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DOE OSTI2023

Increasing the bulk of the 1TEL–target linker and retaining the 10×His tag in a 1TEL–CMG2-vWa construct improves crystal order and diffraction limits

TELSAM-fusion crystallization has the potential to become a revolutionary tool for the facile crystallization of proteins. TELSAM fusion can increase the crystallization rate and enable crystallization at low protein concentrations, in some cases with minimal crystal contacts [Nawarathnage et al. (2022), Open Biol. 12 , 210271]. Here, requirements for the linker composition between 1TEL and a fused CMG2 vWa domain were investigated. Ala-Ala, Ala-Val, Thr-Val and Thr-Thr linkers were evaluated, comparing metrics for crystallization propensity and crystal order. The effect on crystallization of removing or retaining the purification tag was then tested. It was discovered that increasing the linker bulk and retaining the 10×His purification tag improved the diffraction resolution, likely by decreasing the number of possible vWa-domain orientations in the crystal. Additionally, it was discovered that some vWa-domain binding modes are correlated with scrambling of the 1TEL polymer orientation in crystals and an effective mitigation strategy for this pathology is presented.

1TEL↗

DOE OSTI2017

Anodic processes in the chemical and electrochemical etching of Si crystals in acid-fluoride solutions: Pore formation mechanism

The interaction of heavily doped p- and n-type Si crystals with hydrofluoric acid in the dark with and without contact with metals having greatly differing work functions (Ag and Pd) is studied. The dependences of the dissolution rates of Si crystals in HF solutions that contain oxidizing agents with different redox potentials (FeCl{sub 3}, V{sub 2}O{sub 5} and CrO{sub 3}) on the type and level of silicon doping are determined. Analysis of the experimental data suggests that valence-band holes in silicon are not directly involved in the anodic reactions of silicon oxidation and dissolution and their generation in crystals does not limit the rate of these processes. It is also shown that the character and rate of the chemical process leading to silicon dissolution in HF-containing electrolytes are determined by the interfacial potential attained at the semiconductor–electrolyte interface. The mechanism of electrochemical pore formation in silicon crystals is discussed in terms of selfconsistent cooperative reactions of nucleophilic substitution between chemisorbed fluorine anions and coordination- saturated silicon atoms in the crystal subsurface layer. A specific feature of these reactions for silicon crystals is that vacant nonbonding d{sup 2}sp{sup 3} orbitals of Si atoms, associated with sixfold degenerate states corresponding to the Δ valley of the conduction band, are involved in the formation of intermediate complexes. According to the suggested model, the pore-formation process spontaneously develops in local regions of the interface under the action of the interfacial potential in the adsorption layer and occurs as a result of the detachment of (SiF{sub 2}){sub n} polymer chains from the crystal. Just this process leads to the preferential propagation of pores along the <100> crystallographic directions. The thermodynamic aspects of pore nucleation and the effect of the potential drop across the interface, conduction type, and free-carrier concentration in the crystal on the pore size and structure are discussed. The concepts developed in the study can consistently account for experimental facts characterizing the etching of silicon crystals with various electrical parameters under various conditions providing the anodic polarization of crystals in HF-containing solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2005

Measurable characteristics of lysozyme crystal growth

The behavior of protein crystal growth is estimated from measurements performed at both the microscopic and molecular levels. In the absence of solutal flow, it was determined that a model that balances the macromolecular flux toward the crystal surface with the flux of the crystal surface well characterizes crystal growth observed using microscopic methods. Namely, it was determined that the model provides accurate estimates for the crystal-growth velocities upon evaluation of crystal-growth measurements obtained in time. Growth velocities thus determined as a function of solution supersaturation were further interpreted using established deterministic models. From analyses of crystal-growth velocities, it was found that the mode of crystal growth varies with respect to increasing solution supersaturation, possibly owing to kinetic roughening. To verify further the hypothesis of kinetic roughening, crystal growth at the molecular level was examined using atomic force microscopy (AFM). From the AFM measurements, it was found that the magnitude of surface-height fluctuations, h(x), increases with increasing solution supersaturation. In contrast, the estimated characteristic length, xi, decreases rapidly upon increasing solution supersaturation. It was conjectured that the magnitude of both h(x) and xi could possibly determine the mode of crystal growth. Although the data precede any exact theory, the non-critical divergence of h(x) and xi with respect to increasing solution supersaturation was nevertheless preliminarily established. Moreover, approximate models to account for behavior of both h(x) and xi are also presented.

Muramidase/chemistry↗

DOE OSTI2016

Effect of B on Crystallization of Li and Na aluminosilicates - 16323

The vitrification of Hanford high-level waste (HLW) requires careful balance of glass-forming additives and nuclear waste components to maximize the waste loading but prevent adverse effects such as crystallization of aluminosilicates upon cooling in canisters. Aluminosilicate crystallization removes chemically durable glass-formers from the melt, leaving behind a residual glass that is enriched in less durable components, such as alkali and boron. In our previous work, it has been shown that the composition of the starting melt has a large influence on the phase and composition of the nucleating crystals, typically nepheline (NaAlSiO{sub 4}) when wastes are simultaneously high in Na and Al. Chemical partitioning allows for additional crystallization in the residual glass. Interestingly, in HLW glass the primary phases to form are those of sodium or lithium aluminosilicates despite the presence of boron, a common additive known to reduce crystallization and lower viscosity and melting point. In this work, we seek to better understand aluminosilicate crystallization in the presence of boron. Twelve glasses were prepared along the tie lines of NaAlSiO{sub 4}-NaBSiO{sub 4} and LiAlSiO{sub 4}-LiBSiO{sub 4}. Glasses were heat-treated following a schedule that traversed the crystallization temperatures of carnegieite (NaAlSiO{sub 4}), nepheline, and eucryptite (LiAlSiO{sub 4}) as determined by thermal analysis. Samples were analyzed using X-ray diffraction (XRD), Raman spectroscopy, and differential scanning calorimetry (DSC). It was observed that Li glasses tended to crystallize at higher boron levels than Na glasses. This behavior may result from the relationship between the structure of the glass network and the structure of the resulting crystal and the relative need for atomic rearrangement prior to crystallization in the Na bearing glass. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2018

Effect of oxygen vacancies and Ag deposition on the magnetic properties of Ag/N co-doped TiO2 single-crystal films

Highlights: • Photochemical deposition method to prepare Ag-doped TiO{sub 2} samples. • TiO{sub 2} single crystal films are used for studying room temperature ferromagnetism origin. • Ag element is deposited on TiO{sub 2} single crystal films surface in the form of Ag particles. • Oxygen vacancies and Ag particles synergy influence the ferromagnetism in samples. - Abstract: We employ TiO{sub 2} single-crystal films as a substrate and use a photochemical deposition method to prepare Ag-doped and Ag/N co-doped TiO{sub 2} single-crystal films. We also investigate the optical and magnetic properties of the samples using various measurements. No diffraction peaks related to silver oxide appear in the X-ray diffraction (XRD) spectra, which implies the existence of Ag atoms in Ag-doped TiO{sub 2} single-crystal films. X-ray photoelectron spectroscopy (XPS) spectra indicate the existence of Ti{sup 4+} and Ag° in Ag/N co-doped TiO{sub 2} single-crystal films. It is found that Ag is deposited on a TiO{sub 2} single-crystal film surface in the form of Ag particles. Meanwhile, Ag particles can slightly enhance ferromagnetism in Ag-doped TiO{sub 2} single-crystal films compared with the TiO{sub 2} single-crystal film sample. Oxygen vacancies and Ag particle synergy influence ferromagnetism in Ag/N co-doped TiO{sub 2} single-crystal films.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

In Silico Prediction of Structural Properties of a Racemic Porous Organic Cage Crystal

Porous organic cage (POC) solids are porous materials made up of individual porous molecules held together by noncovalent forces. While many examples of POCs have been made in homochiral forms (i.e., crystals in which every molecule has the same chirality), crystallization of POCs that contain mixtures of chiral molecules can also yield useful properties. For example, our previous work has demonstrated that a POC crystal [cage crystal 3 (CC3)-racemic] synthesized using a racemic mixture of diaminocyclohexane has improved sorption properties and stability than a similar POC crystal synthesized with homochiral diaminocyclohexane. The main purpose of this paper is to predict the structure of CC3-racemic with atomic detail because it is challenging to fully resolve the structure of this racemic crystal experimentally since only subtle differences exist between the racemic structure and the known crystal structure of homochiral CC3. Here, we introduce an in silico prediction method that combines electronic structure calculations and atomistic calculations to predict the structure of CC3-racemic. We first enumerate types of cage molecules that can be present in this material and establish their concentrations. A key observation from these calculations is that CC3-racemic is not made up of only CC3-R and CC3-S molecules and that an additional class of heterochiral cages is also present. By studying the packing energy of cage pairs in CC3-racemic, a lattice model representation of the racemic crystal is developed and used in MC simulations to assess the structure of extended crystals. By expanding the lattice model into atomic detail, fully detailed CC3-racemic crystal models are obtained. These models provide the most thorough description available to date of the composition and cage packing of this interesting material.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Comparing crystal structures with symmetry and geometry

Abstract Measuring the similarity between two arbitrary crystal structures is a common challenge in crystallography and materials science. Although there are an infinite number of ways to mathematically relate two crystal structures, only a few are physically meaningful. Here we introduce both a geometry-based and a symmetry-adapted similarity metric to compare crystal structures. Using crystal symmetry and combinatorial optimization we describe an algorithm to arrive at the structural relationship that minimizes these similarity metrics across all possible maps between any pair of crystal structures. The approach makes it possible to (i) identify pairs of crystal structures that are identical, (ii) quantitatively measure the similarity between crystal structures, and (iii) find and rank structural transformation pathways between any pair of crystal structures. We discuss the advantages of using the symmetry-adapted cost metric over the geometric cost. Finally, we show that all known structural transformation pathways between common crystal structures are recovered with the mapping algorithm. The methodology presented in this study will be of value to efforts that seek to catalogue crystal structures, identify structural transformation pathways or prune large first-principles datasets used to parameterize on-lattice Hamiltonians.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Rotating lattice single crystal architecture on the surface of glass

Defying the requirements of translational periodicity in 3D, rotation of the lattice orientation within an otherwise single crystal provides a new form of solid. Such rotating lattice single (RLS) crystals are found, but only as spherulitic grains too small for systematic characterization or practical application. Here we report a novel approach to fabricate RLS crystal lines and 2D layers of unlimited dimensions via a recently discovered solid-to-solid conversion process using a laser to heat a glass to its crystallization temperature but keeping it below the melting temperature. The proof-of-concept including key characteristics of RLS crystals is demonstrated using the example of Sb 2 S 3 crystals within the Sb-S-I model glass system for which the rotation rate depends on the direction of laser scanning relative to the orientation of initially formed seed. Lattice rotation in this new mode of crystal growth occurs upon crystallization through a well-organized dislocation/disclination structure introduced at the glass/ crystal interface. Implications of RLS growth on biomineralization and spherulitic crystal growth are noted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Rapid assessment of crystal orientation in semi-crystalline polymer films using rotational zone annealing and impact of orientation on mechanical properties

Crystal orientation in semi-crystalline polymers tends to enhance their performance, such as increased yield strength and modulus, along the orientation direction. Zone annealing (ZA) orients the crystal lamellae through a sharp temperature gradient that effectively directs the crystal growth, but the sweep rate (V ZA ) of this gradient significantly impacts the extent of crystal orientation. Here in this work, we demonstrate rotational zone annealing (RZA) as an efficient method to elucidate the influence of V ZA on the crystal morphology of thin films in a single experiment using isotactic poly(1-butene), PB-1, as a model semi-crystalline polymer. These RZA results are confirmed using standard, serial linear ZA to tune the structure from an almost unidirectional oriented morphology to weakly oriented spherulites. The overall crystallinity is only modestly changed in comparison to isothermal crystallization (maximum of 55% from ZA vs. 48% for isothermal crystallization). However, the average grain size increases and the spherulites become anisotropic from ZA. Due to these structural changes, the Young's modulus of the oriented films, both parallel and perpendicular to the spherulite orientation direction, is significantly increased by ZA. The modulus does become anisotropic after ZA due to the directionality in the crystal structure, with more than a threefold increase in the modulus parallel to the orientation direction for the highest oriented film in comparison to the modulus from isothermal crystallization. Lastly, RZA enables rapid identification of conditions to maximize orientation of crystals in thin polymer films, which could find utility in determining conditions to improve crystallinity and performance in organic electronics.

36 MATERIALS SCIENCE↗

DOE OSTI2017

X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, in this work, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, `naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Channeling, Volume Reection and Gamma Emission Using 14GeV Electrons in Bent Silicon Crystals

High energy electrons can be deflected with very tight bending radius using a bent silicon crystal. This produces gamma radiation. As these crystals can be thin, a series of bent silicon crystals with alternating direction has the potential to produce coherent gamma radiation with reasonable energy of the driving electron beam. Such an electron crystal undulator offers the prospect for higher energy radiation at lower cost than current methods. Permanent magnetic undulators like LCLS at SLAC National Accelerator Laboratory are expensive and very large (about 100 m in case of the LCLS undulator). Silicon crystals are inexpensive and compact when compared to the large magnetic undulators. Additionally, such a high energy coherent light source could be used for probing through materials currently impenetrable by x-rays. In this work we present the experimental data and analysis of experiment T523 conducted at SLAC National Accelerator Laboratory. We collected the spectrum of gamma ray emission from 14 GeV electrons on a bent silicon crystal counting single photons. We also investigated the dynamics of electron motion in the crystal i.e. processes of channeling and volume reflection at 14 GeV, extending and building off previous work. Our single photon spectrum for the amorphous crystal orientation is consistent with bremsstrahlung radiation and the volume reflection crystal orientation shows a trend consistent with synchrotron radiation at a critical energy of 740 MeV. We observe that in these two cases the data are consistent, but we make no further claims because of statistical limitations. We also extended the known energy range of electron crystal dechanneling length and channeling efficiency to 14 GeV.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Channeling, volume reflection and gamma emission using 14GeV electrons in bent silicon crystals - Oral presentation [Slides]

36 MATERIALS SCIENCE↗

NASA NTRS1973

Study of single crystals of metal solid solutions

The growth of single crystals of relatively high melting point metals such as silver, copper, gold, and their alloys was investigated. The purpose was to develop background information necessary to support a space flight experiment and to generate ground based data for comparison. The ground based data, when compared to the data from space grown crystals, are intended to identify any effects which zero-gravity might have on the basic process of single crystal growth of these metals. The ultimate purposes of the complete investigation are to: (1) determine specific metals and alloys to be investigated; (2) grow single metal crystals in a terrestrial laboratory; (3) determine crystal characteristics, properties, and growth parameters that will be effected by zero-gravity; (4) evaluate terrestrially grown crystals; (5) grow single metal crystals in a space laboratory such as Skylab; (6) evaluate the space grown crystals; (7) compare for zero-gravity effects of crystal characteristics, properties, and parameters; and (8) make a recommendation as to production of these crystals as a routine space manufacturing proceses.

Doty, J. P.↗

NASA NTRS1986

Protein crystal growth; Proceedings of the First International Conference, Stanford University, CA, August 14-16, 1985

Papers are presented on mechanisms of nucleation and growth of protein crystals, the role of purification in the crystallization of proteins and nucleic acids, and the effect of chemical impurities in polyethylene glycol on macromolecular crystallization. Also considered are growth kinetics of tetragonal lysozyme crystals, thermodynamic and kinetic considerations for crystal growth of complex molecules from solution, protein single-crystal growth under microgravity, and growth of organic crystals in a microgravity environment. Papers are also presented on preliminary investigations of protein crystal growth using the Space Shuttle, convective diffusion in protein crystal growth, and the growth and characterization of membrane protein crystals.

Feigelson, R. S.↗

NASA NTRS1990

Crystallization of proteins by dynamic control of supersaturation

The growth of protein crystals is known to be the limiting factor in the determination of the three-dimensional structures of most proteins. It is expected that the kinetics of supersaturation, which is directly related to solvent evaporation, will affect protein crystal growth and nucleation and accordingly determine the quality, number, size, and morphology of the crystals. With a technique that controls the evaporation of solvent from a protein solution with N2(g) it is possible to determine the effect of different evaporation profiles on hen egg white lysozyme crystals. Hen egg white lysozyme was chosen as the model protein because it crystallizes easily and has solubility data available for most salt, pH, and temperature ranges. Commercially available lysozyme was further purified by a number of methods. Crystals grown with the purified lysozyme and with the unpurified lysozyme in citrate buffer were different shapes but were found to be of the same symmetry space group by precession photos. Differences were seen in the lysozyme crystals grown using different evaporation rates. At three of the four initial conditions for lysozyme crystal growth, longer evaporation times yielded better crystals. The evaporation times required to see a change in the appearance of the crystals was much longer than expected. The number of rates studied so far represent only a small fraction of the ones now available with the gas evaporation device. The technique also provides for control of both solution pH and temperature which are related to the solubilities of proteins.

Wilson, Lori June↗

NASA NTRS1995

Growth and characterization of crystals for room temperature I.R. detectors and second harmonic generation devices

One of the major objectives of this program was to modify the triglycine sulfate (TGS) crystals with suitable dopants and variants to achieve better pyroelectric properties and improved infrared detectivities (D(sup *)), and higher Curie transition temperature compared to undoped TGS crystals. Towards these objectives, many promising dopants, both inorganic and organic, were investigated in the last few years. These dopants gave significant improvement in the D(sup *) value of the infrared detectors fabricated from the grown crystals with no significant increase in the Curie temperature (49 C). The IR detectors were fabricated at EDO/Barnes Engineering Division, Shelton, CT. In the last one year many TGS crystals doped with urea were grown using the low temperature solution crystal growth facility. It is found that doping with urea, the normalized growth yield increased significantly compared to pure TGS crystals and there is an improvement in the pyroelectric and dielectric constant values of doped crystals. This gave a significant increase in the materials figure of merits. The Vicker's hardness of 10 wt percent urea doped crystals is found to be about three times higher in the (010) direction compared to undoped crystals. This report describes in detail the results of urea doped TGS crystals.

Lal, R. B.↗

NASA NTRS1994

Crystallization history of the 1984 Mauna Loa lava flow

During a 3-week eruption in 1984, Mauna Loa produced vent lavas that increased in crystallinity from less than 1 to 30%, and 27-km-long flows that increased in crystallinity as they moved downstream. We examined the crystallization history of these lavas using crystal size distribution (CSD) analysis to study the rates of crystallization, viscosity increase, and latent heating. Typical average growth and nucleation rates were 5 x 10(exp -9) cm/s and 5/cu cm/s for microphenocrysts (20- to 500-micron size crystals nucleated in the rift zone) and 5 x 10(exp -8) cm/s and 5 x 10(exp 4)/cu cm/s for microlites (1- to 20-micron size crystals nucleated in the channel). These crystallization rates are high compared with those found in other CSD studies of igneous rocks, probably due to highly nonequilibrium conditions brought on by rapid degassing in the rift zone and cooling in the lava channel. Growth and nucleation rates decreased with time at the vent and with distance downstream. The maximum downstream total crystallinity measured is 39% (25% microlites, 14% microphenocrysts) in a quenched sample 14 km from the vent. Growth and nucleation rates cannot be calculated for postemplacement samples, but they place upper limits of 53-58% on the amount of crystallization in the channel 9-20 km from the vent. Crystallization could have been mostly responsible for the 10(exp 5)-fold downstream increase in apparent viscosity, although degassing and increasing incorporation of solid lava fragments also contributed. Another effect of crystallization on the lava flow was the sizeable latent heating (0.01 J/g/s over the first half of the flow length, if the crystallinity of downstream quench samples is representative of the hot fluid core), which may have been counteracted by entrainment of cooler material. Measurements of crystallization are shown to be crucial in the study of lava flow emplacement dynamics.

Crisp, Joe↗