Isomorphous Replacement Research Articles

Achieving Superprotonic Conduction in Metal–Organic Frameworks through Iterative Design Advances

Two complementary design strategies, isomorphous ligand replacement and heterocycle doping, have been applied to iteratively enhance the proton conductivity of a metal-organic framework, β-PCMOF2. The resulting materials, PCMOF21/2(Pz) and PCMOF21/2(Tz) (Pz = 1H-pyrazole, Tz = 1H-1,2,4-triazole), have their proton conduction raised almost 2 orders of magnitude compared to β-PCMOF2. The bulk conductivities of these materials are over 10-1 S cm-1 at 85 °C and 90% relative humidity (RH), while maintaining the parent MOF structure. A solid state synthetic route for doping 1-D channels is also presented.

Review on Cement Stabilization/Solidification of Municipal Solid Waste Incineration Fly Ash

Municipal solid waste incineration (MSWI) fly ash must be treated properly prior to being disposed in the security landfill due to its serious pollution toxicity. Nowadays, lots of studies have demonstrated that cement‐based stabilization/solidification could reduce the toxicity pollution effectively by encapsulating the heavy metals into cement matrix, which leads to greater capacity and weight. This paper compares and discusses the MSWI fly ash treatment with the mostly used matrix materials such as Portland cement, phosphate cement, aluminate cement, and alkaline activated cement. Moreover, immobilization mechanism introduced by the interaction between the MSWI fly ash and hydrated cement matrix materials, such as the physical cementing effect, adsorption, isomorphous replacement, and complex precipitation, was explored in depth. The paper also pointed out some reasonable development directions for cement‐based stabilization/solidification technology to improve the effectiveness and application of cement‐based stabilization/solidification technology.

TMV-Templated Formation of Metal and Polymer Nanotubes.

Metals and polymers are probably the most important construction materials, but also have many more functions, e.g., for electronics. The interaction of metal ions with tobacco mosaic virus (TMV) was originally used for the preparation of heavy metal isomorphic replacement for structural analysis. Metal ions can also be the precursors for metal clusters, particles, and layers. Various strategies have been developed, which allow the creation of metal layers on the external surface of TMV. Such layers can be made as metal tubes, enveloping a complete virion. An alternative strategy is adsorption of metal nanoparticles. If a dense coating of TMV is achieved, again a tube results. Nanoscale tubes have various physical properties that depend on size, crystallinity, uniformity, but especially on the nature of the metal. Polymer coatings are as yet rarely investigated, though they can be prepared quite easily.Here, a series of exemplary protocols is provided, which covers all of these different concepts.

Introducing site-specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures.

The generation of high-quality protein crystals and the loss of phase information during an X-ray crystallography diffraction experiment represent the major bottlenecks in the determination of novel protein structures. A generic method for introducing Hg atoms into any crystal independent of the presence of free cysteines in the target protein could considerably facilitate the process of obtaining unbiased experimental phases. Nanobodies (single-domain antibodies) have recently been shown to promote the crystallization and structure determination of flexible proteins and complexes. To extend the usability of nanobodies for crystallographic work, variants of the Nb36 nanobody with a single free cysteine at one of four framework-residue positions were developed. These cysteines could be labelled with fluorophores or Hg. For one cysteine variant (Nb36-C85) two nanobody structures were experimentally phased using single-wavelength anomalous dispersion (SAD) and single isomorphous replacement with anomalous signal (SIRAS), taking advantage of radiation-induced changes in Cys-Hg bonding. Importantly, Hg labelling influenced neither the interaction of Nb36 with its antigen complement C5 nor its structure. The results suggest that Cys-Hg-labelled nanobodies may become efficient tools for obtaining de novo phase information during the structure determination of nanobody-protein complexes.

Electrical conductivity of potassium titanyl phosphate KTiOPO4 pure crystals and those doped with Na+, Rb+, and F– ions

KTiOPO4 crystals, both pure and doped with rubidium Rb+ and fluorine F– ions, were grown in temperature range from 1060 to 846°С from salt solvent containing potassium metaphosphate КРО3 and potassium orthophosphate К3РО4 by using a Czochralski modified method. Potassium–sodium titanyl phosphate crystals were obtained from KTiOPO4 crystals by the potassium isomorphic replacement with sodium; to this purpose, sodium chemical diffusion from NaNO3 melt was used. Their ionic conductivity was studied by the electrochemical impedance spectroscopy method. The KTiOPO4 crystal doping with rubidium and sodium ions was shown to lower the conductivity, whereas the doping with fluorine ions results in increased conductivity.

Production, Physicochemical and Catalytic Properties of Gallium-Containing Zeolite Catalysts

<p>Crystalline galloalumino- and gallosilicates with pentasil structure were synthesised under hydrother-mal conditions. The influence of gallium concentration and binder amount both on physicochemical and catalytic properties of a zeolite in the process of C<sub>2</sub>-C<sub>4</sub> light alkanes aromatization and on catalyst deacti-vation due to carbidization has been studied. Acidic properties of gallium-containing pentasils with differ-ent composition were studied using the method of thermoprogrammed ammonia desorption. The forma-tion of strong aproton acidic sites whose composition includes gallium ions was found. It has been shown that isomorphic aluminium replacement by gallium in the pentasil lattice leads to a significant increase in aromatizing activity and period of stable catalyst operation. A decrease in intensity of coking and the formation of less condensed coke deposits with a wide distribution by the structure are observed with the increase in gallium concentration. The introduction of a binder to galloaluminosilicate results in a signifi-cant increase in mechanical strength of a catalyst. It was established that the most efficient catalyst of the above process is a zeolite containing 2.2% of gallium oxide and 1.3% of aluminium oxide and mixed with 20% of the pseudobeumite. The selectivity of the formation of aromatic hydrocarbons reaches 55-60%, the period of stable operation exceeds 350 h. In accordance with the data obtained suggested are the principles of the selection of efficient catalysts of light alkanes aromatization and optimum conditions of the process.</p>

Mixing energies (interaction parameters) and decomposition temperatures in solid solutions of monazites of rare earth elements with structure La1–x Ln x PO4

The mixing energies (interaction parameters) of solid solutions in orthophosphates La1–x Ln x PO4 of rare earth elements (REE) with monazite structure are calculated within the framework of the crystal energy theory of isomorphous replacement. Their values and contributions to the mixing energy depending on the size of replaceable structural units and the degree of ionicity of the chemical bond within the row of lanthanides from Ce to Dy expectedly increase. Accordingly, there is an increase in critical temperatures of solid solution decomposition (stability). This agrees with the previous results of ab initio quantum chemical calculations.

Crystal chemical and geochemical features of genetically different paleozoic dolomites in the Volga–Ural region

The comparative analysis of primary sedimentary and secondary catagenetic dolomites revealed that they differ in many typomorphic properties. Sedimentary dolomites are characterized by the pelitomorphic and fine-grained structure, high stoichiometry, and presence of the electron-hole (p-n) centers [SO2]– and [SO3]– in the structure. Secondary dolomites have a fine- to medium-grained structure and distinguished by a lower degree of stoichiometry. Their crystal lattice shows isomorphous replacements Mg ↔ Fe and Mg ↔ Ca. They can be divided into two (massive and porous) varieties. The massive varieties are characterized by the conformal structure and xenomorphic habitus of the closely packed idiomorphic and hypidiomorphic grains. The Ca–Mg and Fe–Mg isomorphism in the massive dolomites is less expressed than in the porous varieties. These specific features of dolomite varieties are related to their different formation settings. The porous dolomites were formed in a free environment that fostered slow growth of the relatively large equant crystals with a high degree of isomorphism, whereas the massive dolomites were formed under “stringent constraints” during a faster growth of crystals.

Structure determination of contaminant proteins using the MarathonMR procedure.

In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons. It might be difficult to obtain multiple isomorphous replacement or multi wave length anomalous dispersion data or the crystal may have defects such as twinning or pseudo translation. Apart from these usual difficulties, more frequent difficulties have been encountered in recent years because of the large number of projects handled by structural biologists. These new difficulties usually result from contamination of the protein of interest by other proteins or presence of proteins from pathogenic organisms that could withstand the antibiotics used to prevent bacterial contamination. It could also be a result of poor book keeping. Recently, we have developed a procedure called MarathonMR that has the power to resolve some of these problems automatically. In this communication, we describe how the MarathonMR was used to determine four different protein structures that had remained elusive for several years. We describe the plausible reasons for the difficulties encountered in determining these structures and point out that the method presented here could be a validation tool for protein structures deposited in the protein data bank.

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

A complex magmatic system beneath the middle and northern Okinawa Trough: evidence from pyroxene characteristics

The Okinawa Trough is an initial marginal back‐arc basin. In this paper, we present a comparative study of pyroxenes in white and black pumice from the Okinawa Trough to explore the magmatic evolution of the region and the characteristics of the magmatic system. The results show two species of pyroxenes in the white pumice (clinopyroxene and orthopyroxene) but only one species in the black pumice (orthopyroxene). Many isomorphic replacements among the cations occurred during clinopyroxene crystallization. Clinopyroxene‐melt thermobarometry yielded a temperature of 847–988°C and a pressure of 2.73–7.42 kbar, which vary considerably and correspond to a maximum depth of approximately 24 km. All of the orthopyroxenes in both the white and black pumice crystallized at similar pressures ranging from 0.67 to 4.59 kbar, which correspond to a maximum depth of approximately 15 km. The clinopyroxenes crystallized mainly in the lower crust, whereas the orthopyroxenes formed at the boundary depth between the upper crust and the lower crust. The similarities in the pyroxene chemical compositions and the whole‐rock characteristics between the two types of pumice indicate that both types of pumice are linked to the same magmatic system at depth. The pyroxenes crystallized from genetically related melts within a magmatic system that had undergone various degrees of differentiation. The physicochemical characteristics of the pyroxenes show that the magma chamber module changed during the crystallization process from clinopyroxenes to orthopyroxenes. This change most likely resulted from local characteristics of the near‐surface structure. These observations support the model of a ‘two‐layered magma chamber’ in the northern Okinawa Trough. Copyright © 2016 John Wiley & Sons, Ltd.

Unique paragenesis of cerium and yttrium allanites in tourmalinite of the Severny massif (Chukotka)

A description of hydrothermal allanite-(Y) and its unique association with allanite-(Ce) from tourmaline metasomatic rock of the Severny granite massif in Chukotka is presented in the article. Examination of the composition of metasomatic rims in allanite-(Y) allowed us to estimate the limit of isomorphic replacement in allanite of Y and heavy lanthanides by LREE, reaching 25%.

Synthesis and characterization of Mn intercalated Mg-Al hydrotalcite

Mn intercalated hydrotalcite was prepared using a reconstruction method. And Mn intercalation was confirmed by XRD, FTIR, and thermal analyses. The different valences of Mn were present as determined by XPS. Calcination slightly promoted the isomorphic replacement of Mn2+ and Mn3+ for Mg2+ and Al3+, especially the replacement of Mn2+ for Mg2+ and Al3+, and to some extent, reduced Mn intercalation. Ultrasonic treatment significantly increased Mn intercalation in permanganate form (Mn7+), and promoted the replacement of Mn2+ for Mg2+ and Al3+. XRF analysis showed that ultrasonic treatment decreased the unbalanced layer charge of Mn intercalated hydrotalcite, while prolonged calcination increased it. These results may provide guidance on the preparation and application of Mn intercalated hydrotalcite. Extended calcination time and ultrasonic vibration increased the interlayer spacing of hydrotalcite, as a result of reduction in layer charge. As the layer charge was not completely balanced after Mn intercalation, a certain amount of CO32− was re-adsorbed into the interlayer space. Mn-hydrotalcites with different layer charges, different contents of Mn with varying valences are expected to have different performances in the process of adsorption, degradation, and catalysis.

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.

The Degradation of Indigo Sodium Disulphonate by Chromium Isomorphic Replacement in Magnetite

AbstractThis study was designed to investigate the degradation of indigo sodium disulphonate (ISD, a kind of indigoiddyes) in heterogeneous Fenton system (H2O2/Fe3‐xCrxO4). The co‐precipitation was employed to synthesize a series of Cr‐doped magnetite. The result of XRD indicated that Chromium isomorphic replacement will not cause significant changes in the structure of the magnetite. The thermogravimetric (TG) and differential scanning calorimetry analysis was applied in the samples. The adsorption data showed that strong acidic condition and high concentration Cr‐containing magnetite contributed to the enhancement of adsorbing capacity. The degradation experiment was carried out in consideration of 4 aspects, including pH, Fe3‐xCrxO4, H2O2 concentration and catalyst dosage, stating that Cr‐doped magnetite made for degrading indigo sodium disulphonate.

Stabilization of refining slags by correction of their phase composition

The stabilization of refining slags in ladle treatment with alumina fluxes is studied. In refining, the slag is stabilized in the presence of alumina fluxes thanks to isomorphic replacement of a calcium ion by alkali-metal ions and to decrease in the dicalcium-silicate content in the melt as a result of its replacement by aluminum-bearing phases.

Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS.

Understanding how DNA carries out its biological roles requires knowledge of its interactions with biological partners. Since DNA is a polyanionic polymer, electrostatic interactions contribute significantly. These interactions are mediated by positively charged protein residues or charge compensating cations. Direct detection of these partners and/or their effect on DNA conformation poses challenges, especially for monitoring conformational dynamics in real time. Small-angle x-ray scattering (SAXS) is uniquely sensitive to both the conformation and local environment (i.e. protein partner and associated ions) of the DNA. The primary challenge of studying multi-component systems with SAXS lies in resolving how each component contributes to the measured scattering. Here, we review two contrast variation (CV) strategies that enable targeted studies of the structures of DNA or its associated partners. First, solution contrast variation enables measurement of DNA conformation within a protein-DNA complex by masking out the protein contribution to the scattering profile. We review a specific example, in which the real-time unwrapping of DNA from a nucleosome core particle is measured during salt-induced disassembly. The second method, heavy atom isomorphous replacement, reports the spatial distribution of the cation cloud around duplex DNA by exploiting changes in the scattering strength of cations with varying atomic numbers. We demonstrate the application of this approach to provide the spatial distribution of monovalent cations (Na+, K+, Rb+, Cs+) around a standard 25-base pair DNA. The CV strategies presented here are valuable tools for understanding DNA interactions with its biological partners.

A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction.

While structure determination from micrometre-sized crystals used to represent a challenge, serial X-ray crystallography on microfocus beamlines at synchrotron and free-electron laser facilities greatly facilitates this process today for microcrystals and nanocrystals. In addition to typical microcrystals of purified recombinant protein, these advances have enabled the analysis of microcrystals produced inside living cells. Here, a pipeline where crystals are grown in insect cells, sorted by flow cytometry and directly analysed by X-ray diffraction is presented and applied to in vivo-grown crystals of the recombinant CPV1 polyhedrin. When compared with the analysis of purified crystals, in cellulo diffraction produces data of better quality and a gain of ∼0.35 Å in resolution for comparable beamtime usage. Importantly, crystals within cells are readily derivatized with gold and iodine compounds through the cellular membrane. Using the multiple isomorphous replacement method, a near-complete model was autobuilt from 2.7 Å resolution data. Thus, in favourable cases, an in cellulo pipeline can replace the complete workflow of structure determination without compromising the quality of the resulting model. In addition to its efficiency, this approach maintains the protein in a cellular context throughout the analysis, which reduces the risk of disrupting transient or labile interactions in protein-protein or protein-ligand complexes.

Advances in experimental phasing.

Advances in experimental phasing.

Impact of pH Value and Temperature on Cement-Based Materials Adsorbing Heavy Metal Ions

The development of the city traffic and its increasing traffic flux are the signs of the development of the society, but causing a serious pollution on the city's ecological environment. Cement hydration reactions are needed to generate Ca (OH)2, C-S-H gel, and AFt, as well as other hydrated products. Meanwhile, heavy metal ions are contained and fixed in a cement paste under physical encapsulation, absorption, isomorphous replacement, and double decomposition. This paper mainly discusses the impact of hydration environment on the adsorption law of materials adsorbing heavy metal ions and the adsorption mechanism under different pH values and temperatures, analyzing specific reasons from the perspective of micro-structure. Through the analysis it can be seen that, in addition to zinc ions, the cement-based materials’ capacity of adsorbing heavy metal ions increases as the pH value and the temperature increase. Micro-structure analysis shows that cement-based materials’ main adsorption methods are different when pH values are different.