for the antiferroelectric smectic-Z phase

Abstract We present a new ferroelectric nematic material, 4-((4′-((trans)-5-ethyloxan-2-yl)-2′,3,5,6′-tetrafluoro-[1,1′-biphenyl]-4-yl)difluoromethoxy)-2,6-difluorobenzonitrile (AUUQU-2-N) and its higher homologues, the molecular structures of which include fluorinated building blocks, an oxane ring, and a terminal cyano group, all contributing to a large molecular dipole moment of about 12.5 D. We observed that AUUQU-2-N has three distinct liquid crystal phases, two of which were found to be polar phases with a spontaneous electric polarization P s of up to 6 µC cm –2 . The highest temperature phase is a common enantiotropic nematic (N) exhibiting only field-induced polarization. The lowest-temperature, monotropic phase proved to be a new example of the ferroelectric nematic phase (N F ), evidenced by a single-peak polarization reversal current response, a giant imaginary dielectric permittivity on the order of 10 3 , and the absence of any smectic layer X-ray diffraction peaks. The ordinary nematic phase N and the ferroelectric nematic phase N F are separated by an antiferroelectric liquid crystal phase which has low permittivity and a polarization reversal current exhibiting a characteristic double-peak response. In the polarizing light microscope, this antiferroelectric phase shows characteristic zig-zag defects, evidence of a layered structure. These observations suggest that this is another example of the recently discovered smectic Z A (SmZ A ) phase, having smectic layers with the molecular director parallel to the layer planes. The diffraction peaks from the smectic layering have not been observed to date but detailed 2D X-ray studies indicate the presence of additional short-range structures including smectic C-type correlations in all three phases—N, SmZ A and N F —which may shed new light on the understanding of polar and antipolar order in these phases.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Scalable ultrafast epitaxy of large-grain and single-crystal II-VI semiconductors

A general problem for semiconductor applications is that very slow deposition on expensive single-crystal substrates yields high crystalline quality with excellent electro-optical properties, but at prohibitive costs and throughput for many applications. In contrast, rapid deposition on inexpensive substrates or nanocrystalline films yields low costs, but comparatively inferior crystallinity, carrier transport, and recombination. Here, we present methods to deposit single-crystal material at rates 2-3 orders of magnitude faster than state-of-the-art epitaxy with low-cost methods without compromising crystalline or electro-optical quality. For example, single-crystal CdTe and CdZnTe films that would take several days to grow by molecular-beam epitaxy are deposited in 8 minutes by close-spaced sublimation, yet retain the same crystalline quality measured by X-ray diffraction rocking curves. The fast deposition is coupled with effective n- and p-type in-situ doping by In, P, and As. The epitaxy can be extended to nanocrystalline substrates. For example, we recrystallize thin CdTe films on glass to deposit large grains with low defect density. The results provide new research paths for photovoltaics, detectors, infrared imaging, flexible electronics, and other applications.

14 SOLAR ENERGY↗
NASA NTRS2004

Solution-Phase Processes of Macromolecular Crystallization

We have proposed, for the tetragonal form of chicken egg lysozyme, that solution phase assembly processes are needed to form the growth units for crystal nucleation and growth. The starting point for the self-association process is the monomeric protein, and the final crystallographic symmetry is defined by the initial dimerization interactions of the monomers and subsequent n-mers formed, which in turn are a function of the crystallization conditions. It has been suggested that multimeric proteins generally incorporate the underlying multimers symmetry into the final crystallographic symmetry. We posed the question of what happens to a protein that is known to grow as an n-mer when it is placed in solution conditions where it is monomeric. The trypsin-treated, or cut, form of the protein canavalin (CCAN) has been shown to nucleate and grow crystals as a trimer from neutral to slightly acidic solutions. Under these conditions the solution is composed almost wholly of trimers. The insoluble protein can be readily dissolved by weakly basic solution, which results in a solution that is monomeric. There are three possible outcomes to an attempt at crystallization of the protein under monomeric (high pH) conditions: 1) we will obtain the same crystals as under trimer conditions, but at different protein concentrations governed by the self association equilibria; 2) we will obtain crystals having a different symmetry, based upon a monomeric growth unit; 3) we will not obtain crystals. Obtaining the first result would be indicative that the solution-phase self-association process is critical to the crystal nucleation and growth process. The second result would be less clear, as it may also reflect a pH-dependent shift in the trimer-trimer molecular interactions. The third result, particularly for experiments in the transition pH's between trimeric and monomeric CCAN, would indicate that the monomer does not crystallize, and that solution phase self association is not part of the crystal nucleation and growth path. Results are presented for crystallization experiments of CCAN over the pH 6.8 to 9.6 range.

Pusey, Marc L.↗
NASA NTRS2004

The Crystallization of Canavalin as a Function of pH and NaCl Concentration

We posed the question of what happens to a protein that is known to grow as an n-mer when it is placed in solution conditions where it is monomeric. The trypsin-treated, or cut, form of the protein canavalin (CCAN) has been shown to nucleate and grow crystals as a trimer from neutral to slightly acidic solutions. Under these conditions the solution is composed almost wholly of trimers. The crystalline protein can be readily dissolved by weakly basic solution, which has been proposed to result in a solution that is monomeric. There are three possible outcomes to an attempt at crystallization of the protein under monomeric (high pH) conditions: 1) we will obtain the same crystals as under trimer conditions, but at different protein concentrations governed by the self association equilibria; 2) we will obtain crystals having a different symmetry, based upon a monomeric growth unit; 3) we will not obtain crystals. Obtaining the first result would be indicative that the solution-phase self-association process is critical to the crystal nucleation and growth process. The second result would be less clear, as it may also reflect a pH-dependent shift in the trimer-trimer molecular interactions. The third result, particularly for experiments in the transition pH's between trimeric and monomeric CCAN, would indicate that the monomer does not crystallize, and that solution phase self association is not part of the crystal nucleation and growth path. Results are presented for crystallization experiments of CCAN over the pH 6.4 to 9.6 range. Fluorescence anisotropy, light scattering, and gel filtration experiments show that the solutions are primarily trimers, with association to form larger species occurring as a function of protein concentration.

Forsythe, Elizabeth L.↗
DOE OSTI2026

Experimental Quantification of Spin–Phonon Coupling in Molecular Qubits Using Inelastic Neutron Scattering

Electronic spin superposition states enable nanoscale sensing through their sensitivity to the local environment, yet their sensitivity to vibrational motion also limits their coherence times. In molecular spin systems, chemical tunability and atomicscale resolution are accompanied by a dense, thermally accessible phonon spectrum that introduces efficient spin relaxation pathways. Despite extensive theoretical work, there is little experimental consensus on which vibrational energies dominate spin relaxation or how molecular structure controls spin−phonon coupling (SPC). We present a fully experimental method to quantify SPC coefficients by combining temperature-dependent vibrational spectra from inelastic neutron scattering with spin relaxation rates measured by electron paramagnetic resonance. We apply this framework to two model S = 1/2 systems, copper(II) phthalocyanine (CuPc) and copper(II) octaethylporphyrin (CuOEP). Two distinct relaxation regimes emerge: below 40 K, weakly coupled lattice modes below 50 cm −1 dominate, whereas above 40 K, optical phonons above ∼185 cm −1 become thermally populated and drive relaxation with SPC coefficients nearly 3 orders of magnitude larger. Structural distortions in CuOEP that break planar symmetry soften the crystal lattice and enhance anharmonic scattering but also raise the energy of stretching modes at the molecular core where the spins reside. This redistributes vibrational energy toward the molecular periphery and out of plane, ultimately reducing SPC relative to CuPc and enabling room-temperature spin coherence in CuOEP. Although our method does not provide mode-specific SPC coefficients, it quantifies contributions from distinct spectral regions and establishes a broadly applicable, fully experimental link between crystal structure, lattice dynamics, and spin relaxation.

Lohaus, Stefan H. [California Institute of Technol↗
DOE OSTI2023

Targeting Oxide Concentration in Tantalum Oxide-Fluoride Anions

The design of both molecular and non-molecular solid materials with specific properties fundamentally relies on the controlled synthesis of crystals with desired functional groups, bonding motifs, polarity, chirality, and more. To this end, fluoride and oxide-fluoride anions have been utilized as basic building units (BBUs) in the synthesis of noncentrosymmetric racemic materials for their ability to create polar axes that facilitate the breaking of an inversion center as demonstrated in a series of compounds with [MF6]2- anions (M = Ti, Zr, Hf). Targeting an analog with a [TaOF5]2- anion, the phase space of (CuO, Ta2O5)/bpy/HF(aq)/H2O (bpy = 2,2′-bipyridine) was investigated and three new compounds with Cu-bpy cations and Ta-fluoride or Ta-oxyfluoride anions were synthesized: [Cu(bpy)2][TaF6], [Cu(bpy)2][Ta2OF10], and [Cu(bpy)F(H2O)2]2[TaF7]∙H2O with the anions [TaF6]-, [Ta2OF10]2-, and [TaF7]2-, respectively. The formation of these anions was found to be a product of both the concentration of hydrofluoric acid in solution and the ratio of metal-oxide starting materials to ligand. This work contributes to the understanding of mixed anion formation in the solid state.

Kamp, Kendall R.↗
DOE OSTI2026

Evolution of Electronic Properties of Graphene Nanoribbons with Progressive Carving: From Straight to Porous to Chevron Ribbons

Graphene nanoribbons (GNRs) are highly versatile materials due to their unique electronic, magnetic, and optical properties, which can be precisely tuned by controlling their width, edge structure, and topology. Here, we report the on-surface synthesis and characterization of a straight N = 15 armchair GNR with periodic annulene nanopores (15-pGNR). It serves as a structural link between two well-established GNRs: the pristine N = 15 armchair GNR without pores (15-AGNR) and the chevron GNR (cGNR). With the addition of the 15-pGNR reported in this study, these three GNRs form a rare experimentally accessible series of ribbons, in which the evolution of electronic properties can be tracked upon progressive carving of a basic 15-AGNR: first, by creating periodic nanopores to form 15-pGNR and then by extending the pore area and producing meandering cGNR. We have designed a molecular precursor for the 15-pGNR and grown the nanoribbons on single-crystal gold substrates by on-surface synthesis in ultra-high vacuum (UHV) conditions. The atomically precise structure of 15-pGNR was confirmed by scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM). The band gap of 15-pGNR was studied by scanning tunneling spectroscopy (STS) and dI/dV mapping, and the occupied electronic levels were investigated by angle-resolved photoemission spectroscopy (ARPES). A theoretical and experimental comparison of 15-pGNRs, 15-AGNRs, and cGNRs demonstrates that the introduction of periodic nanopores into 15-AGNR leads to a more than 2-fold increase in its band gap. In contrast, the band gaps of 15-pGNR and cGNR differ only by about 15%. Such band gap increase can be qualitatively understood to arise from two combined effects, the periodic perforation of the graphene lattice and the confinement effect induced by the GNR width.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Out-of-equilibrium dynamics of a grid-like Fe( II ) spin crossover dimer triggered by a two-photon excitation

The application of two-photon excitation (TPE) in the study of light-responsive materials holds immense potential due to its deeper penetration and reduced photodamage. Despite these benefits, TPE has been underutilised in the investigation of the photoinduced spin crossover (SCO) phenomenon. Here, we employ TPE to delve into the out-of-equilibrium dynamics of a SCO Fe II dimer of the form [Fe II (HL) 2 ] 2 (BF 4 ) 4 ·2MeCN (HL = 3,5-bis{6-(2,2'-bipyridyl)}pyrazole). Optical transient absorption (OTA) spectroscopy in solution proves that the same dynamics take place under both one-photon excitation (OPE) and TPE. The results show the emergence of the photoinduced high spin state in less than 2 ps and with a lifetime of 147 ns. Time-resolved photocrystallography (TRXRD) reveals a single molecular reorganisation within the first 500 ps following TPE. Additionally, variable temperature single crystal X-ray diffraction (VTSCXRD) and magnetic susceptibility measurements confirm that the thermal transition is silenced by the solvent. While the results of the OTA and TRXRD utilising TPE are intriguing, the high pump fluencies required to excite enough metal centres to the high spin state may impair its practical application. Nonetheless, this study sheds light on the potential of TPE for the investigation of the out-of-equilibrium dynamics of SCO complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Effect of ionic disorder on the principal shock Hugoniot

Here, the effect of ionic disorder on the principal Hugoniot is investigated using multiple scattering theory to very high pressure (Gbar). Calculations using molecular dynamics to simulate ionic disorder are compared to those with a fixed crystal lattice, for both carbon and aluminum. For the range of conditions considered here we find that ionic disorder has a relatively minor influence. It is most important at the onset of shell ionization and we find that, at higher pressures, the subtle effect of the ionic environment is overwhelmed by the larger number of ionized electrons with higher thermal energies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Sweep-tracing algorithm: in silico slip crystallography and tension-compression asymmetry in BCC metals

Abstract Direct Molecular Dynamics (MD) simulations are being increasingly employed to model dislocation-mediated crystal plasticity with atomic resolution. Thanks to the dislocation extraction algorithm (DXA), dislocation lines can be now accurately detected and positioned in space and their Burgers vector unambiguously identified in silico, while the simulation is being performed. However, DXA extracts static snapshots of dislocation configurations that by themselves present no information on dislocation motion. Referred to as a sweep-tracing algorithm (STA), here we introduce a practical computational method to observe dislocation motion and to accurately quantify its important characteristics such as preferential slip planes (slip crystallography). STA reconnects pairs of successive snapshots extracted by DXA and computes elementary slip facets thus precisely tracing the motion of dislocation segments from one snapshot to the next. As a testbed for our new method, we apply STA to the analysis of dislocation motion in large-scale MD simulations of single crystal plasticity in BCC metals. We observe that, when the crystal is subjected to uniaxial deformation along its [001] axis, dislocation slip predominantly occurs on the {112} maximum resolved shear stress plane under tension, while in compression slip is non-crystallographic (pencil) resulting in asymmetric mechanical response. The marked contrast in the observed slip crystallography is attributed to the twinning/anti-twinning asymmetry of shears in the {112} planes relatively favoring dislocation motion in the twinning sense while hindering dislocations from moving in the anti-twinning directions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

Organophosphorus hydrolase (OPH) is a metalloenzyme that can hydrolyze organophosphorus agents resulting in products that are generally of reduced toxicity. The best OPH substrate found to date is diethyl p-nitrophenyl phosphate (paraoxon). Most structural and kinetic studies assume that the binding orientation of paraoxon is identical to that of diethyl 4-methylbenzylphosphonate, which is the only substrate analog co-crystallized with OPH. In the current work, we used a combined docking and molecular dynamics (MD) approach to predict the likely binding mode of paraoxon. Then, we used the predicted binding mode to run MD simulations on the wild type (WT) OPH complexed with paraoxon, and OPH mutants complexed with paraoxon. Additionally, we identified three hot-spot residues (D253, H254, and I255) involved in the stability of the OPH active site. We then experimentally assayed single and double mutants involving these residues for paraoxon binding affinity. The binding free energy calculations and the experimental kinetics of the reactions between each OPH mutant and paraoxon show that mutated forms D253E, D253E-H254R, and D253E-I255G exhibit enhanced substrate binding affinity over WT OPH. Interestingly, our experimental results show that the substrate binding affinity of the double mutant D253E-H254R increased by 19-fold compared to WT OPH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1985

Process Research on Polycrystalline Silicon Material (PROPSM)

Results of hydrogen-passivated polycrysalline silicon solar cell research are summarized. The short-circuit current of solar cells fabricated from large-grain cast polycrystalline silicon is nearly equivalent to that of single-crystal cells, which indicates long bulk minority-carrier diffusion length. Treatments with molecular hydrogen showed no effect on large-grain cast polycrystalline silicon solar cells.

Culik, J. S.↗
NASA NTRS2004

Quartz Crystal Microbalance Operation and In Situ Calibration

Quartz crystal microbalances (QCMs) are commonly used to measure the rate of deposition of molecular species on a surface. The measurement is often used to select materials with a low outgassing rate for applications where the material has a line of sight to a contamination-sensitive surface. A quantitative, in situ calibration of the balance, or balances, using a pure material for which the enthalpy of sublimation is known, is described in this Technical Memorandum. Supporting calculations for surface dwell times of deposited materials and the effusion cell Clausing factor are presented along with examples of multiple QCM measurements of outgassing from a common source.

Albyn, K. C.↗
NASA NTRS2011

Lattice Thermal Conductivity of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2 from Atomistic Simulations

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 are candidate materials for applications in extreme environments because of their high melting point, good mechanical properties and reasonable oxidation resistance. Unlike many ceramics, these materials have high thermal conductivity which can be advantageous, for example, to reduce thermal shock. Recently, we developed Tersoff style interatomic potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current. Results at room temperature and at elevated temperatures will be reported.

Lawson, JOhn W.↗