Crystallographic plane-induced selective mineralization of nanohydroxyapatite on fibrous-grained titanium promotes osteointegration and biocorrosion resistance.

The (002) crystallographic plane-oriented hydroxyapatite (HA) and anatase TiO2 enable favorable hydrophilicity, osteogenesis, and biocorrosion resistance. Thus, the crystallographic plane control in HA coating and crystalline phase control in TiO2 is vital to affect the surface and interface bioactivity and biocorrosion resistance of titanium (Ti) implants. However, a corresponding facile and efficient fabrication method is absent to realize the HA(002) mineralization and anatase TiO2 formation on Ti. Herein, we utilized the predominant Ti(0002) plane of the fibrous-grained titanium (FG Ti) to naturally form anatase TiO2 and further achieve a (002) basal plane oriented nanoHA (nHA) film through an in situ mild hydrothermal growth strategy. The formed FG Ti-nHA(002) remarkably improved hydrophilicity, mineralization, and biocorrosion resistance. Moreover, the nHA(002) film reserved the microgroove-like topological structure on FG Ti. It could enhance osteogenic differentiation through promoted contact guidance, showing one order of magnitude higher expression of osteogenic-related genes. On the other hand, the nHA(002) film restrained the osteoclast activity by blocking actin ring formation. Based on these capacities, FG Ti-nHA(002) improved new bone growth and binding strength in rabbit femur implantation, achieving satisfactory osseointegration within 2 weeks.

Analysis of crystallographic phase retrieval using iterative projection algorithms.

For protein crystals in which more than two thirds of the volume is occupied by solvent, the featureless nature of the solvent region often generates a constraint that is powerful enough to allow direct phasing of X-ray diffraction data. Practical implementation relies on the use of iterative projection algorithms with good global convergence properties to solve the difficult nonconvex phase-retrieval problem. In this paper, some aspects of phase retrieval using iterative projection algorithms are systematically explored, where the diffraction data and density-value distributions in the protein and solvent regions provide the sole constraints. The analysis is based on the addition of random error to the phases of previously determined protein crystal structures, followed by evaluation of the ability to recover the correct phase set as the distance from the solution increases. The properties of the difference-map (DM), relaxed-reflect-reflect (RRR) and relaxed averaged alternating reflectors (RAAR) algorithms are compared. All of these algorithms prove to be effective for crystallographic phase retrieval, and the useful ranges of the adjustable parameter which controls their behavior are established. When these algorithms converge to the solution, the algorithm trajectory becomes stationary; however, the density function continues to fluctuate significantly around its mean position. It is shown that averaging over the algorithm trajectory in the stationary region, following convergence, improves the density estimate, with this procedure outperforming previous approaches for phase or density refinement.

Predicting Electrical Conductivity in Bi-Metal Composites.

Generating high magnetic fields requires materials with not only high electric conductivity but also good strength properties in order to withstand the necessarily strong Lorentz forces. A number of bi-metal composites, most notably Cu/Nb, are considered to be good candidates for this purpose. Here, we generalize our previous work on Cu/Nb in order to predict, from theory, the dependence of electric conductivity on the microstructure and volume fraction of the less conductive component for a number of other bi-metal composites. Together with information on strength properties (taken from previous literature), the conductivity information we provide in this work can help to identify new promising candidate materials (such as Cu/Nb, Cu/Ag, Cu/W, …) for magnet applications with the highest achievable field strengths.

Tracing the genealogy of research on the mechanism of blue flower coloration by anthocyanin based on Keita Shibata's work.

K. Shibata is the ancestor of the research on anthocyanins in Japan and proposed metal complex theory against the pH theory by R. Willstätter. Shibata's successors, S. Hattori and K. Hayashi, made efforts to clarify blue flower coloration by metal complexation and found commelinin, a self-assembled supramolecular metal complex pigment, in blue dayflower, Tsuyukusa. The author introduces two key reports on blue flower coloration published in the Proceedings of the Japan Academy and describes the subsequent development of the study.

Toward the Rechargeable Aqueous Zinc Ion Batteries with Improved Overall Performance: Electrolyte with Surface Adsorptive Additive.

Aqueous zinc-ion batteries (AZIBs) with slightly acidic electrolytes process advantages such as high safety, competitive cost, and satisfactory electrochemical performance. However, the failure behaviors of both electrodes, regarding zinc dendrite growth, interfacial parasitic reactions, and the collapse of cathode materials hinder the practical application of ZIBs. To alleviate the issues of both anode and cathode at the same time, D-xylose (DX) is introduced to the electrolyte as a multifunctional additive. As a result, the side reaction of the anode is suppressed and the metallic deposition behavior is regulated due to the hydrogen bonding network reconstruction and preferential surface adsorption of DX; for the MnO2 cathode, the DX adsorption can help the interfacial charge transfer and increase the reactive sites. Benefiting from these merits, DX-optimized Zn//Zn battery displays reveal a prolonged lifespan of 6912 h and an ultra-high cumulative capacity of 17.28 Ah cm-2 at 5 mA cm-2. With the function of water reactivity suppression, the Coulombic efficiency reaches 99.91% at 2 mA cm-2; the Zn||MnO2 full batteries exhibit excellent cyclability over 2000 cycles at 5C with an increased capacity of 118.9 mAh g-1, indicating the dual functions to both of the electrodes for AZIBs.

Towards dynamically configured databases for CIFs: the new modulated structures open database at the Bilbao Crystallographic Server.

This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via JSmol. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework.

Free tools for crystallographic symmetry handling and visualization.

Online courses and innovative teaching methods have triggered a trend in education, where the integration of multimedia, online resources and interactive tools is reshaping the view of both virtual and traditional classrooms. The use of interactive tools extends beyond the boundaries of the physical classroom, offering students the flexibility to access materials at their own speed and convenience and enhancing their learning experience. In the field of crystallography, there are a wide variety of free online resources such as web pages, interactive applets, databases and programs that can be implemented in fundamental crystallography courses for different academic levels and curricula. This paper discusses a variety of resources that can be helpful for crystallographic symmetry handling and visualization, discussing four specific resources in detail: the Bilbao Crystallographic Server, the Cambridge Structural Database, VESTA and Jmol. The utility of these resources is explained and shown by several illustrative examples.

Energy-dispersive Laue diffraction analysis of the influence of statherin and histatin on the crystallographic texture during human dental enamel demineralization.

Energy-dispersive Laue diffraction (EDLD) is a powerful method to obtain position-resolved texture information in inhomogeneous biological samples without the need for sample rotation. This study employs EDLD texture scanning to investigate the impact of two salivary peptides, statherin (STN) and histatin-1 (HTN) 21 N-terminal peptides (STN21 and HTN21), on the crystallographic structure of dental enamel. These proteins are known to play crucial roles in dental caries progression. Three healthy incisors were randomly assigned to three groups: artificially demineralized, demineralized after HTN21 peptide pre-treatment and demineralized after STN21 peptide pre-treatment. To understand the micro-scale structure of the enamel, each specimen was scanned from the enamel surface to a depth of 250 µm using microbeam EDLD. Via the use of a white beam and a pixelated detector, where each pixel functions as a spectrometer, pole figures were obtained in a single exposure at each measurement point. The results revealed distinct orientations of hydroxyapatite crystallites and notable texture variation in the peptide-treated demineralized samples compared with the demineralized control. Specifically, the peptide-treated demineralized samples exhibited up to three orientation populations, in contrast to the demineralized control which displayed only a single orientation population. The texture index of the demineralized control (2.00 ± 0.21) was found to be lower than that of either the STN21 (2.32 ± 0.20) or the HTN21 (2.90 ± 0.46) treated samples. Hence, texture scanning with EDLD gives new insights into dental enamel crystallite orientation and links the present understanding of enamel demineralization to the underlying crystalline texture. For the first time, the feasibility of EDLD texture measurements for quantitative texture evaluation in demineralized dental enamel samples is demonstrated.

A Snapshot of the Most Recent Transthyretin Stabilizers.

In recent years, several strategies have been developed for the treatment of transthyretin-related amyloidosis, whose complex clinical manifestations involve cardiomyopathy and polyneuropathy. In view of this, transthyretin stabilizers represent a major cornerstone in treatment thanks to the introduction of tafamidis into therapy and the entry of acoramidis into clinical trials. However, the clinical treatment of transthyretin-related amyloidosis still presents several challenges, urging the development of new and improved therapeutics. Bearing this in mind, in this paper, the most promising among the recently published transthyretin stabilizers were reviewed. Their activity was described to provide some insights into their clinical potential, and crystallographic data were provided to explain their modes of action. Finally, structure-activity relationship studies were performed to give some guidance to future researchers aiming to synthesize new transthyretin stabilizers. Interestingly, some new details emerged with respect to the previously known general rules that guided the design of new compounds.

Comparison of the global crystallographic texture of minerals in the shells of Bathymodiolus thermophilus Kenk et B.R. Wilson, 1985 and species of the genus Mytilus Linnaeus, 1758.

The global crystallographic texture of calcite and aragonite in the shells of the bivalves Bathymodiolus thermophilus, Mytilus galloprovincialis, M. edulis and M. trossulus was studied by means of neutron diffraction. It was revealed that the general appearance of pole figures isolines of both minerals coincides for the studied species. The crystallographic texture sharpness evaluated by means of pole density on the calcite pole figures ((0006), (101¯4)) and aragonite pole figures ((012)/(121), (040)/(221)) coincides or has close values for deep-sea hydrothermal species B. thermophilus and the studied shallow-water species of the genus Mytilus. The calcite pole figures (0006) and (101¯4) of B. thermophilus show a shift in the position of texture maximum values compared to corresponding pole figures of other mussels. The shell microstructure of all studied mollusks is similar, only the shape of the fibers of B. thermophilus differs. Global crystallographic texture is a stable feature of the family Mytilidae. The extreme habitat conditions of the hydrothermal biotope do not significantly affect the crystallographic texture of B. thermophilus.

Wide-Field Polarimetric Second-Harmonic Imaging for Rapid and Nondestructive Investigation of Laser-Induced Crystallization Phenomena.

The selective and controlled formation of nanocrystals in glass is emerging as a versatile method to achieve functional photonics, optoelectronics, and quantum devices, such as single-photon emitters. Here, we investigate the use of wide-field polarimetric second-harmonic (SH) microscopy as a method to rapidly and nondestructively examine nanoscale crystal arrangements in laser-processed glass. As a case study, we investigate tellurite glass, where the formation of a trigonal tellurium (t-Te) nanocrystalline phase after femtosecond laser exposure was recently demonstrated. Combined with theoretical models, we show that wide-field polarimetric SH microscopy offers comprehensive information on the nanocrystals' orientation, distribution, and chirality. With its high imaging throughput and spatial resolution, this method has the potential not only to significantly accelerate investigations on laser-induced glass crystallization processes but also to provide a valuable tool for in situ process monitoring.

ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.

Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in the absence of a model. In addition, model bias is more severe when independent experimental data are scarce. Our methods solve the phase problem by combining the location of accurate model fragments using Phaser with density modification and interpretation of the resulting maps using SHELXE. From a partial, correct structure, the density modification process and the stereochemical constraints draw the rest of the structure, validating the result. This same principle is now exploited at low resolution. Coiled coils are important, ubiquitous structures but notoriously difficult to phase and to predict. Both correct solutions and incorrect ones are poorly discriminated by the crystallographic figures of merit as long as helices are correctly oriented. We incorporate coiled-coil verification, designed to set up competing, incompatible structural hypotheses to probe both the results and establish the power of the data to discriminate them. Efficiency of coiled-coil phasing and validation in test cases from 3 to 4 Å is demonstrated in ARCIMBOLDO_LITE, placing single helices, and in ARCIMBOLDO_SHREDDER, with fragments derived from AlphaFold models. SHELXE tracing at low resolution has been enhanced, maintaining its local character but extending the environment assessment. For non-helical structures, verification is demonstrated in the fragment location process. Its use is exemplified with the solution of the VSR1 structure at 3.5 Å, depending on LLG optimization and the emergence of new features in the electron density. Relying on verification, we have extended the use of the ARCIMBOLDO software to low resolution.

Broadband spectral cyan emission phosphor for full-spectrum LED caused by interstitial site occupation.

The phosphor with a highly condensed, rigid framework structure and a single crystallographic site often exhibit symmetrical narrow-band emission. It is challenging to achieve broadband emission by doping Eu2+ ions in similar structures. Here, we propose to control the occupation and quenching concentration of Eu2+ ions in a single-site matrix Sc2Si2O7 to increase efficiency and precise regulation of luminescence spectra substantially. The analysis of photoluminescence spectroscopy through steady-state, transient-state, and Gaussian fitting techniques has discovered two emission centers despite the presence of a single rare-earth substitution site. The theoretical calculations and bond valence sum subsequently prove that Eu2+ ions prefer substituting the Sc3+ and interval sites to emit intense cyan light. Under 340 nm excitation, broad cyan-emission (FWHM = 115 nm) is exhibited with a high quantum yield of 60.67 %. The present phosphor exhibits pronounced thermal stability, and the emission intensity can still keep 68.3 % at 170 °C compared to that at atmospheric temperature. The Sc2Si2O7: Eu2+ phosphor boasts exceptional potential as a highly efficient cyan component in full-spectrum WLEDs. By replacing the blue light component commonly found in WLEDs, the intelligent and healthy alternative Sc2Si2O7: Eu2+ phosphor can effectively decrease the harmful blue light. This work also highlights the critical need to analyze local phosphor distortions upon rare-earth substitution, especially in single crystallographic site structures.

New Insights into MAI Additives in 2D-Assisted 3D Controlled Crystallization Toward High-Quality α-Phase FAPbI3 Perovskites.

The highly oriented 2D perovskite templates of n = 1 have typically been created to attain controllable and oriented crystallization of 3D α-phase formamidinium lead triiodide (α-FAPbI3) perovskites. However, the role of methylammonium iodide (MAI), a widely used α-FAPbI3 phase stabilizer, in regulating the growth dynamics of 2D/3D perovskites is generally ignored. Herein, Ruddlesden-Popper type n = 1 2D octylammonium lead iodide (OA2PbI4) perovskites are added into FAPbI3 precursor solution. The template of n = 2 (OA2MAPb2I7), which is spontaneously constructed by the mixture of n = 1 2D and methylammonium chloride (MACl), acts as a skeleton to template the epitaxial growth of α-FAPbI3. However, the volatilization of MACl inevitably causes damage to the 2D structure during thermal annealing. This study reveals that small amounts of less volatile MAI additive enables the creation of stable 2D template, leading to more controlled vertical orientation crystallization. Consequently, the high-quality mixed-dimensional perovskite film delivers a high efficiency of 24.19% together with improved intrinsic stability. This work provides an in-depth understanding of 2D-assisted controlled epitaxial growth of α-FAPbI3.

Mapping protein conformational landscapes from crystallographic drug fragment screens.

Proteins are dynamic macromolecules. Knowledge of a protein's thermally accessible conformations is critical to determining important transitions and designing therapeutics. Accessible conformations are highly constrained by a protein's structure such that concerted structural changes due to external perturbations likely track intrinsic conformational transitions. These transitions can be thought of as paths through a conformational landscape. Crystallographic drug fragment screens are high-throughput perturbation experiments, in which thousands of crystals of a drug target are soaked with small-molecule drug precursors (fragments) and examined for fragment binding, mapping potential drug binding sites on the target protein. Here, we describe an open-source Python package, COLAV (COnformational LAndscape Visualization), to infer conformational landscapes from such large-scale crystallographic perturbation studies. We apply COLAV to drug fragment screens of two medically important systems: protein tyrosine phosphatase 1B (PTP-1B), which regulates insulin signaling, and the SARS CoV-2 Main Protease (MPro). With enough fragment-bound structures, we find that such drug screens also enable detailed mapping of proteins' conformational landscapes.

Titanium: A systematic review of the relationship between crystallographic profile and cell adhesion.

Dental implant surface properties such as roughness, wettability, and porosity ensure cell interaction and tissue integration. The clinical performance of dental implants depends on the crystallographic texture and protein and cell bonds to the substrates, where grain size, orientation, and inclination are parameters responsible for favoring osteoblast adhesion and limiting bacterial adhesion. The lack of consensus on the best crystallographic plan for cell adhesion prompted this systematic review, which aims to answer the following question: "What is the influence of the crystallographic plane on titanium surfaces on cell adhesion?" by evaluating the literature on the crystallographic characteristics of titanium and how these dictate topographical parameters and influence the cell adhesion of devices made from this material. It followed the Preferred Reporting Standards for Systematic Reviews and Meta-Analyses (PRISMA 2020) registered with the Open Science Framework (OSF) (osf.io/xq6kv). The search strategy was based on the PICOS method. It chose in vitro articles that analyzed crystallographic structure correlated with cell adhesion and investigated the microstructure and its effects on cell culture, different crystal orientation distributions, and the influence of crystallinity. The search strategies were applied to the different electronic databases: PubMed, Scopus, Science Direct, Embase, and Google Scholar, and the articles found were attached to the Rayyan digital platform and assessed blindly. The Joanna Bringgs Institute (JBI) tool assessed the risk of bias. A total of 248 articles were found. After removing duplicates, 192 were analyzed by title and abstract. Of these, 18 were selected for detailed reading in their entirety, 9 of which met the eligibility criteria. The included studies presented a low risk of bias. The role of the crystallographic orientation of the exposed faces in a multicrystalline material is little discussed in the scientific literature and its impact is recognized as dictating the topographical characteristics of the material that facilitate cell adhesion.

Crystallographic Pathways to Tailoring Metal-Insulator Transition through Oxygen Transport in VO2.

The metal-insulator (MI) transition of vanadium dioxide (VO2) is effectively modulated by oxygen vacancies, which decrease the transition temperature and insulating resistance. Oxygen vacancies in thin films can be driven by oxygen transport using electrochemical potential. This study delves into the role of crystallographic channels in VO2 in facilitating oxygen transport and the subsequent tuning of electrical properties. A model system is designed with two types of VO2 thin films: (100)- and (001)-oriented, where channels align parallel and perpendicular to the surface, respectively. Growing an oxygen-deficient TiO2 layer on these VO2 films prompted oxygen transport from VO2 to TiO2. Notably, in (001)-VO2 film, where oxygen ions move along the open channels, the oxygen migration deepens the depleted region beyond that in (100)-VO2, leading to more pronounced changes in metal-insulator transition behaviors. The findings emphasize the importance of understanding the intrinsic crystal structure, such as channel pathways, in controlling ionic defects and customizing electrical properties for applications.

Unravelling biochemical and structural features of Bacillus licheniformis GH5 mannanase using site-directed mutagenesis and high-resolution protein crystallography studies.

Glycoside hydrolase family 5 (GH5) encompasses enzymes with several different activities, including endo-1,4-ß-mannosidases. These enzymes are involved in mannan degradation, and have a number of biotechnological applications, such as mannooligosaccharide prebiotics production, stain removal and dyes decolorization, to name a few. Despite the importance of GH5 enzymes, only a few members of subfamily 7 were structurally characterized. In the present work, biochemical and structural characterization of Bacillus licheniformis GH5 mannanase, BlMan5_7 were performed and the enzyme cleavage pattern was analyzed, showing that BlMan5_7 requires at least 5 occupied subsites to perform efficient hydrolysis. Additionally, crystallographic structure at 1.3 Å resolution was determined and mannoheptaose (M7) was docked into the active site to investigate the interactions between substrate and enzyme through molecular dynamic (MD) simulations, revealing the existence of a - 4 subsite, which might explain the generation of mannotetraose (M4) as an enzyme product. Biotechnological application of the enzyme in stain removal was investigated, demonstrating that BlMan5_7 addition to washing solution greatly improves mannan-based stain elimination.

Variations in orientation relationships between rutile inclusions and garnet host relate to magmatic growth zoning.

Rutile inclusions in almandine-spessartine garnet from a peraluminous pegmatoid from the Moldanubian zone (Bohemian Massif, AT) show distinct changes in aspect ratio, shape preferred orientations (SPO) and crystallographic orientation relationships (COR) along the transition between microstructurally different growth zones in the garnet core and rim. For identification of the COR characteristics we pool specific CORs based on their common axial relationship into three COR groups: Group 103R/111G, Group 001R/111G and Group 001R/100G. The rutile inclusions in the garnet core domains are elongated along the four Grt ⟨ 111 ⟩ directions and are dominated by COR Group 103R/111G. The garnet rim zone additionally contains rutile needles elongated along Grt ⟨ 100 ⟩ . Here, Group 001R/111G and 001R/100G are more abundant than in the garnet core. Needle-shaped rutile in the rim shows a systematic correlation between SPOs and CORs as needles elongated parallel to Grt ⟨ 111 ⟩ are dominated by Group 103R/111G and 001R/111G, whereas those needles elongated parallel to Grt ⟨ 100 ⟩ exclusively pertain to CORs of 001R/100G. Furthermore, the frequency of each particular SPO in the garnet rim clearly depends on the local growth direction of the particular Grt{112} sector. Facet-specific variations in rutile SPO frequencies in different sectors and growth zones of garnet were observed even between equivalent directions, indicating that the microstructures and textures of rutile inclusions reflect varying parameters of garnet growth. The characteristic differences in COR groups of different garnet growth zones are referred to compositional changes in the bulk melt or compositional boundary layer, associated with magmatic fractional crystallisation. Supplementary Information: The online version contains supplementary material available at 10.1007/s00410-024-02146-9.

Destruxin E backbone modification effects on osteoclast Morphology: Synthesis and SAR study of N-Desmethyl and N-Methyl analogs.

The design and synthesis of N-desmethyl and N-methyl destruxin E analogs have been demonstrated. The X-ray single crystal structure of destruxin E (1a) revealed a stable three-dimensional (3D) structure, including a s-cis amide bond at the MeVal-MeAla moiety and two intramolecular hydrogen bonds between NH(ß-Ala) and OC(Ile) and between NH(Ile) and OC(ß-Ala). N-Desmethyl analogs 2a (MeAla â†’ Ala) and 2b (MeVal â†’ Val) were synthesized through macrolactonization similar to our previously reported synthesis of 1a. Conversely, for the synthesis of N-methyl analogs 2c (Ile â†’ MeIle) and 2d (ß-Ala â†’ Meß-Ala), macrolactonization did not proceed; therefore, cyclization precursors 10c and 10d were designed to maintain the intramolecular hydrogen bonds described above during their cyclization. The macrolactamization proceeded despite the presence of a less reactive N-methylamino group at the N-terminus in both cases. Analog 2a, which exhibits multiple conformers in solutions, was inactive at 50 µM, whereas analog 2b, which exhibits a conformation similar to that of 1a in solutions, exhibited morphological changes against osteoclast-like multinuclear cells at 1.6 µM. The activity of the MeIle analog 2c, which cannot take the intramolecular hydrogen bond (Ile)NH•••OC(ß-Ala) in 1a, was markedly diminished compared with that of 1a, and that of the Meß-Ala analog 2d, which cannot take the intramolecular hydrogen bond (ß-Ala)NH•••OC(Ile) in 1a, was further reduced to one-fourth of that of 2c. The overall results indicate that both the s-cis amide bond at the MeVal-MeAla moiety and two intramolecular hydrogen bonds (ß-Ala)NH•••OC(Ile) and (Ile)NH•••OC(ß-Ala) are important for constraining the conformation of the macrocyclic peptide backbone in destruxin E, thereby exhibiting its potent biological activity.