An Atomic View of Cation Diffusion Pathways from Single‐Crystal Topochemical Transformations
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Joseph V. Handy↗
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Direct Visualization of Nucleus Structure and Nucleation Pathways in Apoferritin Crystallization
No abstract available
You, S.-T.↗
Structures, Dynamics and Control Pathways of Protein Crystal Nucleation
No abstract available
Vekilov, Peter G.↗
An Atomic View of Cation Diffusion Pathways from Single‐Crystal Topochemical Transformations
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Joseph V. Handy↗
A Proposed Pathway for the Nucleation and Crystal Growth of the Tetragonal Form of Lysozyme
A number of factors, the shape and charge distribution anisotropy, multiple components in the solution (buffer + counter ion, precipitant, protein, and water), conformational flexibility, and large numbers of intermolecular contacts, all serve as complicating variables in understanding the nucleation and growth mechanism for macromolecules. Intermolecular contacts include hydrogen bonds, van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and give specificity while the others are weaker, more prevalent, and more promiscuous, i.e., can lead to a range of possible molecular interactions. We propose that for tetragonal lysozyme, and by extension many other monomeric proteins, there is a solution-phase assembly process to form 4(sub 3) helix structures that are the basic unit for nucleation. The formation of these structures is continuous and concentration dependent. They subsequently also servc as growth units, with that process then being a recapitulation of the nucleation process. The advantages of solution phase assembly are the immediate burying of the strongest interactions, removing them from subsequent participation in the nucleation and growth process, and the introduction of symmetry into the system, which also assists in the assembly process.
Pusey, Marc L.↗
Fine-grained Goethite as a Precursor for Martian Gray Hematite
Several isolated deposits of gray, crystalline hematite on Mars were discovered using data returned from the Thermal Emission Spectrometer (TES) instrument aboard the Mars Global Surveyor spacecraft. Christensen et al. provided five testable hypotheses regarding the formation of crystalline hematite on Mars: 1) low-temperature precipitation of Fe oxides/hydroxides from standing, oxygenated, Fe-rich water, followed by subsequent alteration to gray hematite, 2) low-temperature leaching of iron-bearing silicates and other materials leaving a Fe-rich residue laterite-style weathering) which is subsequently altered to gray hematite, 3) direct precipitation of gray hematite from Fe-rich circulating fluids of hydrothermal or other origin, 4) formation of gray hematitic surface coatings during weathering, and 5) thermal oxidation of magnetite-rich lavas. Since this initial work, several authors have examined the hematite deposits to determine their formation mechanism. Lane et al. cited the absence of a 390/ cm absorption in the martian hematite spectrum as evidence for platy hematite grains. Their model for the formation of the deposits includes deposition of any of a variety of iron oxides or oxyhydroxides by aqueous or hydrothermal fluids, burial and metamorphosis to gray platy hematite grains, and exhumation in recent times. Based on a detailed geomorphic examination of the Sinus Meridiani region, Hynek et al. conclude that the most likely method of hematite formation was either emplacement by a hydrothermal fluid or oxidation of a magnetite-rich pyroclastic deposit. Similarly, Arvidson et al., favor a model involving the alteration of pyroclastic deposits by aqueous or hydrothermal fluids. Finally, based on geochemical modeling and an examination of Aram Chaos, Catling and Moore favor emplacement by hydrothermal fluids with a minimum temperature of 100 C. Comparison of the average martian hematite spectrum measured by TES to hematite emissivity spectra for a variety of naturally occurring hematites shows small but potentially important differences. In particular, band shapes, positions and relative band emissivities of hematite spectra vary over the range of samples. These differences imply that the natural variability of thermal infrared hematite spectra has not been fully characterized, especially with respect to the reaction pathway and crystal structure.
T D Glotch↗
Nucleation of Protein Crystals: Structures, Dynamics and Control Pathways
No abstract available
Vekilov, Peter G.↗
Reverse Micelle Based Synthesis of Microporous Materials in Microgravity
Formation of zincophosphates from zinc and phosphate containing reverse micelles (water droplets in hexane) has been examined. The frameworks formed resemble that made by conventional hydrothermal synthesis. Dynamics of crystal growth are however quite different, and form the main focus of this study. In particular, the formation of zincophosphate with the sodalite framework was examined in detail. The intramicellar pH was found to have a strong influence on crystal growth. Crystals with a cubic morphology were formed directly from the micelles, without an apparent intermediate amorphous phase over a period of four days by a layer-bylayer growth at the intramicellar pH of 7.6. At a pH of 6.8, an amorphous precipitate rapidly sediments in hours. Sodalite was eventually formed from this settled phase via surface diffusion and reconstruction within four days. With a rotating cell, it was possible to minimize sedimentation and crystals were found to grow epitaxially from the spherical, amorphous particles. Intermediate pH's of 7.2 led to formation of aggregated sodalite crystals prior to settling, again without any indication of an intermediate amorphous phase. These diverse pathways were possible due to changes in intramicellar supersaturation conditions by minor changes in pH. In contrast, conventional syntheses in this pH range all proceeded by similar crystallization pathways through an amorphous gel. This study establishes that synthesis of microporous frameworks is not only possible in reverse micellar systems, but they also allow examination of possible crystallization pathways.
Dutta, Prabir K.↗
Preliminary Work in Obtaining Site-Directed Mutants of Hen Egg White Lysozyme
Protein crystal growth studies are recognized as a critical endeavor in the field of molecular biotechnology. The scientific applications of this field include the understanding of how enzymes function and the accumulation of accurate information of atomic structures, a key factor in the process of rational drug design. NASA has committed substantial investment and resources to the field of protein crystal growth and has conducted many microgravity protein crystal growth experiments aboard shuttle flights. Crystals grown in space tend to be larger, denser and have a more perfect habit and geometry. These improved properties gained in the microgravity environment of space result largely from the reduction of solutal convection, and the elimination of sedimentation at the growing crystal surface. Shuttle experiments have yielded many large, high quality crystals that are suitable for high resolution X-ray diffraction analysis. Examples of biologically important macromolecules which have been successfully crystallized during shuttle missions include: lysozyme, isocitrate lyase, gamma-interferon, insulin, human serum albumin and canavalin. Numerous other examples are also available. In addition to obtaining high quality crystals, investigators are also interested in learning the mechanisms by which the growth events take place. Crystallization experiments indicate that for the enzyme HEWL, measured growth rates do not follow mathematical models for 2D nucleation and dislocation-led growth of tetragonal protein crystals. As has been suggested by the laboratory of Marc L. Pusey, a possible explanation for the disagreement between observation and data is that HEWL tetraconal crystals form by aggregated units of lysozyme in supersaturated solutions. Surface measurement data was shown to fit very well with a model using an octamer unit cell as the growth unit. According to this model, the aggregation pathway and subsequent crystal growth is described by: monomer < ------ > dimer < ------- > tetramer < ------ > octamer < ------ > higher order. It is believed that multimer aggregation of lysozyme occurs by interaction at specific binding sites on the surface of the protein crystals. If the presence of discrete binding sites and the aggregation hypothesis is true, then it follows that the alteration of the binding site(s) should have significant effect on the measurements obtained during growth experiments. Site-directed mutagenesis allows the specific alteration of proteins by replacement, deletion or addition of specific amino acid residues. This report outlines the approach for this strategy and the progress made thus far toward that end.
Holmes, Leonard D.↗
Nucleation of Protein Crystals: Critical Nuclei, Phase Behavior, and Control Pathways
No abstract available
Galkin, O.↗
Mechanical twinning of monazite expels radiogenic Pb
Mechanical twins form by the simple shear of the crystal lattice during deformation In order to test the potential of narrow twins in monazite to record the timing of their formation, a ~1,700 Ma monazite grain deformed at ~980 Ma was investigated by electron backscattered diffraction (EBSD), transmission electron microscopy (TEM) and atom probe tomography (APT). APT 208Pb/232Th ages indicate that the twin was entirely reset by radiogenic Pb-loss during its formation at conditions far below the monazite closure temperature. The results are consistent with a model where Pb is liberated during rupture of REE-O bonds in the large REEO9 polyhedra during twinning. Liberated Pb is likely to migrate along fast diffusion pathways such as crystal defects. The combination of a quantitative microstructural investigation and nanogeochronology provides a new approach for understanding the history of accessory phases.
monazite↗
Preparation and Analysis of RNA Crystals
The crystallization of RiboNucleic Acids (RNA) was studied from the standpoint of mechanisms of crystal growth in three tasks: (1) preparation of high-quality crystals of oligonuclotides for X-ray diffraction, (2) finding pathways to the growth of high-quality crystals for X-ray diffraction and (3) investigation of mechanisms of action of inertial acceleration on crystal growth. In these tasks: (1) RNA crystals were prepared and studied by X-ray diffraction; (2) a pathway to high-quality crystals was discovered and characterized; a combination of kinetic and equilibrium factors could be optimized as described below; and (3) an interplay between purity and gravity was found in a combination of space and ground experiments with nucleic acids and proteins. Most significantly, the rate of concentration of precipitant and RNA can be controlled by membrane-based methods of water removal or by diffusion of multivalent cations across an interface stabilized by a membrane. Oligonucleotide solutions are electrokinetically stabilized colloids, and crystals can form by the controlled addition of multivalent cations.
Todd, Paul↗
Aerosol–Ice Formation Closure: A Southern Great Plains Field Campaign
Prediction of ice formation in clouds presents one of the grand challenges in the atmospheric sciences. Immersion freezing initiated by ice-nucleating particles (INPs) is the dominant pathway of primary ice crystal formation in mixed-phase clouds, where supercooled water droplets and ice crystals coexist, with important implications for the hydrological cycle and climate. However, derivation of INP number concentrations from an ambient aerosol population in cloud-resolving and climate models remains highly uncertain. We conducted an aerosol-ice formation closure pilot study using a field-observational approach to evaluate the predictive capability of immersion freezing INPs. The closure study relies on co-located measurements of the ambient size-resolved and single-particle composition and INP number concentrations. The acquired particle data serve as input in several immersion freezing parameterizations, that are employed in cloud-resolving and climate models, for prediction of INP number concentrations. We discuss in detail one closure case study in which a front passed through the measurement site, resulting in a change of ambient particle and INP populations. We achieved closure in some circumstances within uncertainties, but we emphasize the need for freezing parameterization of potentially missing INP types and evaluation of the choice of parameterization to be employed. Overall, this closure pilot study aims to assess the level of parameter details and measurement strategies needed to achieve aerosol-ice formation closure. The closure approach is designed to accurately guide immersion freezing schemes in models, and ultimately identify the leading causes for climate model bias in INP predictions.
ice formation↗
Crystalline Silicates in Comets: Modeling Irregularly-Shaped Forsterite Crystals and Its Implications on Condensation Conditions
Crystalline silicates in comets are a product of the condensation in the hot inner regions (T > or approx. equals 1400 K [1]) of our proto-planetary disk or annealing at somewhat lower temperatures (T > or approx. equals 1000-1200 K) [2, 3, 4] in shocks coupled with disk evolutionary processes that include radial transport of crystals from their formation locations out to the cold outer regions where comet nuclei formed. The grain shape of forsterite (crystals) could be indicative of their formation pathways at high temperatures through vapor-solid condensation or at lower temperatures through vapor-liquid-solid formation and growth [5, 6, 7]. Experiments demonstrate that crystals that formed from a rapidly cooled highly supersaturated silicate vapor are characterized by bulky, platy, columnar/needle and droplet shapes for values of temperature and supersaturation, T and sigma, of 1000-1450 C and < 97, 700-1000 C and 97-161, 580-820 C and 131-230, and <500 C and > 230, respectively [7]. The experimental columnar/needle shapes, which form by vapor-liquid-solid at lower temperatures (<820 C), are extended stacks of plates, where the extension is not correlated with an axial direction: columnar/needles may be extended in the c-axis or a-axis direction, can change directions, and/or are off-kilter or a bit askew extending in a combination of the a- and c-axis direction.
Wooden, Diane H.↗
Estimation of the initial equilibrium constants in the formation of tetragonal lysozyme nuclei
Results are presented from a study of the equilibria, kinetic rates, and the aggregation pathway which leads from a lysozyme monomer crystal to a tetragonal crystal, using dialyzed and recrystallized commercial hen eggwhite lysozyme. Relative light scattering intensity measurements were used to estimate the initial equilibrium constants for undersaturated lysozyme solutions in the tetragonal regime. The K1 value was estimated to be (1-3) x 10 exp 4 L/mol. Estimates of subsequent equilibrium constants depend on the crystal aggregation model chosen or determined. Experimental data suggest that tetragonal lysozyme crystal grows by addition of aggregates preformed in the bulk solution, rather than by monomer addition.
Pusey, Marc L.↗
Femtosecond resolution of soft mode dynamics in structural phase transitions
The microscopic pathway along which ions or molecules in a crystal move during structural phase transition can often be described in terms of a collective vibrational mode of the lattice. In many cases, this mode, called a 'soft' phonon mode because of its characteristically low frequency near the phase transition temperature, is difficult to characterize through conventional frequency-domain spectroscopies such as light or neutron scattering. A femtosecond time-domain analog of light-scattering spectroscopy called impulsive stimulated Raman scattering (ISRS) has been used to examine the soft modes of two perovskite ferroelectric crystals. The low-frequency lattice dynamics of KNbO3 and BaTiO3 are clarified in a manner that permits critical evaluation of microscopic models for their ferroelectric transitions. The results illustrate the advantages of ISRS over conventional Raman spectroscopy of low-frequency, heavily damped soft modes.
Dougherty, Thomas P.↗
Characterization of the Effects of Precursor Mineralogy on Hematite Spectra: Application to Martian Hematite Mineralization
The Thermal Emission Spectrometer (TES) instrument aboard Mars Global Surveyor discovered several isolated deposits of gray, crystalline hematite in Sinus Meridiani, Aram Chaos, and Valles Marineris. A variety of formation mechanisms has been proposed for the martian hematite deposits, including aqueous and nonaqueous processes. Comparison of the average Sinus Meridiani hematite spectrum measured by TES to laboratory emissivity spectra for a variety of naturally occurring hematites shows small but potentially important differences. In particular, the emissivity minimum at 300 and 445/cm in the Sinus Meridiani (SM) spectrum is displaced 10-25/cm to lower frequencies compared to some natural hematite samples. In addition, these bands in the TES data are narrower than the broad bands seen in many natural hematite spectra. These differences may imply that the natural variability of hematite spectra has not been fully characterized, especially with respect to the reaction pathway (precursor mineralogy and temperature of hematite formation) and crystal morphology. Here, we describe the thermal infrared spectral characteristics of several series of synthetic hematite samples derived by direct precipitation, dehydroxylation of fine-grained goethite and the oxidation of magnetite. Several natural hematite sample spectra are also presented for comparison. Transmission electron microscopy (TEM) and Mossbauer spectral analyses of selected samples were performed in order to help determine the causes of the changes seen in the infrared spectra.
Glotch, Timothy D.↗
Investigation of Magmatic Activities on Early Mars Using Igneous Mineral Chemistry in Gale Crater, Mars
One objective of rover missions is exploring the geological context of the surroundings. Over the years, igneous petrology and sedimentology have been disconnected, the first investigating magmatic processes and volcanic activities, and the second seeking environmental conditions in the past and assessing the habitability of the planet. Although different, one is related to the other: igneous rocks are altered and broken down, leading to the formation of sedimentary rocks, which can in turn be used to back out the nature of their magmatic source. The Curiosity rover that landed in the 3.7 Gyr old impact crater Gale is traveling through sedimentary rocks. About fifty float rocks have been observed, and several of them with ambiguous texture and composition have been classified as igneous or sedimentary depending on studies such as Jake_M. The composition of several unambiguous igneous rocks has been analyzed [4- 6] but their heterogeneity at a larger instrumental (measurement size < 2 cm) scale prevents the measurement of a bulk composition as performed on Earth. An original approach avoiding these two last issues is to consider igneous mineral chemistry analyzed within igneous and sedimentary rocks to assess magmatic processes that could have formed them. Most Curiosity data are used to explore ancient environmental conditions, and a significant number of compositional analyses are under-explored for constraining magmatic activities. We will present how we can make use of sedimentary data for investigating igneous processes in the vicinity of Gale crater. Geological Context: We focus on the first 750 martian days, corresponding to measurements in a coherent lacustrine sedimentary unit called Bradbury, because all sedimentary rocks were sourced from the same watershed and appear to have a consistent source with minimal alteration [2-3]. Igneous detrital minerals including feldspar and pyroxene, are observed in sedimentary rocks. Monte Carlo models showed that minimal cation loss is observed based on the composition of all Bradbury rocks, implying negligible weathering [3]. Although clay minerals are detected in few rocks [7], chemical compositions of rocks can be explained by a mixture of primary igneous minerals [3]. Variation of composition within Bradbury rocks can be explained by mineral sorting and one distinct source component. While a common magmatic source is suggested, Bradbury sediments likely come from several volcanic eruptions from a single magmatic chamber [9- 10]. The occurrence of alkali minerals like sanidine and K-rich rocks throughout Bradbury supports the presence of a potassic component, likely trachytic, while plagioclase and a mafic composition suggest a basaltic component [8-9]. Instruments: Mineral chemistry can be estimated by three instruments onboard Curiosity. The CheMin instrument enables detection of mineral assemblages using X-ray diffraction (XRD). Using Rietveld refinement, each mineral is identified according to their 1D XRD pattern [11]. Note that distinction between pyroxene minerals is challenging with the CheMin instrument due to overlapping peaks on XRD patterns and low angular resolution of the instrument [12]. Then, using least square regression and optimization algorithms based on unit-cell parameters, mineral chemistry has been estimated by [11]. Plagioclase composition has been estimated using the NaAlSi3O8- CaAl2Si2O8 system and alkali feldspar is based on the NaAlSi3O8-KAlSi3O8 system (stars in Fig.1). Two mudstone samples (John Klein and Cumberland) and one sandstone sample (Windjana) were analyzed by CheMin at Yellowknife Bay and Kimberley, respectively. Figure 1. Ternary diagrams of feldspars (top) and pyroxene (bottom) quadrilateral. Stars correspond to CheMin composition and the gray patches to ChemCam composition. The colored dots are the composition of feldspar and pyroxene that crystallized during fractional crystallization at FMQ+1 of a melt extracted at distinct melting degree during the adiabatic ascent of a primitive mantle composition, without any water (left panels) and with 0.5 wt.% of water (right panels) at distinct pressure. The ChemCam instrument enables the analysis of the chemical compositions of rocks at hundreds of micrometer scale (350-550 μm) using laser induced breakdown spectroscopy (LIBS), which may provide the composition of minerals when they are larger than the beam spot (>550 μm) [13]. Within >5000 LIBS points, we performed a typical stoichiometric filtering allowing us to distinguish 56 feldspar and 10 pyroxene mineral compositions (grey patches in Fig. 1). Finally, the Alpha Particle X-ray Spectrometer (APXS) analyzes the composition of rocks with a 1.6 cm diameter spot size. Monte Carlo mass balance modeling allowed [3] to decipher a feldspar range varying between An30 and An40 (Fig. 1). Discussion: Although there could be a more complex history and other ways to form the whole compositional range of igneous minerals analyzed within the Bradbury formation, we are presenting here simple magmatic pathways commonly occurring on Earth using the thermodynamical softwares pMELTS and rhyoliteMELTS [14]. The objective is to find reasonable igneous processes that produce minerals that parallel the compositions of feldspar and pyroxene analyzed by the Curiosity rover. As commonly observed for mid-ocean ridge basalts, the adiabatic ascent of a primitive mantle composition [15] partially melting at 2 GPa has been modeled, followed by the extraction of a liquid at distinct degrees of partial melting, which undergoes fractional crystallization at an oxygen fugacity +1 log unit above the fayalite-magnetite-quartz (FMQ) buffer within the crust (0.02-0.4 GPa) with H2O = 0- 0.5 wt. %. These latter conditions correspond to those recorded within igneous clasts from the Noachian martian breccia NWA 7034 and paired and within Gale igneous rocks (colored dots in Fig. 1) [16-17]. To check the reliability of these 2-step models, we also tested fractional crystallization at similar conditions (FMQ+1; P=0.02-0.4 GPa; H2O = 0-0.5 wt. %) of starting compositions corresponding to that of magmas with distinct melting degrees obtained from isobaric experiments at 2 GPa [18]. Mineral compositions obtained from both models are similar. As shown on Fig. 1, the whole range of observed feldspar compositions cannot be reproduced by fractionation of one magma only. Indeed, while alkali feldspar and Na-plagioclase likely crystallized from fractional crystallization of a low-degree melt (here <15%), plagioclase and pyroxene can only be formed by fractional crystallization of a higher degree melt (here >19%). The corresponding liquid descent lines are broadly in agreement with compositions estimated by ChemCam corresponding to float igneous rocks (Fig. 2) [4-6]. Figure 2. Silica versus alkali content. Lines show the liquid lines of descent from magmas with distinct degrees of melting. Gray patches represents the composition of Gale igneous rocks [4-6]. Trachytic to rhyolitic magmas crystallize alkali feldspar, and andesite to dacite magmas likely form plagioclase. Therefore, at least two starting magmas at distinct melting degrees, which could easily come from a single mantle source, are necessary to explain the whole compositional range of feldspar and pyroxene analyzed within Bradbury rocks. Conclusion: Because rocks from the Bradbury formation are likely originating from the same magmatic source with minimal weathering as supported by several studies using different approaches, igneous mineral chemistry analyzed by CheMin and ChemCam allows us to back out reasonable magmatic pathways that could have crystallized them. Fractional crystallization of at least two starting magmas originating from distinct melting degrees of a single mantle source can explain the whole range of feldspar and pyroxene composition. Both alkaline and sub-alkaline liquids can be produced, with compositions corresponding to those of the igneous rocks analyzed by ChemCam within the Bradbury formation, highlighting the complexity of Mars magmatism.
Payre, V.↗