In the realm of high energetic materials, 5-aminotetrazole (H2N–CN4H) is a well-established chemical [1]. In contrast, dodecahydro-closo-dodecaborates are renowned for their exceptional stability within the hydroborate family, owing to their quasi-aromatic high-symmetry structure. Simple salts of [B12H12]2– with alkali and alkaline-earth metals exhibit thermal stability up to around 700 °C....
Scapolites are usually formed under metamorphic conditions in the presence of fluids, but are also reported as constituents of upper mantle xenoliths [1,2]. The scapolite series of minerals represents a complex non-binary solid solution, whose end members are: marialite [Na4Al3Si9O24Cl], meionite [Ca4Al6Si6O24CO3] and silvialite [Ca4Al6Si6O24SO4]. The members whose composition falls on the...
I interpret the title of this microsymposium ‘How to address questions, doubts and struggles of a young crystallographer’ as meaning that young crystallographers are curious, critical and perseverant. Of course, sometimes you get stuck, you can’t find the answers to your questions, you doubt about what you are doing and you struggle to get out of your problems. I don’t know what your...
2,4-diaminopyrimidine antifolate drugs [e.g. pyrimethamine (PYR, Fig. 1a), and trimethoprim(TMP)] are mainly used for the treatment of parasitic diseases, such as toxoplasmosis and malaria. They work by inhibiting plasma dihydrofolate reductase (DHFR). In their protonated form, they inhibit DHFR by generating hydrogen bonds between the aminopyrimidine group and the hydroxyl group of the enzyme...
The Weaver research group are engaged in the synthesis of potential new drugs for the treatment of tropical diseases. As part of this programme, PhD student Yuqi Li first synthesised and characterised the compound shown in Fig. 1. [1] Initial characterisation was via the usual ‘sporting methods’ including 1H NMR spectroscopy. Yuqi was also able to grow some small single crystals with a thin...
So-called 3D electron diffraction (3D ED) approaches [1] have become an alternative for overcoming the size limitations of single-crystal X-ray diffraction. Nevertheless, the literature remains poor on the limits of 3D ED and what can be expected for the analysis of very small crystals. To address this point, we report here our results on the accurate structure analysis of individual...
3D-electron diffraction (3DED) is a powerful technique for solving the structure of nanoparticles using Transmission electron microscopes (TEM). Typically, 3DED is performed in TEM mode on particles with the size of several hundreds of nanometers. However, as the size of the particle or the region of interest decreases further, some complications appear in acquiring ideal 3DED data. First,...
Garnet-supergroup phases are among the most widespread minerals in the Earth, growing in rocks with composition from ultra-mafic to felsic (e.g. mantle peridotites, metamorphic rocks and granulites) and occurring as detrital minerals in sediments. Their broad P-T stability field (T up to 2000 °C and P ⁓25 GPa) allows garnet crystallization from the Crust to the deep Mantle, at depths...
One of the most mysterious and fascinating animal species to have ever lived on Earth were dinosaurs. The proof of their existence can be found in the fossils that have been discovered all across the world. A thorough structural and morphological investigation of several dinosaur eggshells from 70 million years ago is presented in this work. These ancient dinosaur eggshells from the Late...
1Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (CNR-ICCOM),
2Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi (CNR-ISC)
andrea.ienco@cnr.it
Robotics in education is a powerful tool for presenting scientific concepts as well as for building interdisciplinary activities for high school students in STEM. [1-2] Crystallography is only...
The simple hydrolysis of the amide group at the side chain of L-asparagine, leading to L-aspartate and ammonia, has at least three enzymatic solutions in the living organisms, catalyzed by enzymes classified in three structural Classes and five types. Class 1 L-asparaginases, formerly known as bacterial-type (a misnomer, as representatives are found in all domains of life), have been...
Obtaining diffraction-quality crystals is the rate-limiting step in biological macromolecular X-ray crystallography. Here, an innovative approach that increases the yield of useful protein crystals is presented. The approach is based on the preparation of a mixture that integrates a multitude of different protein crystal fragments. The fragments represent a heterogeneous set of nanotemplates...
Interacting proteins usually bind 5-6 base pairs of DNA. We looked at distributions of 5/6-mer DNA motifs, in whole chromosomes and in smaller sections, across the whole genome to get insights into how proteins read genomic sequences. The distribution of motifs in the genome is non-random as established by their observed to expected (OE) ratios at all examined length scales. We correlated the...
Fragment-based drug discovery (FBDD) [1] is now a widely used technique for developing potent and selective small-molecule binders to macromolecular targets. FBDD comprises probing the molecular surface of macromolecules with a library of low-molecular weight ligands to characterise protein-ligand interactions. This information is exploited throughout the drug development cycle to inform...
The presence of disorder in MOFs is a field of growing importance, with a profound impact on their pore networks [1,2]. Correlations in this disorder cannot be measured by traditional crystallography, requiring local probes such as diffuse scattering [3,4]. We report the recent synthesis and characterization of a dysprosium MOF, which contains both disordered nodes and linkers. This disorder...
Multifunctional materials combine in a single high tuneable system a set of different remarkable properties, controllable by distinct stimuli. Owing the strong structure/properties interplay in these materials, a detailed structural study is a prerequisite to shed light on the miscrosopic origin of their properties and design strategies to optimize their functionalities. To this purpose, it is...
Museo di Cristallochimica, Università di Parma
Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Parco Area delle Scienze 17/A, 43124 Parma, Italy
alessia.bacchi@unipr.it
We all remember the sheer excitement of our first experience in seeing and being able to rotate molecules on a screen, the curiosity to explore molecular architectures, the beauty of the...
Chiral MOF materials are being intensively studied for specific applications such as chiral recognition, separation and catalysis. One of the main challenges of their preparation is to find suitable chiral linkers with proper size and rigidity. Spiranes are aliphatic molecules that contain at least two rings with only one common atom. This structure gives these twisted molecules exceptional...
Diamond anvil cells (DAC) are the primary pressure cell design that has dominated high pressure science when kbar pressures are required. They have made data collection (both single-crystal and powder) routine; however, they are not without their limitations. Fine control of pressure is difficult to achieve and measure accurately, particularly at lower pressures (> 1kbar) where in softer...
Mechanochemical synthesis is emerging as one of the most interesting routes to obtain crystalline materials. As of today, it is abundantly clear that this method can often replace solution-based approaches thanks to its minimal to no solvent use and generally mild conditions. At the same time mechanochemical strategies, due to being relatively unexplored, can often lead to reaction products...
A novel mechanism of bacterial transcription initiation under HelD-mediated protection
J. Dohnálek1, T. Kovaľ1, N. Borah2,3, P. Sudzinová2, B. Brezovská2, H. Šanderová2, A. Křenková4, M. Hubálek4, M. Trundová1, K. Adámková1, J. Dušková1, M. Schwarz2, J. Wiedermannová2, L. Krásný2, T. Kouba4
1Institute of Biotechnology AS CR, Průmyslová 595, 25250 Vestec, Czech Republic, 2Institute of...
The prediction of the phase behaviour of a mixture of solid components when the materials come into contact is attracting a high interest in fastly growing research fields such mechanochemistry (MC) and deep eutectic solvents (DES). In MC processes, reactions implying breaking and forming covalent bonds or supramolecular aggregation occur by grinding dry components together; the mechanism of...
Intermetallic antimonides containing rare-earth (RE) and transition (TM) metals show a large variety of compositions and crystal structures. A representative group of such antimonides are compounds of the composition RE TM Sb3.
Single crystals of these compounds can be grown in multiple ways. In this study, we used a Bi flux synthesis followed by hot centrifugation, which gives access...
It is often considered that the birth of quantum chemistry coincides with that of the Schrödinger equation in 1925-1926[1]. This possibility of predicting the wavefunction paved the way to calculating the quantum expectation value of a range of measurable properties in atoms, molecules, and crystals. Nevertheless, it quickly became apparent that an N electron wave-function often contained more...
In crystallographic diffraction experiments, outlier reflection intensities occur as a result of unaccounted-for or partially masked beamstop shadows and are a known issue in both manual and automatic data reduction [1,2]. Traditional statistical diagnostics have only limited effectiveness in identifying these outliers, termed Not-Excluded-unMasked-Outliers (NEMOs). The diagnostic tool AUSPEX...
A seventh blind test of crystal structure prediction methods
L. M. Hunnisett1, J. Nyman1, N. Francia1, G. Sadiq1, I. Sugden1, J. Cole1
1 The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK
lhunnisett@ccdc.cam.ac.uk
Crystal Structure Prediction (CSP) – generating and ranking plausible crystal structures from a chemical diagram – is a rapidly evolving field,...
Zeolite molecular sieves with at least eight-membered rings are widely applied in industrial applications, while zeolite crystals with six-membered rings are normally regarded as useless products due to the occupancy of the organic templates and/or inorganic cation in the micropores that could not be removed. Herein, we showed that a novel six-membered ring molecular sieve (ZJM-9) with fully...
We demonstrate from first-principles calculations and symmetry analysis that a structural phase transition from an achiral to a chiral crystalline phase can be mediated by a soft phonon mode. This possibility is illustrated in the case of the K3NiO2 crystal, where an unstable and doubly degenerate zone boundary phonon mode is shown to lower the symmetry to a pair of enantiomorphic space...
Abstract for a poster
The CrystalGraphAnalyzer [1] is a script designed to analyze the structural features of crystalline materials and identify low-dimensional substructures. The CrystalGraphAnalyzer takes cif file as input and initiates the analysis by constructing a graph representation of the crystal structure by computing the interatomic connectivity using the Voronoi algorithm. The constructed graph, referred...
The Cambridge Structural Database (CSD) [1], the crystallographic database for organic and metal-organic molecules, now contains over 1.25 million crystal structures. This wealth of data makes it an invaluable resource both in research and in education, both in crystallography and chemistry as well as other subjects.
In this poster, we will focus on resources and activities from the...
Magnetic systems play an essential role in modern life, serving as the foundation for the advancements of technology ranging from electric engines to data storage systems. This fundamental dependency motivates the exploration for materials that demonstrate beneficial and unique magnetic properties. While there are several magnetic materials that are well-established, i.e. inorganic magnets...
Powder X-ray diffraction is a widely used technique, but almost always using relative intensities. Even when extracting the absolute content of a specific crystalline component in a complex sample, typically a reference is used [1]. For neutron powder diffraction, some attempts for absolute intensity measurements have been made [2]. Modern photon-counting detectors facilitate the use of...
X-ray crystallography is a very powerful method for the determination of the absolute structure of compounds that contain elements heavier than oxygen [1, 2]. For all other compounds, absolute structure determination becomes more challenging and sometimes authors revert to chemical derivatisation [3], though this also can fail, e. g. in the case of tertiary alcohols [4]. Additionally, the...
Every academic career is different, just as different as every researcher is. After one year as professor at a German university of applied sciences, I will try to give a very personal witness report of my way to secure an academic position and reflect on some of the joys, but also of the difficulties I met in the last year.
As much as the individuals, university systems in the different...
A. Meents1, M. Hachmann1, V. Hennicke1, P.Y. Reinke1, P.B. Klar2, K. Floettmann1
1Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany, 2Faculty of Geosciences, University of Bremen, 28359 Bremen, Germany
alke.meents@desy.de
Electron diffraction (ED) is an extremely powerful tool for 3D structure determination of crystalline materials like 2D-layered transition...
The recent SARS-CoV-2 pandemic caught us unprepared for a global health emergency. Structure-based drug discovery, while often effective for identifying new drugs, wouldn't have been suitable in such a situation due to the lengthy timeline from hit identification to a drug reaching the market. A valid alternative is repurposing drug discovery. Using a high-throughput screening (HTS), among a...
Many of the compounds in the solid state can exist in a form of different polymorphs, which differ by the arrangement of the molecules or ions in the crystal structure. As polymorphs are different phases, they differ in various properties such as melting point, solubility, stability, etc. Polymorphs can exist both in single-component as well as in multi-component systems, including co-crystals...
In our research group, we focus on improving the analysis of large protein complexes using electron diffraction. Our aim is to achieve higher resolution for flexible proteins, surpassing the limitations of current methods. We believe that electron diffraction holds great promise based on previous results and fundamental principles.
One major challenge we face is the vast amount of data...
Proteins, as highly dynamic macromolecules, adopt specific conformations to perform biological functions. Understanding these conformations is vital for elucidating disease mechanisms. Factors influencing protein structural states include experimental techniques, ligand presence, oligomeric state, and experimental conditions. AI-based computational methods, like AlphaFold[1] and ESMFold[2],...
In recent years, we have seen remarkable progress in the field of 3D Electron Diffraction (3D ED). These improvements encompass various aspects, including instrumentation, data collection strategies, mitigation of radiation damage, data processing, handling of dynamical scattering, and refinement. During the refinement stage, it seems to be essential to use appropriate atomic scattering...
Serial crystallography (SX) has emerged as a leading technique for protein structure determination and studies of protein dynamics at room temperature. Due to the small changes that must be resolved, successful SX data collection necessitates an optimized experimental setup. Among the various sample delivery approaches for synchrotron-based SX (SSX), the fixed target method is particularly...
Structural biology is key to understanding basic processes of life and a major driver for the development of new therapies. However, these structures are merely models which interprete and explain the observed experimental data according to a priori knowledge. Consequently, our structures are only as good as our limited understanding of the underlying principles.
Machine learning methods, in...
NAD(P)H is one of the most important molecules for cell physiology since it is used by a wide variety of proteins as cofactor. As such, the homeostasis of this cofactor must be tightly regulated by the cell, in particular the equilibrium between oxidized and reduced form. Alcohol dehydrogenases (ADHs) are enzymes that can use either NAD+ or NADP+ as a coenzyme whereas others can use both. For...
The recent surge in accuracy of predicted protein structures, particularly those generated by AlphaFold, offers a glimmer of hope in bridging the ever-growing gap between known protein sequences and experimentally determined structures. This newfound potential has not gone unnoticed by the structural biology community, with researchers swiftly recognizing the ability of AlphaFold predictions...
In scattering experiments, phonons manifest themselves as Thermal Diffuse Scattering (TDS). Recent research has focused on phonons due to their role in various properties. This includes interactions like phonon-electron coupling in superconductivity and phonon-spin coupling, which finds application in spintronics, among other significant interactions. Understanding phonons and detecting phonon...
TREX1(Three prime Repair Exonuclease 1) and TREX 2 are the most abundant 3ˈ to 5ˈ exonucleases in mammalian cells and are involved in various DNA metabolism progresses [1, 2]. Dysfunctional TREX1 leads to various autoimmune diseases with accumulation of endogenous ssDNA, dsDNA, and DNA/RNA hybrids in the cytoplasm that trigger immune activation through the cGAS-STING pathway. Although...
Helicases are essential and ubiquitous enzymes, playing a key role in a variety of cellular processes, from DNA replication to repair, recombination, as well as RNA translation and transport. Due to their important role in viruses, bacteria and eukaryotic cells, they are emerging as a new class of antibacterial, antiviral and ant-cancer drug targets. A subset of helicases play specialised...
The anharmonic effects in the description of the atomic/molecular vibrations in the crystal are crucial when predicting various properties of a material from experimental charge density analysis, through precise IR or Raman spectra to thermodynamic characteristics including relative polymorph stability. The presence of vibrations with a non-negligible anharmonic component are one of the major...
With the advent of 3D Electron diffraction (3D ED) data acquisition and processing techniques, electron crystallography has emerged
as a powerful technique for accurate structure solutions and refinements at the atomic level [1]. In data processing of 3D ED data, the
reflection intensities obtained from each frame must be corrected for experimental effects and one of the methods to achieve...
Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy used to determine atomic structures from small crystals. It enables the study of diverse targets such as proteins, polypeptides, and organic compounds, which may exist in aqueous solutions, organic solvents, or as dried powders. Our group has been involved in developing...
ToposPro[1] since 2014 has been used by many MOFs chemists around the world to deconstruct MOFs into underlying nets [2]. Accurate data about MOFs topologies is the base for machine-assisted search for complex reticular correlations and design of new functional materials. We will introduce latest tools that include the database of underlying nets TTD (accessible via TopCryst) [3], the...
I do not what is needed for this field. Abstract is attached (see below).
Over the recent years, our knowledge of the synthesis and the reactivity of metal-organic “modular” materials has grown at a rapid pace, blending organic, inorganic, and physical chemistry together. A rational approach to material design requires the systematic efforts of both experimental and theoretical chemists to understand how a material is formed from the constituents (atoms or...
Since the early beginning of the history of X-ray diffraction it was clear that to describe properly experimental results, thermal motion need to be modelled simultaneously with electron density. Peter Debye proposed to model thermal motion using a temperature factor, which is considered by the refinement of anisotropic displacement parameters (ADPs). This approach had not changed much during...
The design of efficient, low temperature solid oxide fuel cells is necessary to achieve carbon free energy generation and relies on oxide ion conductors to act as the electrolytes. Commercially available fuel cells use yttria-stabilized zirconia and gadolinium-doped ceria as electrolytes which have desirable conductivities, however, require operating temperatures between 700 °C and 1000 °C,...
Many different applications of resonant scattering or anomalous dispersion have been reported in recent decades. When determining the X-ray structure of small molecules in single crystals, it is usually only used to distinguish the absolute structure. To this day, almost exclusively tabulated values are used for the correction of anomalous dispersion, and the accuracy of these thirty-year-old...
Magnetoelectric materials, capable of manifesting a coupling between magnetic and electric properties at the static level, may offer the potential for manipulating one through the other via the application of external magnetic or electric fields. This coupling is symmetry dependent, with the analysis of the material's magnetic space group providing insight into how the coupling will manifest...
The phenomenon of structure modulation is relatively well understood in small-molecule crystallography, but its occurrence in macromolecular protein crystals has been surprising. As a result of modulation, the translational symmetry of the crystal is disrupted in three-dimensional space, and the periodicity of the structure is restored only in higher dimensions. This requires specialized...
The halogen substituted anilines (Fig.1) are key structural blocks of bioactive products, medically important compounds and organic functional materials. Therefore, the study of molecular and crystal structure of such a type of compounds has an immense importance.All modern approaches to the molecular crystal structure analysis base on the comparison of the geometric characteristics of...
Insulin is a well-known and extensively studied hormone consisting of two peptide chains, the A-chain (21 amino acid residues) and the B-chain (30 amino acid residues). These chains are connected by two disulfide bridges and furthermore the A-chain contains an intrachain disulfide bond. In humans, insulin is produced in the beta cells of the pancreatic islets of Langerhans, with a...
Periodic material or crystal property prediction using machine learning has grown popular in recent years as it provides a computationally efficient replacement for classical simulation methods. A crucial first step for any of these algorithms is the representation used for a periodic crystal. While similar objects like molecules and proteins have a finite number of atoms and their...
Electron diffraction experiments, such as 3D electron diffraction (3D ED) and 4D-STEM, provide structural information on materials at the atomic level. The new dedicated scanning transmission electron diffraction microscope TESCAN TENSOR provides rapid 4D-STEM acquisition and processing that can be uniquely combined with precession-assisted 3D ED tomography to obtain and characterize...
There is an increasing urgency to make science more accessible and inclusive as a way of increasing the scientific literacy of the overall population. Article 27 of the Universal Declaration of Human Rights (UDHR) says EVERYONE has the right freely to participate in the cultural life of the community, to enjoy the arts and to share in scientific advancement and its benefits [1] The Convention...
Since the 2010s, three-dimensional electron diffraction (3D ED) has been developed for the structure determination of micro- to nano-meter sized crystals. During the same period, synchrotron X-rays have also used to determine the structure of undersized crystals. Serial femtosecond X-ray crystallography, SX or SFX, with pulses generated by free electron lasers (FELs), is a particularly...
The proposed talk will relate to the study of cultural and natural heritage materials carried out at the SOLEIL synchrotron, where a dedicated scientific section named Cultural Heritage promotes research activities in this field. It aims at the optimization of methodological research and development of synchrotron-based techniques to maintain state-of-the-art experimental setups for the study...
The interactions of aromatic systems are important in crystal form analysis and design, directing and informing properties of the crystalline solid state.[1] In presenting a new Aromatics Analyser (AA2),[2-3] we’ll show how one can quantify these interactions across many heterocycle rings and interaction types, with a simple visualiser in Mercury and a notebook interface with the CSD Python...
It is well know that electron interact with matter through the electrostatic
potential. In principle, the map resulting from electron diffraction experiments
displays the electrostatic potential of the crystalline molecule. For minerals,
this fact was demonstrated in the 1990s, pioneered by Spence et al with the
development of converged beam electron diffraction (CBED). The rise of 3D ED...
Quasicrystals, solids with rotational symmetries forbidden for crystals, are usually synthesized in the laboratory by mixing specific ratios of selected elemental components in the liquid and quenching under strictly controlled protocols. However, the discovery of natural quasicrystals in the Khatyrka meteorite [1,2] showed that these unusual phases could also form in high-velocity...
Advancements in accurate structure refinement from three-dimensional electron diffraction (3D ED) have increased the method's popularity, especially when dealing with very small crystals[1]. However, better approaches have to be developed to extract information on atomic interaction, and charge transfer to fully leverage the advantages of the 3D ED method in the field of material science for...
MicroED enables structures from sub-micro-meter sized crystals and forms a niche complementary to X-ray Crystallography, NMR as well as to CryoEM. By combining MicroED and automation, which enables data collection of thousands of crystals, more of the intrinsically difficult samples can be analyzed. From the selection of thousands of data sets, a few coherent data sets can be found and the...
Three-Dimensional Electron Diffraction (3DED) is an emerging and useful technique for solving molecular structures of small and biological macromolecules from nanometre-sized crystals. We present our automated data processing workflow for 3DED datasets collected at Diamond Light Source's Electron Bio-Imaging Centre. The processing pipeline includes data collection, data analysis, metadata...
There is so much automation all around us, and our daily lives rely heavily on it, but we rarely stop and think about it (mostly only when it goes wrong!).
When driving a car, we take for granted that it ‘just works’. We concentrate on navigating the vehicle from A to B safely. The car ‘just working’ results from many decades of advances in engineering and a great deal of automation.
The...
Several transition metal chalcogenides, boasting diverse structural types like rutile, perovskite, and rocksalt, have exhibited promising thermoelectric properties [1]. Thus, Ba1-pCr2Se4-p selenides [2] have garnered significant attention. Within this family of materials, the crystal structure manifests as an intergrowth of three distinct structural units, sharing a common hexagonal basal...
Barium-cobaltate-based perovskites (BaCoO₃-δ) and barium-cobaltate-based nanocomposites have been extensively studied for energy storage and conversion devices due to their flexible oxygen stoichiometry and tunable oxidation states of non-precious transition metals. Despite a wide array of structural polymorphs reported for these perovskites, the potential structural changes during the oxygen...
The spread of antimicrobial resistance (AMR) might be one of the world’s health biggest problems, jeopardizing the treatment of infections worldwide. Alarming levels of drug resistance have been reported worldwide, with the result that common infectious diseases are becoming untreatable. The bacterial cell wall is an essential gigantic macromolecule that defines the shape of the bacterium and...
Antimicrobial resistant bacteria pose a significant threat to human health. Gram-negative bacteria are particularly difficult to treat with antimicrobials, partly due to the nature of the cell envelope, which consists of an inner and outer membrane, separated by an aqueous periplasm. In particular, the outer membrane of Gram-negative bacteria acts as a physical barrier against antimicrobials....
Bad metal behaviour [1,2] describes the unusual nonlinear dependency of a high specific resistivity of a metallic material with temperature. This feature is important e.g. for the decoupling of thermal and electrical conductivity, a key point for high-efficiency thermoelectrics. Also, giant magnetoresistance is coupled with bad metal behaviour. Despite the high interest in bad metals, concepts...
Understanding structural dynamics and supramolecular assemblies in cocrystals represents a central pursuit in crystallography, spurring the proliferation of screening efforts. This study explores the intermolecular interactions within cocrystals formed by liquid assisted grinding of hydroxybenzoic acids and cyclic amides, focusing on 3-hydroxybenzoic acid (3HBA), 2-hydroxybenzoic acid (2HBA),...
Mechanochemical methods offer a greener alternative to chemical and materials processing. However, these methods are also seen as being 'brute force' methods with little opportunity to fine-tune the outcome. This view has caused many to overlook the potential of mechanochemical technologies with concern over reproducibility, reaction design, and reaction control. This view is the consequence...
3D electron diffraction (ED) is well established as a method for crystal structure analysis of submicron to nanometre crystals, with continuous rotation 3D ED being the predominant experimental protocol [1-2]. This kind of data is mostly used for structure solution and structure model refinement within the kinematical approximation, assuming that electrons are only scattered once. However, ED...
Nowadays, scientists have to work on more and more complicated materials. Description of crystal structures in terms of average structure as obtained from Bragg diffraction data analysis is no longer enough to understand material properties. Pair Distraction Function (PDF) is its natural extension and allows us to look deeper into the real (= both local and average) structure of materials....
A big discussion in the atomic pair distribution function (PDF) community seems to revolve around "big box" vs "small box" modeling. In this framing, a big box is a structural model that contains many thousands of atoms and typically uses a stochastic regression algorithm such as simulated annealing, and "small box" modeling has a greatly reduced number of atoms in the box, similar to...
Glutamate dehydrogenase (GDH) catalyses the reversible oxidative deamination of L-glutamate to produce α-ketoglutarate in all living organisms. Saccharomyces cerevisiae expresses two NADP-specific GDHs: ScGDH1 and ScGDH3. Although these enzymes share 89% sequence identity, ScGDH3 shows pH-dependent cooperativity towards the substrate α-ketoglutarate, whereas the isoenzyme ScGDH1 exhibits...
In the past ten years, biological piezoelectric materials have emerged as the potential next generation of cost-effective, green electromechanical sensors [1, 2]. The piezoelectric voltages produced under an applied force are inversely proportional to the dielectric constant of the material and so even ‘weak’ organic piezoelectrics (with modest piezoelectric constants compared to inorganic...
‘Disordered’ rock salt (DRS) cathodes have attracted considerable attention because of their high first charge capacities with ‘extra’ contributions beyond the transition metal redox activity, and absence of unfavourable phase transformations during cycling. Here we investigate the structure and charge evolution of the several nanostructured Li-excess 〖Li〗(1+x) 〖Mn〗(1-3x)^(3+)...
Nowadays the amount of XRD data to be analysed is drastically increasing by faster and more powerful Lab- as well as Synchrotron equipment. Additionally, the “depth” and complexity of structural analysis is increasing. In the past only well-ordered crystalline materials were deemed worth of analysis, for example by the Rietveld [1] method. Currently analysis shifts more and more to samples and...
Explore nanomaterials that expose protein portions as a new type of nucleant for different proteins crystallization.
The MetalJet X-ray source provides In Kα radiation for in-house diffraction experiments.[1] It has been demonstrated that diffraction setups utilizing In Kα radiation are suitable to collect high quality high-resolution data for experimental electron density investigations.[2] We have now used this setup to collect data on two isomers of dichloro closo-dicarbadodecaboranes. The data were...
Starting from the long-known hexagonal zincides CaZn$_{3+\textit{x}}$ [1] and CaZn$_{5+\textit{x}}$ [2] a small Zn$\leftrightarrow$Cd substitution leads to ternary variants of these partly disordered border compounds. Similar to the border phase 'CaZn3', the ternary derivative Ca$_3$$M$$_8$[Ca]$_\textit{x}$][Zn$_3$]$_{1−\textit{x}}$ [$x=\frac{1}{3}$; hexagonal, space group $P6_3/mmc$,...
With the advent of new and bright light sources, the appetite for extremely focused beams has grown, and is leading to the development of new and exciting capabilities for MX beamlines. Diamond Light Source, the UK National Synchrotron, has embraced this challenge by providing a suite of 7 MX instruments [1], and a number of ancillary laboratories for sample preparation and complementary...
In this day and age single crystal small molecule crystallography has become a household technique in most chemistry departments and crystal structure databases like the CSD reflect this development through a nearly exponential growth of new entries. Several factors have contributed to this increase: Better instrumentation, faster and more powerful computers and user friendly software....
While the elucidation of regulatory mechanisms of folded proteins is facilitated due to their amenability to high-resolution structural characterization, investigation of these mechanisms in disordered proteins is more challenging due to their structural heterogeneity, which can be captured by a variety of biophysical approaches. Here, we used the transcriptional master corepressor CtBP, which...
Controlling different external stimuli to tune the photophysical properties of purely organic molecular crystals toward designing multifunctional materials remains a challenge. Over the years, pyrene-based fluorophores owing to their high charge carrier mobility, complex photoelectronic characteristics in the excited state, and high fluorescence quantum yield, have come up as an attractive...
Please find my oral presentation attached
High pressure is a great tool to be used for studying the crystallographic properties of molecular materials, which has developed remarkably in the past few decades and becomes a well-established technique to be widely applied [1]. And thanks to the invention and developments of the diamond anvil cell (DAC) (Fig. 1) in the 1950-60s [2-4], the generation of high static pressures in the...
Structure models are crucial for the deeper understanding of properties of all sorts of crystalline materials and are usually derived by X-ray diffraction (XRD) methods. Due to the limits of single-crystal XRD experiments however, it becomes increasingly difficult to analyse crystals below the submicrometric border. On the other side, electron diffraction (ED) can be performed on much smaller...
Constraining the size, shape and dimensionality of inorganic structures can lead to enhanced optical, electronic, magnetic, and catalytic properties.[1] One synthetic approach is to grow metal halide nanostructures inside single crystal MOFs.[2] Understanding the links between synthesis and the resulting structures, including how they are arranged on a local scale, is vital for establishing...
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Piezoelectric materials are utilized in various applications, including ultrasonic transducers, sensors, actuators, and frequency generators. The extrinsic contribution from the domain wall motions plays an essential role in the piezoelectric effect. However, the detailed understanding of the domain-wall mechanisms still needs to be improved and expanded, especially for the complex coexistence...
Compounds with phase transition characters are possible to prepare materials with controllable properties for application of nanotechnology nowadays. Among of them, spin-crossover (SCO) compounds represent a class of switchable coordination complexes which can change their electronic configurations between low spin (LS) and high spin (HS) states by different stimuli such as temperature, light,...
Intermetallic compounds with the BaAl4 structure type have attracted a lot of attention for their properties as topological quantum materials. The compounds R(Al1-xGax)4 (where R= Eu, Sr) have a tetragonal crystal structure with space group I4/mmm at room temperature[1]. The temperature dependence of electrical resistivity of these compounds suggests the formation of a charge density wave...
The BaAl4 structure type has tetragonal symmetry I4/mmm with three crystallographically independent atom sites. Several solid solution series RAl4-xGax (R = Eu, Sr, Ca, Ba; 0 < x < 4) crystallize in this structure type [1], where Ga preferably occupies one of the two independent Al sites. Accordingly, complete chemical order is found for x = 0, 2, 4. Incommensurate charge-density waves (CDWs)...
π-hole interactions involving metal-bound electron donor are studied for the first time on four isomorphous co-crystals of [Cu(terpy)ClX] (terpy = 2,2′:6′,2′′-terpyridine; X = Br, I) and perhalogenquinone X'4Q (X' = Cl, Br). Close contact between the halide X from [Cu(terpy)ClX] and the quinoid ring (Fig. 1a) has geometry similar to those observed previously for free halides [1,2]. This is an...
Chirality is an intrinsic property of the matter and is important in chemistry, biology, and physics, because it can affect the properties and reactivity of molecules. Coordination metal complexes which combine chirality with magnetic, optical, and electrical properties, have found great attention in recent years and constitute a new and fast-growing class of multifunctional molecular...
Access to chiral compounds is a crucial fundamental technology in industry, and among various methods, crystallization-based chiral resolution is an economically advantageous approach suitable for mass production. Classical methods such as preferential crystallization, diastereomer method, and the deracemization all require crystal structures where the desired isomer is contained in a single...
Ferroelectric materials have many applications in the electronics industry from capacitors to data-storage. These require a polar point group which can be preferentially selected by using chiral substituents. Ferroelectrics undergo a phase transition upon heating to a paraelectric phase which can be of the order-disorder type, whereby the molecular substituents become disordered at high...
The interaction of members of the transcription factor family myocyte enhancer factor 2 (MEF2) with class IIa histone deacetylases (HDAC) has been implicated in a wide variety of diseases. Although considerable knowledge on this topic has been accumulated over the years, a high-resolution and detailed analysis of the binding mode of multiple class IIa HDAC derived peptides with MEF2D was still...
The neodymium(III) oxidoantimonate(III) chloride NdSb2O4Cl is accessible from solid-state reactions of Sb2O3 with Nd2O3 and NdCl3 at 750 °C for two days. It crystallizes like SmSb2O4Cl and EuSb2O4Cl[1] in the centrosymmetric tetragonal space group P4/ncc with the lattice parameters a = 793.85(4) pm and c = 1767.56(12) pm (c/a = 2.227) with Z = 8 (CSD number: 2350399). Thus it can also be...
During the International Year of Crystallography, in 2014, Uruguay held the first National Crystal Growing Competition (CNCC, for Concurso Nacional de Crecimiento de Cristales). It was organized by an interdisciplinary team of professors, students and outreach officers grouped at Facultad de Química and Centro Universitario Regional Este of Universidad de la República. The main goal, aligned...
The object of the present work is the detection of binding interactions and co-crystallization of palindromic DNA sequences from promoter regions of genes responsible for the development of neurodegenerative diseases with fluorescent markers and new/modified ligands.
Neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's disease (AD) are progressive diseases that lead to serious...
It is known that metal nanoparticles (NPs) can undergo surface and/or structural rearrangements in the presence of adsorbates, and this has relevance both in catalysis and in the field of NPs characterization. A typical example is the structural rearrangement of Pd NPs in the presence of CO, which has been reported to occur mostly at elevated temperature (e.g. during CO oxidation reaction)...
In the attachment
Molecules that change their colour, structure, and electronic properties in response to an external stimulus represent an emerging class of ‘smart’ material with potential applications in sensing, actuating and cooling technologies. The spin crossover (SCO) phenomenon leads to a redistribution of electrons within the d-orbitals of some transition metal complexes as a result of an external...
AA lot of meteorites and rocks transformed by meteorite impacts exhibit a crystalline texture that goes well beyond the usual limit for standard analysis in an SEM. For the study of these textures and the determination of the crystalline phases present in the sample, a technique with a spatial resolution in the nanometer range is required. At the same time the sample should be studied avoiding...
Mechanochemistry finds application in the synthesis of new organic and metal-organic materials such as molecular crystals, salts, cocrystals and polymeric structures. This method allows the formation of products, polymorphs and topologies different from those obtained in solution. However, the structural characterisation of the obtained products is one of the main challenges related to this...
3D-Electron Diffraction (3D-ED) has captured the attention of many within the pharmaceutical industry due to the ability to determine crystal structures from sub-micron crystals [1]. Here, we combine 3D-ED with low dose Scanning Electron Diffraction (SED) to elucidate the crystal structure and unveil crystal defects from nanocrystals of cabotegravir (GSK1265744), a potent integrase strand...
In the past years, mechanochemistry has been proved to be an environmentally friendly strategy for the preparation of organic and metal−organic materials, spanning from molecular crystals to framework structures. Typically, this synthetic method reduces the use of solvents, while minimising energy consumption and chemical waste.[1,2] However, the structural characterization of new materials...
In recent years, computer modelling and simulations become more and more indispensable in scientific research, as an alternative or a complementary method to the experimental one. In particular, ab initio Molecular Dynamics (AIMD), based on Hartree-Fock (HF) or Density Functional Theory (DFT), has become established since its early days as an important tool for simulations of an increasingly...
Nucleotides are one of the most important low-molecular-weight organic compounds in biochemistry. Their multi-functionality (nucleic acids biosynthesis, cellular energy transformations, signal transduction processes [1-3]) provided the basis for many of today's antiviral and anticancer drugs, which are their synthetic analogues [4,5]. These systems are still poorly understood from a structural...
The Cambridge Structural Database (CSD) [1] is the most comprehensive collection of information on the crystal structures of organic compounds. In addition to crystallographic data, CSD records may contain supplementary information about the shape of the crystals, the conditions for their preparation or their properties. The melting points of the crystals and their colors are indicated...
Computational Crystal Structure Prediction (CSP) methods have evolved over the past few decades from studying small rigid molecules to being able to predict polymorphs of molecules of increasing molecular size and conformational complexity, attracting the interests of pharmaceutical and functional materials companies [1]. This is reflected in the targets for the recent 7th CSP Blind Test,...
Ferrocene (FeCp2), [1] ruthenocene (RuCp2) [2] and osmocene (OsCp2) [3] are the only known simple metallocenes, which crystallize in orthorhombic system with eclipsed conformation of cyclopentadienyl rings. The structures at 0.1 MPa/ 296 K of RuCp2 (α-RuCp2) and OsCp2 (α-OsCp2) and low-temperature phase of FeCp2 are isostructural (space group Pnma) and mostly stabilize by CH‧‧‧π contacts. We...
Manganite perovskites exhibit a plethora of different charge and orbital ordering schemes, all of which control the emergence of various technologically-relevant properties such as metal-insulator transitions, magnetism and colossal magnetoresistance (CMR). La$_{1-\textit{x}}$Ca$_{\textit{x}}$MnO$_{3}$ (LCMO) shows a maximum in the CMR effect, large changes in resistivity under an applied...
The rapid development of 3DED techniques[1] has culminated in dedicated electron diffractometers now being commercially available. The recently established UK National Electron Diffraction Facility aims to harness the significant potential of employing electrons as a radiation source for diffraction experiments to expand the scope for structure determination to crystallites too small for...
In multidisciplinary research, the development of new models for X-ray tools holds potential in application areas such as materials and life sciences. Bridging the different worlds of X-ray diffraction, scattering and imaging overcomes gaps between methods, allowing a holistic approach. The combination of 3D morphological and structural understanding of materials is key to the discovery of...
Engineering of non-expensive alloys with perfect combination of physical properties were always the Holy Grail of materials engineering. Two paths were chosen by our group to achieve this goal: study of ternary systems where new intermetallic phases have been discovered and development of novel multi-component alloys (often called high entropy alloys (HEAs)).
Since structure and properties...
Ongoing research in the area of supramolecular chemistry over more than five decades has demonstrated huge structural versatility and various applications of organic macrocycles [1]. Calixarenes are one of the most extensively studied macrocycles, both in solution and in the solid state, as a result of their straightforward synthesis, well-defined and adaptable cavities, high guest binding...
Symmetry and chirality stand in the heart of numerous natural phenomena. In chemistry, it is frequently perceived as a driving force that controls the shape of molecular structures, defines selection rules for the interaction of light and matter, and determine the mechanisms of change. While perfect symmetry is conceptually appealing, numerous experimental and computational studies show that...
Metal-Organic Frameworks (MOFs), constructed by periodic arranged inorganic nodes and bridging organic ligands, have become one of the largest fields of chemistry for over twenty-eight years. The applications of MOF chemistry reach into numerous areas including climate, environment, energy, water, and health. However, all the excellent properties of MOFs fundamentally rely on their structures....
Organic crystalline particles are widely used as active ingredients (AIs) in several industrial sectors, such as, nutraceutical, pharmaceutical and agrochemical.[1,2] Effective control of crystal properties such as size and shape distribution, polymorphism, chemical purity and stability holds paramount importance, as these properties can significantly impact subsequent downstream processes...
Hydrogen bond is arguably the most famous type of noncovalent interactions. The prototypical system for studying hydrogen bonds is water dimer, and the strongest hydrogen bond between two water molecules has interaction energy of -5.0 kcal/mol [1]. Upon coordination to metals, electrostatic potentials on hydrogen atoms of water become more positive [2], leading to stronger hydrogen bonds of...
A series of mononuclear copper CuLBz, CuLT complexes containing unsymmetrical tetradentate Schiff base ligands were synthesized and fully characterized by conventional spectroscopic techniques. Crystal structure data of CuLT, solved by X-ray diffraction, shows a monoclinic system with Cc space group and Z= 4 molecules per unit cell. The central copper ion adopts a nearly ideal square planar...
Abstract submission for consideration at ECM34, MS1.
High-angular resolution powder diffraction, with well-defined and resolved diffraction peaks, is used generally to obtain high-quality data for complex structure refinements. The ID22 beamline at ESRF has very high angular resolution, arising from the combination of the highly collimated beam from the new EBS ring, wavelength selection via a cryogenically-cooled Si 111 monochromator, and use...
Particle properties are important to a range of formulated product industries such as pharmaceuticals, agrochemicals, and dyes, who expend significant effort in mitigating manufacturing bottlenecks and improving product performance. Particle characteristics impact processes such as flow, compaction, and cohesivity. Shape, size, roughness, and hydrophilicity/hydrophobicity are typical...
The barocaloric effect (BCE) is characterized as a thermal response (variation of temperature or entropy) in solid-state materials induced by external hydrostatic pressure and cooling technologies based on the BCE have emerged as a promising alternative to conventional vapor-compression cooling [1]. Recently, spin crossover (SCO) transitions, where the low spin (LS) and high spin (HS) states...
Synchrotron-based resonant inelastic X-ray scattering (RIXS) and X-ray absorption spectroscopy (XAS) experiments were performed to probe the nature of XY-like spin-glass (SG) focusing on the spin-flip (magnon) excitation and lattice distortion in single-crystal Ni0.4Mn0.6TiO3 (NMTO) close to the spin-glass temperature (TSG). RIXS provides clear evidence of crystal field (d-d) excitations at...
Teaching crystallography requires more than just conveying technical skills; it entails fostering an understanding of the scientific discipline as a whole. Drawing from experiences gained through teaching crystallography classes at the higher education level, and by organizing and teaching at diverse summer school settings globally, this abstract offers strategies to design impactful courses...
The following presents the setup of a structure database used for benchmarking parameters for the Hirshfeld Atom Refinement.
In September 2023, the first Young Crystallographers’ Meeting (YCM1), organized by the French Association of Crystallography (AFC) and the German Society for Crystallography (DGK) gathered 63 participants from all over Europe. During this event, young crystallographers from French laboratories and French young crystallographers from foreign laboratories expressed their desire to found a Young...
Rhodium(III) octahedral complexes with amine and chloride ligands are the most common starting compounds for preparing functional and catalytically active rhodium(I) and rhodium(III) species. Despite intensive study during the last 100 years, synthesis and crystal structures of rhodium(III) complexes were described only sporadically. Some [RhClx(NH3)6-x] compounds are still unknown. In the...
Our recent studies have focused on radical-radical cocrystal formation and this presentation reports recent experimental and computational studies using dithiadiazolyl (DTDA), diselenadiazolyl (DSDA) and TEMPONE radicals. The isolation and characterization of the 2:1 cocrystals, [DTDA]2[TEMPONE] and [DSDA]2[TEMPONE] is described. The relative energetics of DTDA…O-N< vs DTDA…O=C< interactions...
The measurement of diffraction data on single crystals requires professional expertise and highly specialised equipment that may not be available at school. But solving and refining of structures is now also possible for students [1, 2] thanks to simplified graphical user interfaces of the structure determination programs [3, 4]. In courses at the student laboratory and in teacher training...
Coordination polymers (CPs) utilizing the anions of benzenepolycarboxylic acids have received significant attention in crystal engineering due to the ability of these anions to form fascinating metal-organic crystal structures with various dimensionality and numerous applications as functional materials [1].
In our continual synthetic strategy of CPs [2-4], a new ongoing challenge was design...
Crystal structure and hydrogenation properties of the Mg6CoSn ternary compound
N. Pavlyuk1, G. Dmytriv1, V. Pavlyuk1,2, H. Ehrenberg3
1Department of Inorganic Chemistry, Ivan Franko National University of Lviv, Kyryla & Mefodia str. 6, 79005 Lviv, Ukraine,
2Jan Długosz University in Częstochowa, Institute of Chemistry, al. Armii Krajowej 13/15, 42200 Częstochowa, Poland
3Karlsruhe...
Crystal structure and phase transition in orthorhombic FeSO4OH
G. Giester1, D. Talla1, J.M. Meusburger2, J.L. Bishop3, M. Wildner1
1Institut für Mineralogie und Kristallographie, Universität Wien, Josef-Holaubek-Platz 2, A-1090 Wien, Austria
2NASA Ames Research Center, P.O. Box 1 Moffett Field, CA 94035-1000, USA
3SETI Institute, 339 Bernardo Ave, Suite 200, Mountain View, CA 94043,...
In the attachment.
Cannabidiol (CBD), a non-psychoactive compound found in cannabis, has been extensively studied for its potential to alleviate anxiety, chronic pain, inflammation, and epilepsy [1]. Encapsulating CBD in cyclodextrins (CDs) significantly enhances its solubility, stability, and bioavailability. This leads to more consistent and efficient delivery, thereby enhancing its therapeutic efficacy....
Bacteriophages (phages) are viruses that infect prokaryotic hosts. The intense arms race between bacteria and phages have led to the development of sophisticated antiphage defense strategies in bacteria. A number of novel antiphage defense systems have been identified, but few of them are thoroughly characterized at molecular level. Gabija system is an antiphage defense system in over 4000...
Several platinum(II) complexes have been established anticancer metallodrugs for a long time, but due to various side effects as well as acquired resistance of tumor cells, drugs based on other metals with the possibility of acting by other mechanisms are being sought. Due to the many similarities between platinum and palladium, there is considerable interest in studying palladium(II)...
The gram-negative bacterium Legionella pneumophila lives in aquatic freshwater environments as a parasite of free-living amoebae or in the form of biofilms. As accidental pathogen, it may cause life-threatening lung infections in humans. L. pneumophila secretes more than 300 effector proteins into the cytosol of the host cell that modulate numerous cellular pathways to build and to maintain a...
Diketones and their related derivatives represent a significant class of organic compounds due to their ability to coordinate with several transition metal ions and main group metal centers. Additionally, metal complexes with pyrazole ligands have garnered substantial interest because of their unique coordination properties and their relevance in biological and biochemical contexts [1]....
Significant advancements in precise structural analysis using electron diffraction have been made in the past decade, largely attributed to the adoption of 3D electron diffraction (3D ED) methods [1]. In this study, we investigate the constraints linked to the size of crystalline domains and the degree to which we can monitor structural alterations at the nanoscale. For this, we propose an...
Histone deacetylases (HDACs), also known as lysine deacetylases, are enzymes involved in the control of gene expression. They catalyze the removal of acetyl moieties from acetyl-lysine residues in histones and non-histone proteins and the hydrolysis of amides of short and long fatty acids, playing a key role in the regulation of many biological processes, such as cell differentiation,...
The radionuclide technetium-99m, thanks to its ideal physicochemical properties and availability, is the most used radionuclide in clinical practice, for the SPECT imaging (Single Photon Emission Computed Tomography), the first-line imaging modality in nuclear medicine. Recently, the radionuclide 188Re emerged as a very attractive candidate for endoradiotherapy due to its nuclear features.1...
In the ternary systems T–M–M’ (T = Ti, Zr, Hf; M = Al, Ga; M’ = Si, Ge, Sn, Pb, Sb, Bi) in the cross-section T5M3–T5M’3 at 600°C phases with four structure types are observed: Mn5Si3 – A (Pearson symbol hP16, space group P63/mcm), W5Si3 or its ternary ordered variant Nb5SiSn2 – B (tI32, I4/mcm), Yb5Sb3 – C (oP32, Pnma), and Y5Bi3 – D (oP32, Pnma). The closely related structure type Hf5CuSn3 –...
The endeavour to enhance the solubility and stability of essential drugs or vitamins in pharmaceutical and cosmetic contexts has prompted the search for advanced methods in the field of crystal engineering. A lot of valuable research and developed methodologies have recently appeared in this topic, now also supported by machine learning algorithms, but the complexity of crystallization...
There are several routes to produce compounds of single chirality, i.e. enantiopure molecules. Ever since the days of Pasteur, crystallisation has been a very important route. Here we discuss recent, crystallisation-based methods that allow complete deracemization, thus methods in which the unwanted compound is converted into the desired one and that can lead to 100% chiral purity and 100%...
Natural products a rich source of inspiration for the development of new medicines. Natural products and their derivatives have been used to treat a host of diseases and conditions, such as pain management (aspirin and morphine), cancer (paclitaxel and doxorubicin), heart disease (captopril and enalapril) and infection (penicillin and tetracycline).[1, 2] In fact, more than 50 % of small...
The solid form of an active pharmaceutical ingredient (API) is usually governing its material properties such as solubility or tableting characteristics. Several strategies have been put into place to improve solubility as this is often a major issue. Naproxen is a poorly soluble API, but its solubility can be improved by synthetizing corresponding sodium salt. Another alternative to improve...
Klebsiella pneumoniae (Kp) is a sepsis-inducing dangerous nosocomial pathogen, which causes life-threatening infections. Its success is due to an arsenal of tools acquired through multiple resistance mechanisms [1,2]. In this work, we structurally characterised by X-ray Kp-lin, an encapsulin from K. pneumoniae. The crystal structure and the biophysical studies show that Kp-lin is a protein...
Crystallographic and quantum chemical studies of xanthene-1,8(2H)-dione derivatives
L. Radovanović1, A. Lazić1, I. Đorđević2, N. Trišović3, J. Rogan3
1Innovation Centre of the Faculty of Technology and Metallurgy, Karnegijeva 4, Belgrade, Serbia, 2Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia, 3University of Belgrade, Faculty of...
Zinc, known for its non-toxicity and exceptional biocompatibility, with various coordination geometries, is an ideal metal for constructing Metal-Organic Frameworks (MOFs). MOF-5 is a highly representative Zn MOF, which is distinguished by its high specific surface area and thermal stability. However, the application of MOF-5 is significantly limited as it undergoes irreversible degradation...
The Coronavirus Replication/Transcription Complex (RTC) is composed of 7 proteins, in addition to the viral polymerase. One of these proteins is the non-structural protein 14 (nsp14), a bi-functional multi-domain enzyme.
The N-terminal domain of nsp14 is a viral 3'-to-5' exonuclease (ExoN), which enables the correction of errors generated by the polymerase. Its activity is regulated by the...
The achiral ionic salts, NaClO3 and NaBrO3, readily form large cubic crystals from aqueous solution in the chiral space group P213. Isomorphous crystals of these salts which have the same absolute configuration rotate polarised light in opposite directions. For most undergraduate students, this is counterintuitive. Generally, the only exposure undergraduate students have to chirality is in...
Georg-August-University Göttingen, XLAB – Experimental Laboratory for young people,
Justus-von-Liebig-Weg 8, D-37077 Göttingen, Germany
erhard.irmer@chemie.uni-goettingen.de
Although the method of crystal structure analysis and working with its results offer many possible applications in chemistry, physics or biology lessons, this topic is very rarely found in school classes. From the...
Presence of K-rich carbonatitic melts in upper mantle and discovery of dense K-Ca carbonates as mineral inclusions in diamonds [1] demonstrated the rising importance of understanding the role of potassium within our planetary deep carbon cycle. Within the K2CO3-CaCO3 system [2], there are two selected phases, i.e. K2Ca(CO3)2 and K2Ca2(CO3)3 of which structural polymorphism was investigated...
People’s curiosity about crystals and the beautiful science of crystallography means there is an exciting opportunity for creative outreach. The types of outreach activities available can be broadly classified into three models: Deficit, Dialogue and Participatory. There has been a shift away from deficit model in public engagement, where the public are perceived to be deficient in awareness...
1Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Como, Italy.
2Dipartimento di Scienza dei Materiali, Università degli Studi di Milano-Bicocca, Milano, Italy.
3Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milano, Italy.
simona.galli@uninsubria.it
On the occasion of the International Year of Crystallography 2014...
In the past few years, remarkable advancements in data-driven models and the accessibility of extensive experimental data from various sources have facilitated the development and implementation of Artificial Intelligence in materials science, particularly machine learning (ML) algorithms for diffraction data analysis. These algorithms have proven to be particularly useful and effective in...
Proteins crystallize surprisingly often within living cells and across all domains of life. [1] Our research focuses on refining a systematic approach, InCellCryst, to leverage in cellulo crystallization in insect cells for structural biology. This crystallization approach can rapidly generate millions of micron-sized, high-quality protein crystals within the densely populated environment of...
Self-healing is an intrinsically exciting concept as it applies to the process of recovery, an almost commonplace effect found in living organisms, and extends to inanimate objects. Self-healing of artificial materials is as beneficial as it is to living creatures, as the effect significantly prolongs the lifetime of both. Self-healing polymers, cementitious materials, and coatings have...
Pressure and temperature are key variables to explore the physical properties of matter, allowing to access new reactivity paths, tuning properties, and modifying both length and angles and thus crystal structures. The effects of these variables can be studied directly using specific devices, such as diamond anvil cells (DACs), or more indirectly exploiting natural samples, like mineral...
The Curious Chemist summer research camp has been organized in thirteen consecutive years so far for secondary school students in the Research Centre for Natural Sciences (RCNS). We only accept the application of 24 students a year and the number of supervisors dealing with the students is comparable to this. The supervisors are the enthusiastic researchers and PhD students of the RCNS. They...
In the macromolecular crystallography beamline AR-NW12A at the Photon Factory, we have been developing instruments for UV-visible absorption spectroscopy and Raman spectroscopy and improving their utilization environment to establish the beamline where X-ray crystallography and spectroscopic methods can be used seamlessly. The UV-visible absorption and Raman microspectroscopic systems in an...
Many polymorphic forms of organic compounds, in particular of drug molecules, are notoriously difficult to crystallize. This often hinders their crystal structure characterization and hence also our understanding of polymorphism and crystallization phenomena. We have recently developed a protocol for reliable crystallization of three elusive polymorphs of meloxicam (MLX), an anti-inflammatory...
Molecular recognition plays a crucial role in a wide range of chemical and biological processes, encompassing phenomena such as crystallization, molecular assembly, enzyme catalysis, cellular signaling, and protein-protein interactions. Despite often being characterized as a binary association between two partners, molecular recognition typically occurs within an aqueous environment...
Cation arrangement, disorder and defects substantially impact the optoelectronic properties of multinary semiconductors [1]. While often an inconvenience, this also provides opportunities to enhance optical properties such that improved absorption coefficient and photovoltaic device efficiency can be achieved [1]. Due to the fundamental relationship between atomic geometry, electronic...
In Structural Biology, Cryo-electron microscopy (cryoEM) has emerged as a pivotal technique for understanding the intricate structures of biological macromolecules at near-atomic resolution. The advent of deep learning has revolutionized the processing of cryoEM images, offering unprecedented accuracy and efficiency. This presentation delves into our contributions to applying deep learning...
A large number of written and illustrated papyruses from Ancient Egypt have survived through the ages, providing numerous details about stories, practices, and everyday life in Egypt several millennia ago. We investigated a series of fragments of illustrated papyruses from the collection of the Champollion museum (Vif, département de l’Isère, France), showing scenes from the Book of the Dead,...
Advances in crystallography software have made structural determination more accessible and less reliant on understanding complex principles of macromolecular crystallography (MX). This opens up opportunities for researchers and eases access for those who are new to the field. While newcomers benefit from streamlined processes, they may be unfamiliar with efficient utilisation of computational...
We present a method for achieving high-quality anomalous powder X-ray diffraction (AXRD) by employing a flat panel imaging detector scanning over a large angular range, coupled with transmission X-ray absorption spectroscopy (XAS) (Fig. 1). Maintaining an adequate Q-range becomes particularly challenging in experiments involving the collection of AXRD data at atomic absorption edges, which are...
When capturing atomic resolution imagery, such as that taken via scanning tunnelling microscopy (STM), systematic errors are not unusual. For example, a sample and probing tip are moved relative to each other in STM by piezoelectric actuators. These actuators often have the shape of a tube and allow for both sample movements up to hundreds of nanometers while selecting scanning areas and...
This would be the story of a woman who grew up in a small town in Poland with dreams of becoming a doctor. However, she discovered her passion for chemistry instead, thanks to a supportive mentor who introduced her to the world of crystallography. Despite facing challenges and struggling with a rare neurological disorder causing chronic pain, she persisted in her studies, earning her...
A procedure is presented to exactly obtain the apparent average crystallite size (ACS) of powder samples using standard in-house powder diffraction experiments without any restriction originating from the Scherrer equation [1]. Additionally, the crystallite size distribution within the sample can be evaluated. To achieve this, powder diffractograms are background corrected and long-range...
The organization of Al atoms in zeolites, alongside their topology, is a critical parameter that defines the presence and behaviour of catalytically active centres. Al atoms introduce a negative charge in the zeolitic lattice, which needs to be balanced by extra-framework counter-ion species serving as active sites, including acid (protons) and redox (transition metal ions) sites.[1] In...
NSDHL, a crucial enzyme involved in human cholesterol synthesis and the regulation of epidermal growth factor receptor (EGFR) trafficking pathways, has garnered attention as a promising therapeutic target due to its significant implications in cholesterol-related diseases and carcinomas. However, the lack of atomic-level details has impeded the development of pharmacological agents targeting...
Time-resolved structural analysis allows us to understand the detailed reaction mechanism of proteins. At SPring-8 BL41XU, we are proceeding with the development of time-resolved structural analysis using serial crystallography targeting reactions slower than milliseconds, which is complementary to the serial femtosecond crystallography at SACLA.
So far, we have completed the introduction of...
X-ray crystallography is the gold standard of protein structure determination. Diamond's XChem facility has enabled high throughput collection of crystal datasets, allowing the acquisition of over 1000 structures during a single screen. That advancement brought new opportunities in fragment-based drug design, allowing the creation of a fast-acting drug design platform for emergencies (e.g.,...
Single crystals of two new 1D bimetallic oxalate compounds with the formula [ACr(C2O4)2(H2O)4]n, A = Li, Na have been synthesized and the crystal structures elucidated by X-ray diffraction analysis and compared [1]. The compound (I) with Li atom crystallizes in the monoclinic space group C2/m, while the compound (II) with Na atom crystallizes in the triclinic space group P1 ̅, however with...
Sanidine is the high-temperature, monoclinic polymorph of potassium feldspar. It is typically found in felsic rocks, often incorporating significant amounts of sodium due to rapid cooling. Sanidine's crystal structure has four non-equivalent tetrahedral sites where Al and Si are tetrahedrally coordinated by four oxygen ions, forming a framework of corner-sharing AlO4 and SiO4 tetrahedra. In...
Nanosizing TiO2-rutile has been shown to improve its Li-ion storage capacity significantly. During the initial discharge, the nanocrystalline material distorts monoclinically and disorders gradually. Upon deep discharge (high degree of lithiation), the material undergoes an irreversible structural reconstruction into a layered α-NaFeO2-like structure with grain boundaries possessing a...
Zeolites are microporous aluminosilicate materials that are widely utilized as industrial catalysts or sorbents since the micropore confinement along with the presence of acid sites enables the shape-selective catalysis and adsorption of various guest entities [1]. The high commercial demand for zeolites has fuelled extensive efforts to develop innovative synthetic variations, surpassing the...
Direct real-space determination of atomic parameters from inhomogeneous cryoEM and crystallographic maps
A.G. Urzhumtsev1,2, N.L. Lunina3, V.Y. Lunin3
1Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM-UdS, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France, 2Université de Lorraine, Faculté des Sciences et Technologies, BP 239,...
Gaining precise control over the structure and dynamics of matter is still an open challenge, which can give access to architectures of ever-increasing complexity and, hence, to new functional materials with desired physicochemical properties.
sigma/pi-hole interactions have garnered significant attention in contemporary research across various domains of supramolecular science and crystal...
A new mineral with the composition Al2(PO4)(SO4)(OH,F)(H2O).6H2O was found on the dump of the Lichtenberg open cast, Ronneburg, Thuringia, Germany. In the open cast and surrounding mines uranium bearing alumn shale was mined from 1950"s to 1990"s. The Ronneburg mining area was one of the largest uranium producers in Europe. The new mineral is an alteration product and was formed on the mine...
Metal-inorganic clusters represent a highly varied class of cofactors, ranging from simple two-iron-two-sulfur clusters to highly complicated structures containing more than one metal such as the nitrogenase iron-molybdenum cofactor. As such, they convey a multitude of abilities to the proteins binding them, ranging from simple electron transfer to catalyzing complicated reactions.
Here we...
Chemical warfare nerve agents and pesticides, known as organophosphorus compounds inactivate cholinesterases (ChEs) by phosphorylating the serine hydroxyl group located at the active site of ChEs. Over the course of time, phosphorylation is followed by loss of an organophosphate-leaving group and the bond with ChEs becomes irreversible, a process known as aging. Differently, structurally...
Within the K2CO3-CaCO3 system on P,T variation relevant to the Earth's geotherm [1], trigonal K2Ca2(CO3)3 is one of the known solid key phases with an apparent stability under the conditions of formation. Early descriptions report on intensive polysynthetic twinning in morphologically trigonal crystals [2], and the structure was later solved according to acentric R3 space-group symmetry, but...
Active pharmaceutical ingredients (APIs) can form different crystalline solid forms. [1] These include single component solid forms (polymorphs) and different types of two and multi component systems such as solvates, co-crystals etc. Solvates and co-crystals usually have physicochemical properties different from those of the pure API. These properties have an impact on the drug dosage form...
Diversity of the host-guest crystalline assemblies of p- sulfonatocalix[n]arenes with benzamidines
K. Kravets1,2, L. Contini2, F. Grepioni2, O. Danylyuk1
1Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
2Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126, Bologna,...
Supramolecules, or giant metallasupramolecular cages, are formed upon coordination of metal cations and organic ligands and possess various molecular structures. [1] Thanks to the hollow structure many of them are successfully used as molecular containers, and current research focuses mainly on exploring host-guest interactions aiming to use them for effective inclusion-release cycle as well...
Time-resolved serial crystallography demands the production of millilitres of micron-sized crystals, alongside robust strategies for reaction initiation. This necessitates the crystallographer to transition from vapour diffusion to batch methods [1]. Droplet microfluidics has traditionally been employed for crystallization screening and generating large crystals suitable for standard,...
Upon the introduction of Dui[1] within the CCP4 software suite[2], it was demonstrated that using a graphical user interface (GUI) significantly enhances the practicality of image processing with DIALS[3]. Moreover, Dui emerged as a valuable instructional tool for helping with the comprehension of DIALS and data processing principles. A key attribute of Dui lies in its facilitation of...
The presentation will address the structural peculiarities of early carbon minerals in the light of their formation processes. It will emphasize the importance of crystal chemistry and structural defects to decipher the early cosmic processes that prevailed during the formation of the solar system.
Traditional earth-based mortars used in buildings of the 17th and 19th centuries placed in the historical centres of Vegueta and Triana, emblematic districts located in the city of Las Palmas of the volcanic island of Gran Canaria (Spain), have been characterized through a multi-analytical study.
Such traditional earth-based mortars were both filling the masonries and coating the façades...
Epstein Barr Virus (EBV), one of the most common human viral infections, is one of the few viruses known to lead to the development of cancers, such as Hodgkin lymphoma, Burkitt’s lymphoma, and nasopharyngeal carcinoma (NPC) [1]. NPC has a high mortality of patients with advanced and recurrent disease but very few druggable targets [2].
EBV encoded nuclear antigen 1 (EBNA1) has been shown...
The interaction of intense synchrotron radiation with molecular crystals frequently modifies the crystal structure by breaking bonds, producing fragments and hence inducing disorder. Moreover, X-ray radiation may strongly affect physical properties such as electronic configurations [1], colour, compressibility, thermal expansion [2], and stability of certain structural forms [3, 4]....
The phenomenon of polymorphism is well studied in molecular solids, thanks mainly to its relevance to pharmaceutical science, yet it remains understudied in covalent network solids such as coordination networks. In this contribution, we will highlight how subtle changes in crystal packing can profoundly influence certain bulk properties more than others:
(i) Aqueous solubility and melting...
Among the well-established methods for protein crystallization, in cellulo crystallography has a special place, as it allows for investigation of protein structure in the cellular milieu. However, due to current limits in current understanding why some proteins undergo spontaneous ordered assembly, in cellulo crystallization has remained a niche technique to date. Many protein targets that can...
The electric vehicle rechargeable battery market has seen a substantial boost due to the green energy transition. This surge has sparked a high demand for raw materials such as cobalt and nickel, both vital constituents in lithium-ion batteries (LIBs) [1]. However, the current mining protocols and the concentrated localization of these ores have transformed cobalt and nickel into mineral...
The prototypical methylammonium lead iodide (MAPbI3) belongs to the class of hybrid organic-inorganic perovskites (HOIP), and has been a material of intensive scientific interest due to the technological relevance in fabricating state-of-the-art solar cells (cite). Much of the structural characterization of MAPbI3 to date are carried out based on diffraction and electron microscopy techniques,...
Development molecule-based magnetic materials built of metal-organic coordination frameworks requires their structural characterization [1]. However, large enough single crystal suitable for X-ray diffraction are notoriously difficult to grow hampering structure determination and discouraging research in the field.
To address this obstacle we show here that the structure of two novel...
Biogenic crystals encompass crystals produced by living organisms. Examples include calcium oxalate crystals in plant tissues, magnetite crystals forming within diverse bacteria and animals, and various crystals within the human body. These crystals are intriguing due to their unique properties, yet extracting them from the parent organism poses challenges for structure determination. Their...
Hybrid Organic-Inorganic Halide Perovskites (HOIHP) have emerged as promising materials in semiconductor technology. Their easy and low-cost production together with their unique optoelectronic properties make them promising materials, for a multitude of applications including light-emitting diodes, lasers, photodetectors, scintillators, field-effect transistors and photovoltaics (PVs) [1,2]....
SESEAME is the first Synchrotron light source in the middle east and an intergovernmental organisation established under the auspices of the UNESCO. This contribution highlights the advantages and new experimental capabilities of Synchrotron X-ray tomography for cultural heritage science at the newly build ID10-BEATS (BEAmline for Tomography at SESAME) beamline. X-ray tomography offers a...
Exposure to both UVA and UVB radiation from the sun stands as the primary cause of skin cancers. Sunscreen products have become ubiquitous in personal-care products, packaging, plastics, dyes, and many other sectors. Ideal UV filters should be photostable and dissipate the absorbed energy efficiently. However, most organic UV filters are photolabile upon protracted UV exposure, leading to the...
The performance and durability of solid oxide fuel cells (SOFCs)1 are paramount for their successful application in sustainable energy technologies. This study examines the impact of introducing cerium and nickel2,3 into the PrBaMn2O5+δ (PBM) structure and investigates the influence of gadolinia-doped ceria (GDC) buffer layer thickness, applied via physical vapor deposition, on anode...
Hydrogen atoms represent a large fraction of the total atomic content of macromolecules. They often play critical roles in enzyme ca-talysis, ligand recognition processes, and protein-protein interactions. However, their direct visualisation by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localisation of only the most ordered hydrogen atoms at...
As a first-year phD candidated I attended my first Erice School of Crystallography in 2021 in Powder Diffraction. Although I had an intense training in crystal engineering and crystallography, I approached the Erice course aiming at deeply understanding all the secrets of the powder diffraction directly by all the scientists whom I only have read about. After spending 10 days in a wonderful...
In this oral presentation I will share with the community the amazing experience I had during the the 58th International School of Crystallography (Structural Drug Design 2023) at the Ettore Majorana Center in Erice.
This short presentation will include personal reminiscences and photos of the Erice schools on crystallography since 1998.
The overall diffraction precision index (DPI) of a biological macromolecule crystal structure was first described by Durward Cruickshank in 1999 [1]. Additional developments were introduced by the availability of a webserver http://cluster.physics.iisc.ernet.in/dpi/ , which provides a transformed PDB entry with individual atom coordinate errors derived from applying the DPI method, using the...
Naturally occurring minerals provide examples of unique nanoscopic tubular units based upon silicate oxyanions. The crystal structure of eveslogite (first described in [1]), a chemically and structurally complex natural Ca-K-Ba-Ti-Fe-Nb silicate from the Eveslogchorr Mt., Khibiny massif, located in the Russian Arctic, solved using 3D electron diffraction (3D ED) provides an amazing example of...
The ‘great oxidation event’ that occurred about 2.4 BYA led to the permanent accumulation of O2 in the atmosphere, putting significant evolutionary pressure on many organisms. Adaptation led to the appearance of novel enzymes able to take advantage of this new molecule and its electron-acceptor capabilities. However, other O2-utilising enzymes evolved from classes whose original functions were...
Best practices in the usage of linear position-sensitive detectors for advanced measurements and experiments at large scale facilities will be discussed, with a focus on the Mythen system and its recent upgrade.
Sulfur(VI)-fluoride exchange, so-called SuFEx, is an all-encompassing term for substitution events that replace fluoride at an electrophilic sulfur(VI), allowing rapid and flexible assembly of linkages around a SVI core.
In the late 1990s, many key articles on activity-based protein profiling (ABPP) were published, highlighting its ability to detect active enzymes in complex proteomes like...
Dynamic organic crystals are rapidly gaining traction as a new class of smart materials for energy conversion, however, they are only capable of very small strokes (<12%) and most of them operate through energetically cost-prohibitive processes at high temperatures. We report on the exceptional performance of an organic actuating material with exceedingly large stroke that can reversibly...
The crystal structure of bis(1,2diaminepropane) di-μ-chloro-bis[diaquadichloromanganate(II)] dichloride (1) is built as layers of cen-trosymmetric binuclear units made of two (MnIICl4(H2O)2)- octahedra sharing one edge along the a direction and distributed in the a,c basal plane (P-1 triclinic space group). These doubly negative charged layers are separated along the b axis by posi-tive...
The magnetic properties of heavy transition metal complexes are poorly explored, even though they possess huge potential for different applications, including quantum information technology. We decided to study a simple but versatile system: Osmium(III) acetylacetonate, ([Os(acac)3]). We isolated crystals of two different shapes, which turned out to correspond to two polymorphs (Fig. 1a)....
Co-crystals, systems of two or more neutral compounds crystallizing in one structure (with all the due reservations – excluding solvates, hydrates etc, cf. quite a vivid discussion some time ago), are recently subject of quite intensive studies due to their expected properties, for instance solubility of pharmaceutically important compounds. Due to the very nature of these crystals the number...
Metal–organic frameworks (MOFs) are porous crystalline materials that consist of metal ions or clusters linked by organic ligands. MOFs have been synthesised using several elements including rare-earth (RE) elements such as scandium, yttrium and terbium. RE-MOFs are attractive not only due to their permanent porosity, tuneable pore size/shape and accessible Lewis acidic sites but also due to...
The bitter taste of pharmaceuticals majorly impacts patient adherence. Co-crystallisation has been proposed as a novel way for taste masking using sweetener-based co-formers, while other co-formers also have a positive effect. We hypothesise that the sweetness of the co-formers is not the key factor but rather the supramolecular interactions between the drug and co-former. These interactions...
Three-dimensional microcrystal electron diffraction (3D ED/MicroED) has become a powerful technique for unravelling complex structures of sub-micron crystals. As the first dedicated, commercially available electron diffractometer, Rigaku’s XtaLAB Synergy-ED stands at the forefront of nanometer-scale crystallography, offering an accessible platform for structure determination [1]. With its...
The historical utilization of organic molecules (ligands) coordinated to transition metals, such as platinum (Pt), rhodium (Rh), rhenium (Re) and technetium (Tc), spans several decades particularly in the field of catalysis and medicine [1-2]. However, due to factors such as global warming, virus mutations and evolving catalytic technologies, the global demand for novel organometallic...
We live in a contradictory society where, on the one hand, we face devastating environmental consequences caused by excessive use of non-renewable fossil resources, but at the same time, we are heavily dependent on them and are depleting our reservoirs. Research into environmentally friendly and renewable resources is therefore of utmost importance, and a great interest is focused on biomass...
Highly ordered structural arrangement in crystalline solids, which can be modified in a controlled manner, has proven to be an exceptionally useful feature in achieving and adjusting a specific material property, such as electric or magnetic [1]. Relatively recently, it has been demonstrated that the introduction of slight changes in the structure of 1-D crystalline coordination polymers on a...
Background. BET (Bromodomain and Extra-Terminal) proteins are chromatin-associated proteins that recognize acetylated histones via their two bromodomains (BDs). Small molecules that target the BDs of human BET proteins are intensely pursued as potential therapeutics against cancer and other diseases. We previously identified the fungal BET protein Bdf1 as a potential antifungal target...
The physico-chemical properties of active pharmaceutical ingredients, agrochemicals, and other useful chemicals can be altered and optimised by forming multi-component crystals, such as salts, solvates and cocrystals. Discovering suitable multi-component crystals, especially cocrystals, is time-consuming and labour-intensive. The Cambridge Structural Database (CSD) contains a massive number of...
In recent times, there have been notable advancements in refining crystal structure models using electron diffraction data [1, 2], thanks to improved experimental setups and modelling techniques. However, compared to typical R-factors observed in X-ray diffraction experiments, there remains a significant gap. This suggests that there are parameters overlooked in the model that have a notable...
Two-electron multicentre bonds (2e/mc or pancake bonds) are strong intermolecular interactions which occur between planar organic radicals [1−3]. They involve the pairing of spins of contiguous radicals due to the extension of the highest occupied molecular orbital (HOMO) between both radicals; this implies a significant covalent contribution to the total interaction, which often exceeds −15...
The bacterium Streptococcus pyogenes employs several enzymes in its evasion of the human immune system. Such enzymes include IgG-degrading enzyme of S. pyogenes (IdeS) [1], a protease which deactivates IgG antibodies by cleaving within the lower hinge region, thereby separating the antigen-binding F(ab')2 regions from the immune-engaging Fc region. Additionally, the bacterium utilises two...
In modern quantum chemistry and quantum crystallography, the Noncovalent Interaction (NCI) index [1, 2] has recently emerged as a prominent and useful tool for discerning noncovalent interactions within molecular systems. Initially, its application was merely con-fined to qualitative descriptions. However, recent advancements have expanded its capabilities to provide quantitative insights [3,...
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Identifying the crystal structures that govern their properties is essential when developing new materials. Rietveld analysis is commonly used to identify the crystal structures, namely the symmetry, lattice parameters, atom sites, and the occupancy rates. This analysis involves deciphering crystal structures from powder X-ray or neutron diffraction profiles. Finding lattice parameters and the...
Electron diffraction of 3D nanometer sized crystals, most commonly named microED or 3D ED, has recently emerged as a new technique to solve the structure of both small organic molecules and proteins [1–3]. 3D ED is clearly a promising technique in structural biology, both quite easy to implement and very complementary to X-ray crystallography and single particle cryo-EM. Electrons are actually...
Due to the computational cost of quantum mechanical simulations for large and electron-rich systems, semiempirical methods have been developed to provide a better compromise between accuracy and computational cost. The xTB program package is a collection of semiempirical quantum chemical methods based on the tight-binding approximation. The methods are designed to be computationally...
Time-resolved X-ray crystallography using the serial approach has received increased attention over the past years at synchrotron and XFEL sources worldwide. Developments in instrumentation, data collection strategies and data processing have lowered the entry barrier to a wider user community seeking insight to a wide range of biological targets. Existing methods have effectively been used to...
The introductions of [c2] daisy chain rotaxanes with extended/contracted conformations and different polymerization active sites into mechano-fluorophoric polyurethane (PU) networks were carried out via the step-growth polymerizations to gain PU films with interesting mechanical and optical properties upon stretching. As expected, the distinctive stretchabilities and toughnesses of PU films...
Shigella are highly infectious bacteria and cause the severe disease bacillary dysentery. It occurs predominantly in developing countries, affecting mainly small children, and causes several 100,000 lives per year. The bacteria are able to penetrate into the epithelial cells of the colon and thus develop their pathogenicity. The Shigella-specific chaperone IpgC plays an essential role in the...
A key feature of metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) is their ability to capture, convert, and release guest molecules. This capability is governed by multiple factors such as pore volume and surface area, chemical environment, and the nature of the host-guest intermolecular interactions. X-ray diffraction (XRD) experiments are essential to resolve the atomic...
The binary compounds A$^{\mathrm{II}}$M$_2$ (M=Mg/In) belong to different structure families such as Laves phases, which are dominated by packing effects (FK phase), and Zintl phases, like e.g. the CaIn$_2$- or KHg$_2$-type structure which obey the well-known electron counting rules. As the crystal structure formation strongly depends on geometric (radii) [1] as well as electronic (e.g....
Navigating the early stages of one's career often resembles a journey through a landscape of local minima, each promising but potentially trapping. From a “unripe” scientist perspective, what are the critical junctures and key events that determine when a trajectory becomes locked into a particular path? How are the individual aspirations, external opportunities, and structural constraints...
Biological function is intimately tied to dynamic changes in protein conformations and interactions with other molecules. The recent upgrade to the Linac Coherent Light Source (LCLS-II) marks a transformative leap for structural biology by providing unprecedented opportunities to study these dynamic processes. The high repetition rate of LCLS-II enables real-time observation of macromolecular...
The RAS/MAPK signalling pathway is one of the most extensively studied pathways, mainly due to its fundamental role in the regulation of cell cycle, proliferation, or senescence. Mutations in RAS/MAPK are primary drivers of cancer [1]. They also contribute to developmental syndromes known as RASopathies. These syndromes are associated with body malformations of different severity and with...
Solid-state luminescent materials based on pure fluorescent organic molecules have received considerable attention due to their potential applications in the field of optics, optoelectronics and bioimaging. Yet, their rational design is challenging because the photoluminescence properties, which strongly depend on molecular conformation and non-covalent interactions (NCI) in the solid state,...
In the continual pursuit of enhancing cooling efficiency and lowering CO2 emission in aeroengines, reliable experimental methods are essential for temperature profiling of hot gas components. High temperature responsive materials have assumed a significant role in advanced technological applications such as microelectronics, cell biology, and diagnostics for their potential use in thermometry....
Metal-organic frameworks are porous compounds consisting of metal nodes and bridging organic ligands.1,2 MOFs are potential candidates for application in gas storage, catalysis, and drug delivery due to their unique properties such as large surface areas, large pore volumes, tuneability, and flexibility.3,4 Our research focuses on the synthesis and investigation of gas sorption properties of...
In an attempt to synthesize Gd5F3[AsO3]4[1–4] under high-pressure conditions from appropriate molar mixtures of GdF3, Gd2O3 and As2O3, which were filled into a gold ampoule with a drop of deionized water, colorless lath-shaped crystals of what turned out to be Gd2F[CO3][AsO3] emerged. After seven days in a piston-cylinder high-pressure cell at 10 kbar and 850 °C, some CO2 dissolved in the...
Human glucokinase (GK) is a hexokinase isozyme (hexokinase IV) active in the liver and the pancreas.1 In the beta cells of the pancreas, GK acts as a glucose sensor for insulin secretion, while in the liver it facilitates the transformation of glucose into glycogen, which allows glucose to be stored for later use (Fig. 1).2 The role of GK in the reduction of glucose levels in the body leads to...
To the end of twentieth century, gold supramolecular chemistry, especially in the solid state, but also in solution, has known a renewed interest.[1] The discovery of the powerful tool of the “aurophilic interaction”, for which gold cationic centers are attracted together, made possible a new word of possibilities of engineering crystal structures or supramolecular entities in solution.[2]...
The need for a more effective wastewater treatment is necessary to minimize dyes content in the wastewater and produce maximum amount of treated water that is suitable to be discharged into open water course. Photodegradation, is one of the used technologies due to its relatively simple design and cost effectiveness. Photodegradation involves the breakdown or decomposition of different organic...
Structural studies of thin films of several different hexaferrites have been a subject of our research in last years [1-3]. In this contribution, the growth of epitaxial thin films of Sr4$_2$Co$_2$Fe$_28$O$_46$ (X-phase) on a SrTiO$_3$(111) (STO) by a chemical solution was studied. This phase was prepared in the form of a thin film for the first time. The orientation relation between film and...
To solve the folding problem, the attention algorithm, encoded in the transformer succeeded in relating pairwise evolutionary conservation and structural data in the PDB. AlphaFold succeeded in harnessing this knowledge, in many cases matching the accuracy of close homologs in its predictions, as assessed in CASP14-15 experiments. AlphaFold derives information from three sources: learned...
Water (H2O) is the third most abundant molecule in the Universe following dihydrogen and carbon monoxide. Travelling through the Solar System, water ice is a constant companion from the polar regions on Earth and the asteroid belt to the icy satellites of the gas giants and the Kuiper belt. The presence of ice across the Solar System is important for a variety of reasons: Firstly, ice can...
Fifty years ago, Dr. Leo Merrill and Professor Bill Bassett developed a miniature Diamond Anvil Cell for single crystal diffraction (Merrill and Bassett, 1974). They used this simple but innovative tool to determine the crystal structure of CaCO3-II, a high-pressure polymorph of one of Earth's most common minerals that cannot be retained at ambient conditions. This groundbreaking device...
Following a need for increased hands-on experience with technical analytical instrumentation for undergraduate students, the University of Southampton has offered just such a practical course to third year students for the past 10 years. This involves the preparation of crystalline materials, with subsequent analysis including the collection of single crystal X-ray diffraction data and work-up...
Since 1994, the Elettra hard X-ray diffraction beamlines dedicated to material science are supporting a large community of users coming from different scientific and technological sectors. These beamlines are playing a pivotal role in the scientific production of the facility providing our users valuable information on crystal structure and molecular arrangements and their response to changing...
Helicobacter pylori’s proton-gated plasma membrane urea channel and cytoplasmic urease are essential for the survival of this carcinogen the human stomach. The channel is closed at neutral pH and opens at acidic pH to allow the rapid access of urea to cytoplasmic urease. Urease hydrolyzes urea into 2 NH3 and CO2, neutralizing protons and thus buffering its cytoplasm even in gastric juice...
The HeXI project, funded by the Wellcome Trust “Electrifying Life Sciences” grant and Diamond Light Source, aims to build a dedicated electron diffractometer to investigate the potential of Mega-electron volt (MeV) electrons for the determination of molecular structures from nanometre sized crystals.
The HeXI instrument will leverage the increased penetration of MeV electrons and the high...
Small molecule structures and their applications rely on a good knowledge of their atomic arrangements. However, the crystal structure of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis...
The phase transitions of PdBi and PdBi2 structures were studied by in-situ high temperature single crystal X-ray diffraction.
Experimental diffraction data were collected starting from room temperature up to 573 K for PdBi, and 637 K for PdBi2. The special experimental performing conditions were required due to high oxidation possibility of bismuth compounds. The crystals were capsulated in...
P11 is a Macromolecular Crystallography (MX) beamline at PETRA III (DESY, Hamburg) [1]. The instrument can provide variable experimental setups with multiple focus sizes (from 200 x 200 to 5 x 10 μm2), in an energy range from 6 to 28 keV. With a maximum flux of 1013 ph/s at 12 keV, the beamline can be used to perform both standard and serial macromolecular crystallography.
Equipped with an...
Ambient conditions diffraction data of AuSn4 and PtSn4 compounds can be described by an orthorhombic Aba2 (space group 41) structure with identical Wyckoff positions: 4a, for the noble metal and 8b for two types of Sn (I and II), thus making these compounds isomorphous. These compounds come under the new category of materials known as topological nodal line semimetals with non-trivial...
Modern material characterisation at atomic structural resolution is heavily dependent on the availability of single, high-quality crystals for analysis by Single Crystal X-ray Diffraction (SCXRD). However, successful crystallisation, including access to different polymorphs, hydrates, solvates and co-crystals can only be achieved through the rigorous exploration of large areas of experimental...
Metal organic frameworks (MOFs) and covalent organic frameworks (COFs) are polymers which due to their porosity are suitable for various applications, such as gas separation and storage, water harvesting and purification, catalysis, sensing and energy storage. Many of these materials can form crystals amenable to single crystal X-ray diffraction analysis. This provides an opportunity to employ...
Metal-organic frameworks (MOFs) are microcrystalline materials, composed of transition metal nodes connected by organic linker molecules. MOFs are renowned for their applications in gas storage and separation, sequestration of atmospheric greenhouse gases, water purification and degradation of toxic agents, all of these applications stemming from the porous nature of these materials.[1,2]...
Host-guest interactions guide pentamidine folding inside and outside the cavities of macrocyclic hosts
O. Danylyuk1, K. Kravets1
1 Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
odanylyuk@ichf.edu.pl
Pentamidine is the FDA-approved anti-protozoal drug currently rediscovered as a membrane-targeting antibiotic sensitizer helping...
Non-covalent interactions play an important role in the design of new materials, from catalysts to high-energy materials (HEM) [1]. Analysis of non-covalent bonding patterns in crystal structures is especially important in the case of high-energy compounds like explosives since the vast majority of these compounds are used in the solid state. Moreover, crystalline factors like free space per...
One of the processes routinely and frequently used by crystallographers engaged in structure determination is the fully automatic generation of a unit cell, together with crystal orientation, from the initial images obtained on a single-crystal diffractometer. Often there are few user options and only one or just a small number of possible solutions are offered. How does it work, what...
Georg-August Universität Göttingen,, Institut für Anorganische Chemie, Tammannstraße, 37077 Göttingen, Germany
The MetalJet source provides new available Kα radiation wavelength for use in X-ray diffraction experiments.[1] Here we want to demonstrate the application of using indium Kα radiation in independent atom model refinement, as well as approaches using aspherical atomic form factors....
The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation...
Perovskite-type oxides (ABO$_3$) are largely engineered for the realisation of multiferroic materials as they can host proper ferroelectric instabilities. The perovskite framework can also support the more exotic, yet easier to engineer, mechanism of electric polarisation known as hybrid proper improper ferroelectricity. However, this mechanism has been limited to layered structures [1,2]....
Constraining spatial dimensionality of electronically extended systems by tailoring crystal structure, size and shape of inorganic compounds at nanoscale often endows the resulting materials with extraordinary optoelectronic, magnetic and catalytic properties.[1, 2] A recent prominence of inorganic and hybrid – organic-inorganic – lead halide three- and two-dimensional perovskites as...
Hydrogen-bond-donating (HBD) catalysis has emerged as a biomimetic alternative to Lewis acid activation and it is an effective ap-proach for the synthesis of various highly valuable intermediates for pharmaceutical and agricultural industries. HBD catalysts are capable of binding selectively and activating reactive substrates during the reaction process through hydrogen bonding or other...
Temperature-dependent X-ray diffraction (XRD) is employed to study the phase transitions in axially chiral 1,1’-Binaphthalene at various heating and cooling rates. The known phases of 1,1’-Binaphthalene are monoclinic (racemate), a cisoid conformer with a melting temperature of 145°C, and tetragonal (enantiomers), a transoid conformer melting at 158°C[1-4]. Upon melting and recrystallization...
The use of solid-state reactions as a crystal engineering tool in material design has gained traction over the years as chemists continue to pursue greener ways of making chemical compounds. The absence of solvent use in this method is not the only advantage, these reactions have also been found to result in higher product yields with excellent regio- and stereo selectivity in comparison to...
Cultural heritage objects possess immense material and immaterial value, serving as open windows into humankind’s past. Through them, we can grasp how man perceived and depicted the world as it was centuries ago. Many of the questions concerning cultural heritage objects that are addressed with analytical techniques revolve around three main topics: (i) how the object was created, (ii) its...
The first Erice School on Advanced Studies of Direct Methods in Crystallography remains a milestone. Already I had a background in structural determinations developed during my thesis and post-doc stages in USA (UW and NW). At that time, the task was not so easy even if some metal atom allowed a fruitful usage of the Patterson methods. On the other hand, the discovery of Direct Methods (DM)...
Georg-August-Universität Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
ngraw@chemie.uni-goettingen.de
Single crystal X-ray diffraction is not only a powerful tool for structure determination but also an invaluable asset for education. Unlike many analytical methods, it inherently allows the visualization of chemical structures and give us a means by which “we can now "see" the...
In this study, we examined the charge distribution in an organometallic complex using three-dimensional electron diffraction (3D ED), with a focus on modelling charged species like iron. We refined structural model of a metal-organic complex called iron(III) acetylacetonate (FeAcAc), using both the Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM). TAAM refinement...
Cancer is a prevalent disease in many countries and is one of the leading causes of death worldwide.[1] New insights into cancer treatment are needed particularly for treatment against strains which are resistant against current protocols. In the field of anti-cancer pharmaceutical research metalloorganic complexes have been shown to possess several benefits above the traditional carbon,...
This contribution discusses the application of mechanochemistry to the synthesis and conversion of inorganic materials by combining mechanical energy with chemical reactions.
High pressure techniques have proven instrumental in the discovery of new solid forms of materials, including agrochemicals and pharmaceuticals. Traditionally, these discoveries have been supported by high pressure single crystal diffraction studies. However, this method's reliance on relatively large, high-quality crystals (~200 microns) limits its applicability, as many materials of interest...
Despite numerous studies on postcombustion CO2 capture the search for efficient adsorbents continues. Alternative to conventionally applied sorbents can be found in polymeric carbon nitride class of materials, also known as poly(heptazine imides) (PHIs). PHI possesses the following advantages: chemical and thermal stability, easy to scale up, precursors are abundant and inexpensive yielding an...
Metal-Organic Frameworks (MOFs) have attracted significant attention for their diverse applications, particularly in gas absorption and separation. One notable application of MOF-74 is its ability to capture carbon dioxide (CO2), which is crucial for addressing global warming [1]. However, before MOFs can be utilized, they must undergo an activation process to empty their pores and create open...
Thanks to unique 2-dimensional structure, graphene oxide (GO) has attracted much attention in the scientific community and exhibits great potential in energy storage and environmental separation applications. Understanding the interfacial interactions of graphene oxide with metal ions, water or organic molecules will provide valuable insight for these applications. Benefits from synchrotron...
Metallophilic interactions occur between two metal atoms when they are between 2.5A to 3.5A apart. It has attracted recent interest because of its enhancement of the various properties to expand the application potential. [1] The most popular interactions are observed between coinage metals namely gold, silver and copper. These interactions occur in three conformations namely: fully supported...
Thin films of perovskites such as BaTiO3 show different, exceptional behaviour compared to their bulk counterparts [1-5]. The understanding of property changes during the growth process itself is highly desirable. Here we focus on the in-situ characterization of BaTiO3 thin films during the epitaxial growth by pulsed laser deposition (PLD) on different substrates. SrTiO3, LaAlO3 and MgO with a...
MOFs exhibits interesting harvesting water capabilities from the air or as heat pumps as they demonstrate a steep increase in water uptake in the range 10-30 RH% [1]. Optimal water isotherms are represented by an alternation of moderately hydrophilic and hydrophobic sites. However even within MOFs exhibiting such alternation, the required steep uptake of water relevant for real applications is...
Molecular photoswitches bear significant potential for designing functional materials whose properties can be controlled by optical stimulation (see e.g. [1,2]). It is important to understand the underlying switching mechanisms as well as the influence of the photoswitch’s environment on the resulting material properties. Precise knowledge of the photochromic properties is essential for...
Thin films possess complex gradients of residual strains and stresses, which vary laterally and also across film thickness. These originate (i) from self-organized film growth, (ii) from intentionally varying deposition conditions and/or (iii) from inhomogeneous thermal and/or mechanical loads applied during service. In order to reveal those gradients and subsequently optimize functional...
Crystal structure determination from 3D electron diffraction (3D ED) data must deal with the dynamical diffraction effects present whenever electrons interact with a crystal. Although it is possible to perform structure refinement without taking the dynamical diffraction theory into account (a procedure called kinematical refinement), the best results are obtained when the dynamical...
Hexakis(urea-O)iron complexes with different anions have a multitude of applications, e.g. they are used as selective oxidants and catalysts in organic chemistry, nanocomposite materials, and fertilizers [1]. Despite being known for decades; the nitrate complex Fe(urea)63 lacks a proper structure description. We discovered that the structure of hexakis(urea-O)iron(III) nitrate is...
The rich rare-earth (R) intermetallic compounds R3Co exhibit varied physical properties originating from the competition between exchange interactions and crystal field [1,2]. Their complex magnetic behavior, high spin ordering temperatures, magnetocaloric effect, giant magnetoresistance are naturally of fundamental interest, but also of great potential for technological applications such...
Structures of K2V3O8 and Rb2V3O8 mixed-valence vanadate fresnoites are studied with synchrotron single-crystal diffraction at the Swiss Norwegian Beamlines at the ESRF at low temperatures and ambient pressure. K2V3O8 exhibits a phase transition to an incommensurately modulated structure at about 115 K. At 100 K, the satellite reflections can be indexed with two q vectors: q1 = (α,α,0.5) and...
Incommensurate structures in organic-inorganic metal-halides
A. Gągor, D. Drozdowski
Institute of Low Temperatues and Struture Research Polish Academy of Science, Wrocław, Poland
a.gagor@intibs.pl
Organic-inorganic hybris based on protonated polar molecules and complex metal-halide units possess remarkable and tuneable properties that make them suitable for variety of applications...
Multiple myeloma (MM) is an incurable blood cancer affecting antibody-producing plasma cells, whose clonal expansion and dysregulated secretion of immunoglobulins leads to widespread organ failure. The available therapies, including hematopoietic stem cell transplantation and inhibition of the 20S proteasome, have limited efficacy, and relapses occur with high frequency. Thus, the...
Antimicrobial-resistance (AMR) stands nowadays as a pressing concern in public health. A group of six pathogens is named with the acronym 'ESKAPE' because of their ability to evade the biocidal action of traditional clinically used antibiotics [1,2]. Structural insight of molecular factors which play a key role in AMR is fundamental to deeply understand their mechanisms on and develop...
Insight into α-iminoamidines: Hirshfeld atom refinement and evaluation of intermolecular interaction energies
M.V. Rodić 1, M.S. Nešić 2, M. Lozinšek 3, N. Radulović 2
1 University of Novi Sad, Faculty of Sciences, Trg D. Obradovića 3, 21000 Novi Sad, Serbia,
2 University of Niš, Faculty of Sciences and Mathematics, Department of Chemistry, Višegradska 33, 18000, Niš, Serbia,
3...
The ability to adapt the crystalline structure to various conditions underpins the stimuli-responsive properties of materials. Such systems often undergo solid-state reactions such as linkage isomerism. While it was shown in numerous studies that small inorganic moieties, such as NO2, exhibit ability to change the way of bonding to metal centre in response to external stimuli like...
Ylides are a class of chemical compounds classified as zwitterion by having a positively charged atom directly attached to a negatively charged atom. The most common types of ylides involve a positively charged heteroatom like nitrogen, phosphorus, sulphur, or arsenic attached to a negatively charged carbon atom (Figure 1(a)). [1,2] Ylides are textbook examples of the interplay between...
The ParABS system [1, 2], composed of ParA (an ATPase), ParB (a DNA binding protein), and parS (a centromere-like DNA), regulates bacterial chromosome partition. The ParB-parS partition complex interacts with the nucleoid-bound ParA to form the nucleoid-adaptor complex (NAC) [3]. In Helicobacter pylori, ParA and ParB homologs are encoded as HpSoj and HpSpo0J (HpParA and HpParB), respectively....
See the attachment
Structural analysis at atomic and near atomic resolution of biomolecules, organelles, viruses and cells requires high quality sample preparation and characterization prior to and during the experiment. The Sample Environment and Characterization (SEC) group at the European XFEL works closely with visiting users to provide and optimize delivery of samples to the beam for high throughput high...
The process of crystal nucleation can be facilitated by the presence of nucleation centres in solution (pre-existing particulate material) or compliant surfaces that lead to lower interfacial tension of a crystal nucleus formed at the surface than that generated in solution. Heterogeneous nucleation can pose significant problems in the form of pipe scaling, but also pathological...
Since its inception in 2016, the BioMAX beamline [1] has been the only beamline for macromolecular crystallography at the MAX IV Laboratory, a fourth-generation synchrotron located in Lund, Sweden. Since then, BioMAX has been instrumental in supporting various research endeavors, extending its capabilities to encompass serial crystallography investigations conducted at ambient temperature [2]....
CCP4 released version 9.0 of the CCP4 [1] software suite this summer. It delivers an infrastructural upgrade to Python 3.9 and new features in the graphical user interface, ccp4i2. Other highlights of this release include DIALS 3.18+ [2] with its graphical user interface, DUI2, which now supports multitasking and remote control. The release brings deeper integration with Coot scripting [3] and...
Total scattering experiments provide valuable information on the local and intermediate-range order in complex materials. By taking the Fourier transform of a total scattering function, you obtain the pair distribution function (PDF): a weighted histogram of interatomic distances. Given a structure model of a material, consisting of the coordinates of the atoms, it is straightforward to...
The selection of a crystalline solid form for a new Active Pharmaceutical Ingredient (API) is a critical milestone in the development of many commercial drug products. The final selection must be robust and manufacturable as well as provide the desired bio-performance, indeed the expectation to ensure control of the solid form in the specific drug product is described in regulatory...
Over 200 million people in the world are affected by Intellectual Disability (ID) and/or Autism Spectrum Disorder (ASD), debilitating and often co-occurring neurodevelopmental disorders [1; 2]. They have problems with cognitive and adaptive functioning, including learning, communication, and social skills. ID/ASD have mostly monogenic causes. Majority of the mutations (non-sense, frameshift,...
Cataract is the leading cause of blindness worldwide, characterised by progressive opacification of the eye lens due to aggregation of its constituent proteins [1]. The major monomeric protein in the human lens is human gamma D crystallin (HGD). Localised to the lens fibre cells which lack the machinery for protein synthesis, HGD must therefore remain correctly folded and functional for the...
We investigated the organocobalt complexes of B12 models as cobalt based catalysts, which are extensively used in radical polymerization[1]. The complexes of obidoximes possessing an O-BF2-O moiety were prepared (Figure 1a). During crystallization experiments, apart from the crystals of (H2O)Co-(dimethylglyoximeBF2)2 (1, Figure 1b) were obtained, a new one-dimensional cobalt-based coordination...
Our group first time evidence the multiferroicity and magnetoelastic coupling in the aplha-Mn2O3.They have attracted special consideration as they present both intriguing fundamental physics problems and technological importance for potential multifunctional devices. The samples alpha-MnMn1-xMxO3 (X=0, 0.01; M=Cr and Fe) have been investigated for their temperature dependent structural,...
Candida auris has emerged as a significant pathogen due to its increased resistance to antimicrobial agents, warranting heightened attention in the medical community [1]. Developing effective strategies to combat this pathogen necessitates a profound understanding of its molecular biology, including the intricacies of its genetic machinery. The exceptional drug resistance observed in C. auris...
Sulfanilamide’s were the first chemical drugs used as preventive and therapeutic agents against various infection diseases [1]. They generally act as structural analogues of para-aminobenzoic acid and therefore inhibit dihydropteroate synthase [2]. After the discovery of Penicillin [3], their use decreased significantly. Nevertheless, in recent years, their synergistic activity has gradually...
It is well known that the presence or lack of metal ions have a drastic influence upon the crystallisation of a compound, whether the ion will be part of the crystal structure or not. Throughout the past decade our group systematically explored the influence of ions in cocrystal and polymorph screening experiments for pharmaceutically active compounds, as well as various other inorganic and...
The role of the single-crystal X-ray analysis (SC-XRD) in chemistry from 1990’s as a ‘fast, first resort analytical tool’ [1] is even more relevant nowadays, as the structural characterization of novel compounds becomes a pre-requisite for publication in the high-level chemical journals. In this context, the problem of evaluation of crystal structure, either solved during chemical research or...
Isostructurality, supramolecular isomerism, and single-crystal-to-single-crystal transformations in a family of metal complexes with a new bipodal ligand
S. Chaudhary, R. M. Losus, Z. Rafiński, L. Dobrzańska
Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Toruń, Poland,
chaudhary.6@doktorant.umk.pl
Research on metal complexes has enjoyed unflagging interest...
High-end crystallography techniques such as single crystal XRD, high pressure XRD and SAXS rely heavily on the x-ray source brightness for realizing smaller and brighter beams to achieve acceptable signal to noise with acceptable measurement time on ever increasingly difficult samples. Traditional x-ray tubes are typically limited in brightness by when the e-beam power density melts the anode....
Thermal energy storage has a major role to play in the energy transition, because of its potential and its various fields of application: recovery of the waste heat released during industrial processes, optimisation of battery operating points, heat dissipation in power electronics devices, and so on. The thermal storage using solid-solid phase change materials (SS-PCMs) appears interesting in...
The high velocity bombardment of planetary bodies via asteroid, comet, and meteorite impacts contributes to various processes in planetary genesis, evolution, and habitability [1–3]. The determination of the peak shock pressures and temperatures is an essential step to derive the original properties of the impactor and target, interpret magnetic signatures, and study the collision history of...
A2MX6 perovskites materials have shown impressive advances in the last 50 years due on thier photovoltaic application , made
them one of the most-promising technologies for next-generation solar cells.We present in this work a semiempirical model for prediction of mail parametrer of cubic A2MX6 perovskites.It is useful for providing the predicted structural information for estimating the...
$(1-x)Pb(Mg_{2/3}Nb_{1/3})O_3-xPbTiO_3$ (PMN-PT) are relaxor-ferroelectric perovskite-like solid solutions known for their exceptional electromechanical properties. Understanding their complex origins has been the subject of much academic research [1], especially for the compositions near the morphotropic phase boundary (0.28 < x < 0.35). In general, PMN-PT is described by the cubic and...
Development of new Deep Learning techniques have impacted a wide range of research areas [1]. One area where deep neural networks have proven powerful is the processing and interpretation of images [2]. We built on top of these methods to develop a novel technique to streamline the process of aligning crystal samples in the centre of a single crystal X-ray diffractometer.
The neural network...
The Cambridge Structural Database (CSD) [1], the crystallographic database for organic and metal-organic molecules, now contains over 1.25 million crystal structures. This wealth of data makes it an invaluable resource both in research and in education. In particular, educators and learners can use structures from the CSD and the associated CSD software to learn and teach crystallography and...
Over the last decade, MX has seen a prominent shift toward online solutions in both experimental and computational parts of the whole structure determination process. Online approach may start with contracting a crystallisation facility, followed by a remote diffraction experiment at a synchrotron with subsequent data processing and structure solution using a suitable online software setup,...
Climate change is one of the most pressing problems of the 21st century and in order to reduce our reliance on fossil fuels, new materials for energy conversion and energy storage are required. One family of materials receiving significant interest in this area are hybrid perovskites, also known as organic-inorganic metal halides, which can be used in photovoltaic devices. The archetypal...
Local correlations and lattice dynamics in the advanced nuclear fuel system U3Si2
D. A. Chaney1*, A. Castellano2, J. Bouchet3, E. Brando3, G. Lapertot3, L. Harding4, R. Springell4, G.H. Lander4, A. Simonov5 and A. Bosak1
1ESRF, France, 2University of Liège, Belgium, 3CEA, France, 4University of Bristol, UK, 5ETH Zürich, Switzerland
daniel.chaney@esrf.fr
The international fission reactor...
Until now, the comprehensive structural analysis of single crystals of zeolite ECR-1, an aluminosilicate with the EON topology, has been hindered owing to the submicron dimensions of the obtained crystals. Additionally, this zeolite, which is characterized by a topology comprising alternating periodic building units of two other zeolites (MAZ and MOR layers), exhibits stacking faults that...
Long period stacking ordered (LPSO) phases represent a hot topic in the Mg-based alloys research. Despite numerous efforts[1,2], the structural characterization of these intermetallics cannot be yet considered fully satisfactory due both to their intrinsic structural complexity and to several unavoidable experimental difficulties. In this work we present the results of a combined 3D-ED/XRD...
Over the last 30 years, the Crystallographic Information Framework (CIF) has become one of the main means for recording and exchanging crystallographic data. As such, it has been widely adopted by crystallographers, scientific journals and crystallographic databases alike. However, a recent analysis of crystallographic data collected from peer-reviewed sources [1] suggests that the framework...
Calculations of scattering factors from wavefunctions have shown remarkable improvements in the quality of structural models, including accurate hydrogen atom positions from X-ray diffraction data, better precision of disorder models in more straightforward cases, and the treatment of almost any type of crystal structures, and improvement of electron diffraction data interpretation.[1–4] One...
The design and synthesis of water-soluble, synthetic macrocycles as artificial receptors and biomimetic models for enzymes has been a major subject of interest in recent years. Self-assembly of such synthetic receptors with biorelevant molecules is a powerful tool to understand, model and mimic biological systems and developing new materials with specific properties and functions.
The aim of...
The Rigaku XtaLAB Synergy-ED is a proven solution for microED with a seamless workflow from data collection to 3D structure determination. It features a JEOL electron source and optics, a Rigaku HyPix-ED detector, and Rigaku’s CrysAlisPro software. Our previous treatment of macromolecular microED on the XtaLAB Synergy-ED used cryo focused ion beam (cryo-FIB) milling to obtain crystals thin...
Magnetic nanoparticles have been and continue to be the focus of researchers, as it has been observed that the transition from microparticles to nanoparticles leads to huge changes in the physical and chemical properties of the material. Biofunctionalization and reproducibility of nanosystems prepared by various methods usually cost a lot of effort. As a result of these treatments, materials...
Hybrid organic inorganic materials are ideal platforms for the realisation of low-dimensional quantum magnets and the study of model Hamiltonians. In this context, the magnetic properties of the novel S = 1 NiX$_2$(3,5-lutidine)$_4$ materials with X = Cl, Br, or I have recently been reported by some of us.[1] Interestingly, in this family of materials a through-space two-halide exchange...
Resonant Elastic X-ray Scattering (REXS) is a powerful technique successfully employed to investigate a wide range of phenomena both in solids and thin films [1-3]. The particular combination of diffraction and spectroscopy features of this experimental approach allows the study of different charge, spin, and orbital orderings.
The beamline P09 [4] at PETRA III (DESY) is dedicated to the REXS...
Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to poor experimental access. I will describe ligand-, temperature-, and electric-field-based perturbations during X-ray diffraction experiments that make it possible...
A detailed understanding of the structure-property relationship is key to designing materials with tailored properties for specific applications. Single crystal X-ray diffraction is one of the most powerful analytical methods to provide this insight. Modern science benefits from the ability to perform experiments under non-ambient conditions, typically increasing pressure and decreasing...
Metal-organic frameworks (MOFs) are highly diverse polymeric materials, which are formed by strong covalent bonds between the selected metal nodes and organic linkers. It has been demonstrated in numerous instances where MOFs are excellent for gas separation applications1 and the hexafluosilicate (SIFSIX) MOFs are among them. The three-dimensional framework of SIFSIX MOFs is constructed by...
Generally perceived as inflexible, molecular crystals may, under certain circumstances, adapt to a variety of external stimuli whilst maintaining their integrity [1]. Once enriched with adaptable properties, crystals become exceptional candidates for application in advanced technologies where they bring in a range of fine-tunable properties. However, the practical application and...
Scanning/transmission electron microscopes (S/TEMs) are invaluable tools for the characterisation of nanosized matter, in no small part due their flexibility to be configured to perform a wide variety of experiments. The most well-known experiments are conventional high-resolution imaging modes, with a static parallel electron beam or a scanning converged electron probe. In recent years,...
Bacteriophages are the most abundant and diverse biological entities, found in all known ecosystems. However, phage genetic material remains largely uncharacterised. With an estimated population of 10^31, phages are most prolific natural predators of bacteria, outnumbering bacteria 10-fold and causing up to 50% mortality of bacterial cells produced daily. Phage-encoded lytic enzymes are...
Deinococcus radiodurans (Dr) is a Gram-positive bacterium highly resistant to stress conditions. The molecular basis of its resistance has been the subject of several studies [1]. A Dr cell harbours multiple copies of its genome and is equipped with an efficient DNA repair system capable of repairing the entire genome through homologous recombination [1]. Additionally, its capacity to protect...
Despite the tremendous attention that has been paid to metal-organic frameworks (MOFs) over the last few decades, with very few exceptions [1-3], all have been constructed from anionic ligands and metal ions or clusters in moderate to high oxidation states. These structural motifs are vastly different to those encountered in organometallic chemistry and nanoparticle catalysis more generally....
Cancer remains one of the leading diseases with very high mortality rate in the world today [1]. Therefore, the staggering statistics prompts the critical importance of increasing the rate of new radiopharmaceutical approvals. Organometallic complexes, in biomedical field, are well-established anticancer agents, with classic cisplatin and its derivatives commonly used in chemotherapy [2]. The...
Supramolecular architectures constructed via metallophilic interactions (M···M), especially using d8 and d10 metallic centers, constitute an active topic of research due to the rich electronic properties offered by the metal centers and weak nature M···M. Furthermore, the latter can often be modified by external stimuli. In consequence, such materials may find applications e.g. in...
Protein rotamer libraries are extensively used during the protein modelling process and have been shown to greatly improve the prediction of protein-ligand and protein-protein interactions as well as suggest amino acid mutations. Most of the strategies predicting the side-chain conformations involve calculating the dihedral angle averages for each side-chain from a subset of high-quality...
Global plastic production is a major world concern due to the increasing plastic pollution and subsequent negative environmental impacts. Thus, in the last decade enzyme-catalyzed depolymerization of synthetic polyesters has become extremely developing field, providing a chance for plastic recycling. In this research we expressed, purified, and structurally characterized Mgy protein - a novel...
Luminescent smart materials can respond to different types of external stimuli such as temperature, pressure or the presence of solvents, with changes in their emission, and this feature makes these materials likely candidates for applications as sensors. Our research group has already obtained some promising luminescent coordination compounds that present this behaviour [1,2]. Coordination...
Above its charge ordering temperature of 320 K, $\mathrm{LuFe_2O_4}$ becomes disordered with local order indicated by the emergence of diffuse helical scattering in its single crystal x-ray scattering patterns. Here we use 3D-ΔPDF informed Monte Carlo modelling to analyse the diffuse scattering in terms of correlated atomic displacements arising from polarons in the charge-disordered system....
The nature of interactions between entities can be an indicator of different types of multicomponent crystals. In cocrystal the hydrogen bonds most commonly govern aggregation, while in salts Coulomb interactions between ions are the most significant. When the crystal is built of Brønsted-Lowry acid-base pairs the ΔpKa rule can be used to predict which one will be formed. According to the...
Metal-organic magnets offer unique opportunities for control over magnetic function, as chemical functionalisation of the framework structure allows for tuning of the functional behaviour. This is particularly true for van der Waals materials, where the chemical flexibility permitted by the organic component allows for a diversity of structure and function not easily realisable in inorganic...
For the first time, we have determined the crystal structures of all four butene isomers: 1-butene (B), cis-2-butene (CB), trans-2-butene (TB), and isobutene (IB) at high-pressure by single-crystal X-ray diffraction techniques. These compounds, gases under ambient conditions, at high pressure and room temperature froze in their phases α at: 3.65, 1.55, 0.50 and 1.40 GPa,...
Climate change preoccupations motivate researching alternatives to energy-intensive vapor-compression thermodynamic machines, which use gases with tremendous greenhouse effect and are of limited thermodynamic efficiency. Roughly 3 billion systems (refrigeration, air-conditioning, heat pumps) consume around 1/6th of the whole global electricity production, with greenhouse gas emissions...
Quantum materials exhibit exotic phenomena arising from the intricate interplay between electronic, magnetic, and lattice degrees of freedom. Virtually all quantum materials are inorganic in nature and synthesized under conditions that provide nothing but thermodynamic control as a synthetic handle. Molecular chemistry offers the tools for addressing contemporary problems in quantum materials...
Due to the lack of efficient specific molecular interactions, achieving host-guest molecular recognition inside large and neutral metal organic cages (MOCs) is challenging. Preferential molecular recognition of aromatics using the internal binding sites of interlocked icosahedral (i.e., spherical) M12L8[1] MOCs within poly-[n]-catenane (1)[2] is presented (Figure 1).[3] The guest absorption...
The concerted movement of atoms in conjugated systems can produce chiral arrangements of chromophores, but how do we display the resultant symmetry? Our exploration of coordinate transforms in crystallography[1-2] led to a depiction of molecular symmetry and movement which was strongly informed by the work of Piet Mondrian, a pre-eminent Dutch artist of the modernist era. Mondrian’s artworks...
Here we present Moorhen, a next-generation client-side web-based application for the visualisation and manipulation of molecules in structure determination and analysis (Figure 1).
Recent developments in the field of cloud-based computing have enabled a rapid increase in the range of crystallographic tools available on the web, which crystallographers can use without the need for installing...
Sublimation remains an under-utilised technique for the crystallisation of molecular materials [1]. Our group has explored sublimation as a method to produce organic multi-component crystals [2]. We have shown that co-crystals and salts can be selectively crystallised from the gas phase by changing the sublimation conditions [3,4]. We have also investigated the sublimation of hydrates [5], as...
Calcium aluminate cement (CAC) presents several advantages in comparison to other types of cement. Its fast-setting, high-temperature and sulphate attack resistance make it a valuable choice for projects where quick strength development and heat-resistance characteristics are needed. Despite these advantages, CAC does have some limitations. One notable drawback is its initial setting strength...
Multicomponent crystals[1], viz., cocrystals and salts, designed and synthesised following crystal engineering[2] principles, are alternative solid forms of a parent material with altered structures and properties of interest. The number of reported cocrystals has been increasing exponentially in the Cambridge Structural Database every year. In the previous century, designing multicomponent...
See attached document
Cellulases are a group of enzymes that includes endoglucanase, exoglucanase, and β-glucosidase that play an important role in the hydrolysis of lignocellulosic biomass. The combined effect of these three major enzymes determines hydrolysis efficiency [1]. The hydrolysis of cellulose produces simple sugars that are further fermented to bioethanol [2]. β-glucosidase is a rate-limiting enzyme of...
The oxidoreductase myeloperoxidase (MPO) plays a key role in phagocytotic killing of invading pathogens by neutrophils as part of the innate immune response [1]. It is a highly stable dimeric protein, that undergoes a number of post-translational processing steps, including proteolytic cleavage at multiple sites, complex glycosylation and formation of an interdimeric disulphide bridge before...
Ureilites are achondritic meteorites mainly composed of olivine, pigeonite, carbon phases (graphite and diamond) and Fe-Ni compounds. All the ureilitic samples are believed to come from the same parent body, the Ureilitic Parent Body (UPB), which was catastrophically disrupted by impact event(s) [1]. Nowadays, the shock origin of diamonds in ureilites is the most supported and reliable process...
Detailed investigations of light and matter interactions are indispensable to understand mechanisms of many crucial (bio)chemical processes, the nature of excited-states and structural dynamics. Such knowledge can also be successfully applied to designing novel effective functional materials for applications in optoelectronics, solar-energy conversion systems, storage devices, various sensors...
The abstract is attached as a Word file
Electron diffraction acts as a powerful alternative for crystals and samples that are challenging for X-ray diffraction [1]. It can be performed in-house on a transmission electron microscope, and is also easily accessible. Automated data collection is always profitable, and the use of crystal picking algorithms can significantly reduce both the data collection time and radiation damage to the...
The effect of isotope substitution on the properties of materials is quite difficult to study with x-ray diffraction, especially when it involves H/D substitution and the property to investigate is related to the hydrogen bonding in the solid state. Neutron diffraction, is in fact a much better probe to locate the position of light atoms even in the presence of heavy ones. Furthermore, the...
Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP). This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from the ability to facilitate the deprotonation of a carbon next to a carbonyl group...
PETRA III is a 3rd generation synchrotron source operating 25 beamlines with almost 60 experiment station at DESY campus in Hamburg, Germany. In the next years, the accelerator is planned to be upgraded into the world’s most powerful synchrotron radiation source: PETRA IV will act as the ultimate X-ray microscope for nanoresearch, with outstanding potential for users from industry and with...
Non-ambient X-ray diffraction (NA-XRD) is an essential tool for the investigation of crystalline materials. It can provide insights into processes such as phase transitions, catalyst activation and degradation or sintering processes under different temperatures, pressures or gas atmospheres in-situ. These in-situ investigations allow the observation of intermediates or semi-stable phases, that...
Imatinib mesylate was approved by the U.S. Food and Drug Administration (FDA) in 2001, marketed under the trade names Gleevec and Glivec. It is a groundbreaking medication in the treatment of certain types of cancer, particularly in the management of chronic myeloid leukemia and gastrointestinal stromal tumors [1].
There are 10 forms of imatinib mesylate deposited in the Cambridge structure...
The modulation of physicochemical properties of an Active Pharmaceutic Ingredient (API) by means of prospection of new solid forms, such as salts, cocrystals, eutectics, among other, is of great interest to the pharmaceutical industry[1]. The design of a new Multicomponent Pharmaceutic Material (MPMs) can be carried out by means of crystal engineering strategies, once this approach covers the...
CORELLI is a unique instrument designed for measuring diffuse scattering from neutrons with a white beam. This feature enables the utilization of a statistical chopper with energy discrimination, facilitating the separation of the elastic from the total scattering signal. Moreover, CORELLI boasts unparalleled out-of-plane detector coverage, an exceptional neutron flux, and extensive reciprocal...
Multicomponent pharmaceutical crystals are composed of two or more substances, at least one of which is pharmaceutically active (Active Pharmaceutical Ingredients, API). In such crystals, the drug molecule remains chemically unchanged (cocrystals, solvates) or is ionized (salts), and is combined with the molecule(s) of another compound through non-covalent interactions. This changes the...
Over the past few years, the CaSiO3 system has been extensively investigated due to its status as one of the most abundant and pure calcium silicates on Earth. Despite its simple chemical composition, this system exhibits interesting structural complexity, featuring a significant number of polymorphs and polytypes across various pressure and temperature conditions [1-2] (Fig. 1.a). In minerals...
By tilting and rotating a thin single-crystal film (TSCF) in various ways (TSCF lies exactly on the plane of the crystal holder), we obtain an electron diffraction pattern of the type of lamellar oblique textures (Fig. 1a) and acicular textures (Fig. 1b) [1]. From the reflections h00 we determine the value of the parameter a of the crystal lattice, and from the reflections 10l the value of the...
We set out to investigate the structure and function of GbpA, an important colonization factor of Vibrio cholerae. GbpA aids colonization by attaching to chitin in environmental reservoirs as well as mucins in the human host (Fig. 1). Curiously, this colonization factor is secreted. One of the main challenges of this work is the complex crystalline nature of chitin. We sought to overcome this...
Quantum Crystallography (QCr) [1-2] is currently one of the most active research areas in small-molecule crystallography. QCr aims to enhance quantum chemical (QC) computations with experiments, and experiments by information from QC calculations. Starting from 1.) azulene [3], the classical example of a disordered crystal structure, questions arising from studying four selected and peculiar...
Physiological and environmental stress conditions can cause protein unfolding/misfolding in the endoplasmic reticulum (ER stress), where newly synthesized proteins fold and assemble. In eukaryotic cells a strategy to cope with accumulation of unfolded proteins is the induction of molecular chaperones and folding enzymes. This homeostatic response, known as the unfolded protein response (UPR),...
Molecular switches are systems that undergo chemical transformations under the influence of an external stimuli, such as temperature changes, irradiation, or electric field. Changes in molecular structure may be accompanied with alterations in physical properties, making them promising materials for various applications e.g. in materials science [1], optoelectronics [2] and medicine...
The attempt to fine-tune the structural properties requires mastering the supramolecular packing architecture [1-3], while isostructurality of the crystals may be preserved. The investigation of isostructurality leads to a deeper understanding of the close packing principles, the role of molecular conformation, supramolecular interactions and symmetries [4-5]. In isostructural crystals, both...
The contamination of aquatic ecosystems by anthropogenic activities presents a pressing global concern, necessitating effective water purification strategies to mitigate environmental and health risks. Traditional urban wastewater treatment methods often fail to adequately remove micropollutants, emphasizing the need for advanced water treatment solutions. [1-2] In particular, heavy metals...
Nucleic acid electron density interpretation after molecular replacement remains a difficult problem for computer programs to deal with. Programs tend to rely on time-consuming and computationally exhaustive searches to recognise characteristic features. We present NucleoFind, a deep-learning-based approach to interpreting and segmenting electron density. Using an electron density map from...
Over the years, Olex2 has established itself as user-friendly software, enabling novice users to quickly solve and refine X-ray structures. But what also comes in the box - and is often overlooked - is olex2.refine. This presentation will highlight olex2.refine's development directions and the new features it introduces in addition to the well-established refinement performed by ShelXL.
In...
Faster computers allow brute-force calculations that were too time-consuming a while ago, and the development of symmetry operation identification software, represented by spglib [1], makes way for new algorithms and implementations. Surprisingly, very fundamental math at the level of vector and matrix multiplication, inverse matrix calculation, and lattice problems without going deeply into...
Grazing incidence X-ray diffraction (GIXD) is the method of choice for the characterization of crystallographic order in thin films [1]. An essential part of the analysis of GIXD maps is the determination of accurate Bragg peak intensities, as they are directly related to the position of individual atoms within the unit cell. To correct for different measurement parameters a variety of...
Cocrystals are multicomponent crystalline molecular materials made of different chemical entities that crystallize within the same crystal structure held together by intermolecular noncovalent interactions. Cocrystallisation has been largely investigated in the modern literature since the novel intermolecular networks established between the molecular species involved can tune their ultimate...
Our planet is 4.6 billion years old. We call the first 500 million years the Hadean because until recently, it was thought that the surface of the planet at that time was like hell, a dry wasteland covered by rivers of lava, volcanoes, and bombarded by meteorites, a landscape where life has probability zero to emerge. We have no rocks from that time except some crystals of zircon that tell us...
This work summarizes the endeavour to develop an automated platform, named MicroCrys, based on two different macro-scale pipelines [1,2] previously designed and operating in our laboratory for the rational optimization of crystal growth by mapping temperature and/or precipitant concentration crystallization phase diagrams. MicroCrys is a miniaturization of these instruments and constitutes the...
The design and synthesis of molecular crystals is rapidly becoming one of the most active fields in solid-state chemistry, given its enormous economic impact on many fields, such as the production of pharmaceuticals, pigments, fertilizers, pesticides, energy-related materials, magnetic materials, organic semiconductors, porous systems. In this context, controlling polymorphism, namely the...
Homometric structures are distinct structures that possess the same weighted vector-distance set [1]. Pairs of homometric structures therefore cannot be distinguished by classical diffraction experiments. Actual examples of homometric structures have been described for polytypes, i.e. structures built of the same layers arranged in different ways [2]. However, these are exceedingly rare in...
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, remains a significant health concern in Latin America. A potential breakthrough in Chagas disease vaccine development lies in targeting Trypanosoma cruzi 80kDa prolyl oligopeptidase (TcPOP), a validated antigen. In this study, TcPOP was expressed in Escherichia coli, purified, and utilized as an immunogen in mice to...
Are your crystals ever as perfectly round as theory assumes the perfect crystal to be, never twinned, never strongly absorbing, never seeing any icing on your frames? In real life, such perfection is rarely met, and every measurement requires a unique data processing treatment. Making an informed decision on a data processing strategy can be difficult when results are not becoming visible...
PROTACs (Proteolysis Targeting Chimeras) are bi-functional molecules which use the body's own protein degradation system to remove unwanted proteins. They bind an E3 ligase with the “anchor” end and the target protein with the “warhead” end with a linker joining the ends, thereby bringing the target protein into close proximity to an E3 ligase. The E3 ligase then (poly-)ubiquitinates the...
X-ray radiation offers unparalleled advantages in material characterization due to its remarkable ability to penetrate materials with-out destroying them. This unique capability enables researchers to investigate the physical properties of materials in situ and operando, revealing structural transitions that are affected by external factors such as temperature and electric fields....
Sarcomeres are the smallest contractile units found in cardiac and skeletal muscle, where actin and myosin filaments move past each other to generate tension. This molecular machinery is supported by a subset of highly organised cytoskeletal proteins that perform architectural, mechanical, and signalling functions. The ultrastructure of a sarcomere is highly ordered and bordered by Z-disks,...
Order-disorder control in functional oxides
G. Marshall1, J. S. O. Evans1, I. R. Evans1
1University of Durham, Lower Mount Joy, South Rd, Durham, DH1 3LE
george.marshall2@Durham.ac.uk
The exploitable properties of many functional materials (e.g., their electronic, magnetic, or dielectric properties) are intimately linked to their atomic structure. Investigating the order-disorder...
Palladium shows high activity and selectivity in the heterogeneous catalysis of organic reactions which occur on the surface of this metal. As the raw material price of palladium has increased eightfold in the last 20 years, it is an interesting option to reduce the amount of palladium in these reactions. This could be realised by using ultrasmall nanoparticles with a size of less than 3 nm,...
The reversible CO2/formate interconversion by Mo/W-Formate dehydrogenases (Fdhs) is a promising route not only for green-house gas sequestration but also to sustainably produce fuel. Formate is a safe option for hydrogen storage/delivery (53g H2/L) in cell power applications [1].
W-FdhAB (periplasmic heterodimer; W active site: bisMGD, Se(Cys), S ligand; 4x[4Fe-4S]) is the main responsible...
Serial X-ray diffraction (XRD) using free-electron lasers and synchrotron sources has shown great advantages in studying the structure of microcrystals and time resolved structure changes. Recently, serial electron diffraction has also been developed, which shows promise for studying microcrystals, complementing both XRD and 3D electron diffraction methods. Common to all serial diffraction is...
Over the past two decades, there has been an increased interest in halogen-bonded molecular crystals due to their potential use in a variety of applications such as luminescent materials, magnetic materials, soft materials, and pharmaceutical solids [1]. The physicochemical properties of these solids are driven by their crystal packing. Understanding the packing of molecules within the crystal...
Nanotubes (NT) are considered promising materials for future electronics, sensors and nanomechanical devices. However, it is known that the properties of the NT depend on their structure. During the NT synthesis unwanted phases often occur (platelets, amorphic content, etc.) [1, 2] and it is hard or even impossible to disentangle the structural information about the NTs from the data achieved...
Pd(II) and Pt(II) complexes with
N-benzylphenotiazine – Hirshfeld atom refinement and intermolecular interaction energies
M.G. Bogdanović1, T.P. Andrejević2, B.Đ. Glišić2, D.P. Ašanin3, M.V. Rodić1
1University of Novi Sad, Faculty of Sciences, Novi Sad, Serbia, 2University of Kragujevac, Faculty of Sciences, Kragujevac, Serbia, 3University of Kragujevac, Institute for Information...
The pressure induced phase transitions and phase diagram are long term topics in condense matter physics. Many interesting behav-iors, such as high Tc superconductivity under high pressure conditions, were reported in last decade, but the responsible structures are not well studied at correct P-T conditions and mechanisms are far away from fully understood. In this presentation, several...
Binary vanadium oxides exhibit a wide range of magnetic, electronic, and catalytic properties. Their magnetic and electronic transitions have recently been proposed for volatile resistive switching devices and neuromorphic computing [1]. The versatility of a vanadium cation to assume different valence states, its changing local environment, and the flexibility of the framework geometry of...
Titanium-oxo clusters are molecular analogues for bulk and nanomaterial titanium dioxide. They consist of an inner core of titanium oxide, which is supported by coordinated organic ligands. In the solution phase UV light causes clusters with formula [TiO(OiPr)L]n (L = O2CtBu, n = 6; L = O2PPh2, n = 4) to undergo a photochemical transformation.[1, 2] In this process, two Ti(IV) sites become...
Molecular interactions formed between solute and solvent can profoundly affect the optical spectra of solutions, altering the position, intensity, and shape of absorption and emission bands. Solvatochromic dyes, which are particularly sensitive to the physicochemical nature of the surrounding medium, manifest a strong, visible changes in their solution colour.[1] This phenomenon, known as...
In this study, Na2CoxNi1-xSi4O10 (0.0 ≤ x ≤ 1.0) compositions were prepared via the chemical co-precipitation method to minimise the toxic and expensive amounts of cobalt and nickel. Colour in these compositions is due to Co(II) and Ni(II) ions in olivine structure that crystallize together with NaCl and SiO2. The fusion of NaCl since 800 ºC from these compositions coincides with the...
Hybrid photon counting (HPC) X-ray detectors have emerged as crucial tools in synchrotron research due to their ability to provide noise-free detection and rapid readout capabilities [1-3]. The PILATUS4 detectors, designed as successors to the PILATUS3 series [4,5], offer a combination of a large active area and high frame rates, essential for various scientific applications.
The PILATUS4...
The term ‘bad metal’ behavior is used to describe the unusual metallic properties of polar intermetallics. It is the result of a combination of low free electron concentration with a small free electron path length [1,2]. Polar intermetallic phases combine metallic bonding with ionic and covalent bonding contributions [3,4]. Unlike Zintl phases, however, the electron transition from the...
The class of benzothieno-benzothiophene (BTBT) molecules attracts large attention since it shows outstanding performance as organic thin film transistors. One specific derivative of BTBT-type molecules has oligoethylene-side chains attached at the terminal ends of the conjugated core. The chemical structure of the molecule is given in Figure 1. A classical polymorph screening procedure is...
The unique characteristics of lead halide hybrid organic-inorganic compounds (specifically 3D and 2D hybrid perovskites (HOIPs) of the ABX3 and A2BX4 formula, respectively [1]) arise directly from molecular-level interactions and are strictly contingent on the constituents within the structure. Thus, altering the chemical composition is essential for comprehending and modifying their...
Triacylglycerols (TAGs) are among the most abundant lipids in the food and cosmetics industries. Additionally, they are of special interest in controlled drug delivery and sustained release applications in pharmaceuticals, being a key material in the preparation of solid lipid nanoparticles. TAGs exhibit monotropic polymorphism, forming three main polymorphic forms upon crystallization - α, β’...
Exhaustive characterisation of polymorphism and phase transitions in active pharmaceutical ingredients is crucial in the development of solid forms in patient therapy. Polymorphs may differ in physicochemical properties, such as solubility and compressibility, which affect the bioavailability or tabletability of a drug [1]. High pressure offers an attractive method for studying the underlying...
Different packing of molecules in crystals leads to different properties of solids. 3D electron diffraction (3D ED) has been successfully used in two different research projects where the determination of the structure was crucial to explain the observed properties of the prepared materials: (a) nanocrystals blooming on fibers used to fabricate long-lasting bed nets for malaria control (Figure...
One of the famous examples of silver treasures from the late Roman period is the Seuso Treasure, the pieces of which (14 silver objects so far) were found hidden in a large copper cauldron, buried in the ground. The provenance (finding location) of the cauldron is uncertain, but it is currently kept in the Hungarian National Museum. The cylindrical, large-sized cauldron has a diameter of 83...
In analogy to the non-centrosymmetric Ln3OX[AsO3]2 representatives (Ln = Ce – Nd, Sm – Dy; X = Cl and Br)[1–5], the isostructural iodide Pr3OI[AsO3]2 was obtained in synthetic experiments with Pr, PrI3, As2O3 with CsI as flux by means of a partial metallothermic reduction at 850 °C. The green, needle-shaped crystals could be recovered phase-pure after removal of the resulting monolithic...
Carboxylic acids play a pivotal role in crystal engineering, owing to their ability to form hydrogen-bonded cyclic dimers, which route the crystallization process. Benzoic acid (BZA) is the prototype of aromatic carboxylic acids. Recent results from our group [1] point out that several intermolecular recognition modes are present in the liquid phase, where the cyclic dimers that are found also...
A key step in the structure determination process of protein crystals is an estimation of the molecular unit cell content, which can be performed after diffraction data has been indexed with a candidate lattice using modern diffraction reduction software. Identifying the potential number of molecules in the unit cell, and the corresponding solvent content, plays a key role in identifying the...
Single crystal X-ray diffraction experiments under ambient as well as high pressure were performed to investigate the solid state structure of [Ni(Tp)(acac)(MeCN)] (Tp = Tris(3,5-dimethyl)pyrazol-2-ylborate, acac = acetylacetonate, MeCN = acetonitrile). All X-ray diffraction experiments were performed on a unique in-house diffractometer equipped with a Dectris Eiger 2R 1M CdTe detector,...
In the quasi-one-dimensional material Rb2Mo6Se6, a charge density wave (CDW) has long been suspected based on the strong resistivity upturn at low temperatures and based on considerations of Fermi surface nesting. A long range ordered CDW has, however, never been observed and the electrical resistivity does not show any clear transition temperature at ambient pressure. In our recent works, we...
In this presentation, two types of selected engineering oxides, including doped nano oxide and high entropy oxides (HEO) will be introduced for their novel pressure induced phase transition behaviours. In order to detect the local structure distortion and potential phase transition under pressure, in situ high-pressure Raman spectra were measured in a diamond anvil cell (DAC) at room...
Organic semiconductors (OSCs) are receiving significant attention for their potential in photovoltaic applications, owing to their light weight, low-cost production, low-temperature processing, mechanical flexibility, and abundant availability. These materials, primarily consisting of π-bonded molecules or polymers made from carbon, nitrogen, oxygen, and hydrogen, can exist in multiple...
Imogolite metal-oxide nanotubes, with diameters similar to those of single or double-walled carbon nanotubes, are emerging as promising nanostructures in several nanoscience fields, such as nanofluidics [1] and photocatalysis [2]. Compared with carbon nanotubes, they offer the advantage of being synthesized with a well-controlled morphology and monodispersity in diameter and chirality. They...
Based on widely accepted rules of thumb [1, 2] of high-pressure crystal chemistry, elements at elevated pressure increase their coordination number and behave like the elements below them in the periodic table at lower pressures. It was noted already in the highly acclaimed structural chemistry book by Alexander Frank Wells [3] that the crystal structures of gray arsenic (Strukturbericht A7,...
Sugar distribution plays essential roles in energy, signaling, and defense mechanisms. Sugar Transport Proteins (STPs) are part of the Sugar Porter family that also include human GLUTs. In plants, STPs are responsible for proton-driven cellular uptake of glucose, derived from sucrose in the apoplast. Few STPs also facilitate uptake of fructose, the other constituent of sucrose but the...
The isolable relationship between the organometallic compound Cp'''NiP3 and white phosphorus is investigated using multipolar modeling and X-ray restrained wavefunction fitting. The resulting complementary bonding analysis validates the isolobale principle but also explains differences in the reactivity of the two compounds. Cp'''NiP3 is described as metallatetrahedrane.
The work presents an...
Protein crystals, with their ordered assembly of nano-machines, provide a basis for advanced biomaterials design and development. Protein crystallisation, however, remains a challenging, case-by-case endeavour. The challenge arises from the chemical and geometric complexity of protein surfaces. Different strategies are available to overcome this challenge. Water soluble macrocycles are proving...
Macromolecular crystallization occurs in a complex scenario in which several variables such as the solution pH, the precipitant nature, the presence of additives or the temperature, among others, play an essential role. After finding the right crystallization conditions, efforts are focused either on controlling crystal quality to get the best possible diffraction data for the 3D structural...
Serial electron diffraction (SerialED) promises several advantages over traditional rotational data collection methods such as microED/3D ED. By distributing radiation over multiple crystals, SerialED achieves higher signal-to-noise ratios, which lead to higher resolution structures and significantly reduced radiation damage. This improvement is particularly beneficial for addressing...
The Protein Targeting to Glycogen (PTG) facilitates the dephosphorylation and activation of glycogen synthase (GYS) by directing the protein phosphatase (PP1) to glycogen. In the brain, PTG undergoes ubiquitination via the Laforin/Malin complex, leading to its degradation and resulting in minimal glycogen levels in neurons and reduced levels in astrocytes [1]. Mutations in either Laforin or...
The Hofmeister Series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive.
We propose a correlation, based on published data and crystallisation...
In 2023 the Dianthus screening platform was delivered to the joint laboratories of the Biophysical Sciences Institute at Durham University. So far, a number of projects ranging from protein-protein interactions to ligand discovery and optimization have benefitted from this new technology. Here, examples and experiences from our drug discovery campaigns focusing on neglected tropical diseases1,...
Word file is in the attachment.
In this study, we present an integrated experimental-computational approach to explore the solid-form landscape of the highly conformationally flexible molecule, chlorpropamide (CPA). CPA is unusual in the sense that in that it has been subject to significant solid form screening experiments utilising a range of non-traditional approaches that include high pressure and mechanochemistry. ...
Crystal structure prediction (CSP) algorithms serve as indispensable tools for determining stable and metastable phases associated with specific chemical compositions.[1] Despite their utility in structural recognition from experimental data, particularly in powder X-ray diffraction (PXRD), discrepancies between predicted and experimental results persist, especially under compression. These...
3-Dimensional Electron Diffraction (3DED) is a key technique for characterizing nanocrystalline materials, but it is currently limited by not specialized hardware and software. [1] These limitations become relevant when working with low dimensional or highly agglomerated nanocrystals (few tens of nanometres), as the lack of standard reproducible goniometers with precision in the nanometre...
In the crystallographic community refinement using the independent atom model is ubiquitous while more sophisticated methods of describing the aspheric electron density are largely ignored. The slow but consistent adoption of Hirshfeld atom refinement implemented in Olex2 [1] in the form of NoSpherA2 [2] has shown that if the experience of using more sophisticated models is sufficiently...
Crystallographic databases, such as the Crystallography Open Database (COD [1], https://www.crystallography.net/cod/), are important resources for structural knowledge of chemical compounds. With the advent of machine learning methods, quality control in datasets becomes more and more important due to the increased reliance on black box approaches [2]. Here we present the recent developments...
Quantum Crystallography (QCr) uses various types of aspherical atomic electron densities (consequently aspherical atomic scattering factors) in the refinement of the structures of crystals and their electron densities against X-ray diffraction data. The main methods of QCr are: the refinement of multipole model of quantitative electron density distributions, the refinement of experimental...
Crystals are complicated. A thorough model of a crystal must describe not only the atomic positions, but also the atomic and molecular vibrations and possible disorder. Whereas the static models of charge densities refined against high-resolution diffraction data have been compared extensively to high-level periodic ab-initio calculations, there has been less focus on the use of ab-initio...
Owing to the limited quality of experimental data, such as resolution, atomic model refinement using cryo-EM or crystallographic experimental data is often a challenging task. To make refinement practical, a priori information about model geometry is always used as chemical restraints. These restraints originate from standard libraries that are used across most structure solution software in...
Quarter century of the statistical method in crystallography
J. Wolny, R. Strzalka, I. Buganski, J. Smietanska-Nowak
AGH University of Krakow, Faculty of Physics and Applied Computer Science, Krakow, Poland
wolny@fis.agh.edu.pl
Higher-dimensional crystallography first introduced to modulated crystals by de Wolff, Janner, and Janssen is about to celebrate 50 years. The discovery of...
We are at present carrying out a systematic search for quaternary alumosilicides and alumogermanides containing a rare-earth metal (R) and a 3d-metal (T). Alumosilicides of two compositions, R2TAl4Si2, R3TAl3Si2, and alumogermanides of four compositions, RTAl4Ge2, R2TAl4Ge2, R3TAl3Ge2, R5T3Al3Ge4, were synthesized by arc melting under argon and annealed at 873 K for up to three months. The...
Information-theoretic methods for objective classifications of digital images and electron diffraction spot patterns into projected Laue classes and plane symmetry groups [1, 2] as well as 2D point symmetry groups [3] have recently been developed. The objectivity of these crystallographic symmetry classifications is ensured by the selections of the best geometric models for complementing...
Quinolines are molecular species often found in multi-component crystalline systems due to their great ability of participating in intermolecular interactions [1,2], specifically due to the presence of the aromatic nitrogen in the quinolines’ core, known as a reliable supramolecular tool [3]. In addition to the pyridinic nitrogen, the quinoline-derivative, quinoline-6-carbonitrile (Q6CN), used...
New applications for porous coordination polymers (CPs) are continuously emerging due to their tuneable pore size, selectivity, and metal activity. CPs have been investigated for their wide range of properties, like magnetism. Naphthalenediimides (NDIs) are chemically robust and electron deficient ligands. They are very versatile due to the amenability of the NDI core to functionalisation...
RamanCrystalHunter (RCH) is a new program that includes novel techniques for processing, interpretation, and identification of unknown Raman spectra through comparison with reference spectra in the new RamanCrystalHunter Database (RCHDB). RCH features a versatile and intuitive graphical interface where both specialist and non-specialist users can easily perform many visualization and...
Ranolazine (RNL) is an anti-anginal drug widely used in treating cardiovascular diseases, which shows advantages over other anti-anginal agents because it exhibits an anti-ischemic effect [1,2]. Unfortunately, its bioavailability is limited by its low aqueous solubility [3]. Moreover, there is scarcity of scientific results regarding the solid-state forms of RNL. Within this framework, we...
Introducing chiral cations into hybrid organic-inorganic metal halides (HOIMHs) is paving the path for innovative materials combining the benefits of the chiral molecules, as the second-order non-linear optical response [1], and the adjustable absorption and luminescence properties deriving from the HOIMHs structures [2,3]. The heightened design flexibility allows for the creation of materials...
Disclosure of crystallochemical information to rationalize the solid-state performance of bulk materials cannot prescind from the (combined) application of advanced characterization techniques, which is beneficial in both the short and the long term. As a matter of fact, this strategy not only provides a comprehensive picture for the current case of study, but also paves the way to the...
IUCrData, the peer-reviewed open-access data publication from the International Union of Crystallography (IUCr), has launched a new section: Raw Data Letters as a collaborative innovation of IUCr Journals with the IUCr Committee on Data.
Future raw data sets will become increasingly large and no one group will be able to analyse all the scientific content in a timely manner and others will...
Rb$_4$[As$_2$S$_{10}$]: A Rubidium Polythioarsenate(V) with an Unusual Discrete [S$_3$AsS(S$_2$)SAsS$_3$]$^{4−}$ Anion
Since polythioarsenate and -phosphate fluxes were successfully used during the syntheses of quaternary thioarsenates and -phosphates in the past, it is surprising that for thioarsenates just a few [As$_x$S$_y$]$^{n−}$ anions such as [AsS$_4$]$^{3−}$ and...
Suboxides of heavy alkali metals can be described as metal-rich oxides with a surplus of electrons. In their structures regions with ionic bonding as well as regions with metallic bonding can be discerned, and macroscopic metallic behaviour is observed. In this family of ‘complex metals’ or ‘metals with holes’ clusters of [A$_6$O] octahedra occur as discrete units, for example for caesium as...
In situ and operando experiments are the studies of real-time reactions, but while the diffraction measurements might be real-time, the data analysis often take days, weeks, months or even years. At the DanMAX beamline we aim to reduce that time significantly – at least for the preliminary analysis. Part of the motivation for this is of course to reduce the time from experiment to publication,...
Chemical crystallography beamline P24 offers a wide range of crystallographic applications such as charge density analysis, disordered and modulated structures, x-ray standing wave and phase transitions studies under ambient and non-ambient conditions. The beamline consists of two experimental hutches housing a heavy load Kappa diffractometer (EH1) and Eulerian diffractometer (EH2). Both...
Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme of the Calvin–Benson cycle through which oxygenic phototrophs perform carbon fixation. The cycle as well as the light-harvesting reactions of photosynthesis are modulated by different mechanisms to adjust them to rapid environmental changes.
Different GAPDH isoforms exist in higher plants: the most abundant is a...
What would our research look like if everyone had fast access to high quality synchrotron powder diffraction data? How does materials research change when we can measure thousands of samples in the matter of hours? Does more, does better data really make a difference? How does this change our approach to data analysis?
Momentum Transfer has been formed around the ideal of bringing...
In today’s technology, the need for data- and energy storage devices with a high efficiency and capacity, as well as a high writing speed for the former is ever increasing. For such applications, materials with a magnetic nature, i.e. Ferro-, Ferri- and Antiferromagnetic, are indispensable [1]. In such a context, a variety of transition-metal phosphates is receiving a growing interest [2-3]....
Friction welding is a relatively fast joining process, which occurs in a solid-state manner and is often used due to the possibility of achieving lower residual stresses and distortions [1]. The study presented in this paper focuses on employing the direct drive friction welding process to join SAF 2205 duplex stainless steel and API X52 high strength low alloy material and aims to enhance the...
Ferroelectrics form critical components of contemporary electronic devices owing to their appealing electromechanical properties. The cubic perovskite BaTiO3 comprises one of the most renowned ferroelectric materials, where ferroelectricity occurs due to an off-centre displacement of the octahedral Ti4+ cations along the <111> directions [1]. While the cubic polytype of BaTiO3 (3C-BaTiO3) has...
Resorcinol polymorphism: the lattice energy and conformers
A. Katrusiak, S. Batmanghelich, J. Kaczkowski, I. Plowas-Korus
Department of Materials Chemistry, Adam Mickiewicz University of Poznan,
Institute of Molecular Physics of the Polish Academy of Sciences
shibat@amu.edu.pl
Resorcinol, 1,3-benzediol, C6H6O2, is a common building block in the synthesis of numerous polymers and a...
The hole-doped lanthanum cuprates, based on Ruddlesden-Popper n = 1 (RP1) La2CuO4, have attracted intense focus since the discovery of high-temperature superconductivity in La2-xBaxCuO4. The temperature vs doping level (x) phase diagram for these materials includes a region around x = 0.125 (1/8th) featuring a marked drop in superconducting critical temperature (Tc). This region is understood...
Magnetic anisotropy is an essential property of primary importance in areas ranging from molecular magnetism and magneto-optics to magnetoelectric transport. It is an inherent characteristic of magnetic materials that describes the response of magnetization to a magnetic field. Several techniques are currently used to extract information about bulk magnetic anisotropy; the most well-known are...
Square planar rhodium(I) complexes of the type [Rh(L,L’-Bid)(CO)(PPX3)], where L,L’-Bid = monoanionic bidentate ligands and PPX3 are tertiary phosphine ligands, have been extensively investigated as potential catalyst precursors in different conversion reactions. [1-5]
The main objective of this current study is to use solution and solid state 31P NMR spectroscopy in conjunction with X-ray...
Meloxicam (MLX) is an anti-inflammatory drug used to treat arthritis. It is an interesting molecule prone to form diverse polymorphic forms, solvates, salts with organic and inorganic acids and basis, as well as cocrystals. We have recently reported a reliable and repeatable protocol for the crystallization of three elusive forms of MLX [1], with some of the attempts involving crystallization...
For hundreds of years, crystals were studied almost exclusively by discrete tools such as symmetry groups. The classification of 230 space groups into 230 types was a great achievement at the end of the 19th century. These 230 classes were sufficient when hundreds of known crystals could be visually compared by experts until discontinuities were reported in 1965 [1]. In 2024, the Cambridge...
We have structurally analyzed the coordination possibilities of L-carnosine in reaction with copper(II) under different conditions. Three coordination compounds were synthesized. They comprise almost the same building blocks – isoskeletal dimers that differ in the apical ligand coordinated to Cu(II) ions (water or methanol molecule). These can be removed by heating, altering the Cu(II) ion...
When it comes to teaching crystallography, at most stages of education the start and end points are covered. Crystal growing experiments are synonymous with elementary and high school science and the Cambridge Structural Database (CSD) teaching subset [1] exposes students to the 3D structures of chemicals in the form of crystal structure determinations. Little attention has been given to the...
Serial data collection and microED techniques usually require “slurries” of tiny, well-ordered crystals. Neutron diffraction requires very large single crystals. Microseeding effectively generates such samples since the seed stock can be concentrated or diluted as required. During the 16 years since the random microseed matrix-screening (rMMS) method was published, understanding of the...
Serial data collection and microED techniques usually require “slurries” of tiny, well-ordered crystals. Neutron diffraction requires very large single crystals. Microseeding effectively generates such samples since the seed stock can be concentrated or diluted as required. During the 16 years since the random microseed matrix-screening (rMMS) method was published, understanding of the...
ALBA is a 3-GeV synchrotron radiation facility located near Barcelona, Spain, servicing worldwide academic and industrial users with ten operating beamlines and four more in construction. Two of these beamlines are dedicated to macromolecular crystallography (MX): BL13-XALOC, a flexible beamline in operation since 2012, and BL06-XAIRA, a microfocus beamline currently under commission. Each of...
The formation of unknown polymorphs due to the crystallization at a substrate surface is frequently observed. This phenomenon is much less studied for epitaxially grown molecular crystals, since the unambiguous proof of a new polymorph is a challenging task. The existence of multiple epitaxial alignments of the crystallites together with the simultaneous presence of different polymorphs do not...
Long flexible chain organic molecules impose a significant challenge to the experimentalist when crystals are needed, e. g. for crystal structure analysis. A variety of methods, such as the crystal sponge method or the nano-droplets method are valuable tools in the quest for obtaining crystals for structure elucidation. Chaperones can assist in the crystallization of compounds that do not...
This study case deals with structure-related linear and non-linear optical properties of a new solid solution series, Li1(LiXNa5–X)Mo9O30 [1]. Large single crystals grown using the Czochralski were oriented on a X-ray Laue camera and cut into plates parallel to the crystallographic main directions to determine non-linear optical (NLO) coefficients d_ij by means of the rotational Maker fringe...
See attached for abstract
P11 at PETRA III (DESY, Hamburg) is a high-throughput instrument for macromolecular crystallography [1]. P11 has tuneable photon energy between 5.5 - 28 keV having the Eiger2 X 16M as the stationary detector. Beam size from 200x200 μm2 to 4x9 μm2 can be used with a maximum photon flux of 1x1013 ph/s at 12 keV energy.
P11 is a diverse environment able to accommodate various non-standard...
Serial macromolecular crystallography (SMX) has emerged as a highly effective technique for uncovering the structures of biological macromolecules at room temperature (RT). While microfocus beamlines at third-generation synchrotrons are invaluable, their capacity for data acquisition is often restricted to the millisecond time scale due to limitations in photon flux and detector capabilities....
Near-infrared (NIR) emission is of significant importance despite its relative scarcity. It finds numerous applications, particularly in the fileds of optoelectronics and biological imaging, owing to the weak absorption of near-infrared by tissues, commonly referred to as the ‘biological window’. In this study, we synthesized and characterized...
The in-depth understanding of manufacturing technique and corrosion process of cultural heritage materials very often requires reliable structural characterization. Techniques like X-ray diffraction, Scanning Electron Microscopy, Raman, Fourier Transformed Infrared Spectroscopy are usually employed to the study such materials. In recent years, scientific community has also shown a renewed...
Short-Range Order and 3D-ΔPDF in V1-xMoxO2
M. Krogstad1
1Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL, USA
krogstad@anl.gov
A cornerstone of condensed matter physics is the determination of crystal structure, consisting of perfect translational symmetry over long range, which produces sharp Bragg peaks in x-ray scattering. However, locally correlated deviations from the...
The talk consists of two parts, as described below:
The spike-mediated cell entry mechanisms of common cold betacoronaviruses are poorly understood. In contrast to the highly pathogenic SARS-CoV, SARS-CoV-2 and MERS-CoV, which engage proteinaceous receptors via the S1B domain, the spike protein of human betacoronaviruses HKU1 and OC43 have only been visualized in the fully closed, prefusion...
In the innate immune response, activation of the pattern recognition receptors Nucleotide Oligomerization Domain 1 and 2 (NOD1 and NOD2) triggers a proinflammatory response, which plays a crucial role in both bacterial pathogen detection and gut homeostasis maintenance. Dysregulation of NOD signalling is involved in several genetic and non-genetic inflammatory diseases, such as Inflammatory...
The heart of the steelmaking process is the blast furnace, where iron ore is reduced to metallic iron. Following the initial mechanical processing of the ore, two particle fractions can be distinguished: lump (31.5 to 6.3 mm) and fine (<6.3 mm) products [1]. However, the fine fraction (<6.3 mm) cannot be used directly in the blast furnace process. This is primarily due to the loss of particles...
Please see attached document.
Proteins undergo various conformational transitions throughout their lifecycle, that are induced by environmental factors and interactions with other biomolecules. This dynamic behavior severely impedes unraveling the mechanistic details of protein function, because only in rare cases can all the relevant conformations be observed directly with current technology. AI-driven methods, while...
The role of the single-crystal X-ray analysis (SC-XRD) in chemistry from 1990’s as a ‘fast, first resort analytical tool’ [1] is even more relevant nowadays, as the structural characterization of novel compounds becomes a pre-requisite for publication in the high-level chemical journals. On the one hand, fast automatic diffractometers and user-friendly software makes ground to a ‘black box’...
Conventional X-ray single-crystal diffraction measures the reflections, while the crystal is rotated. Similarly, serial crystallography at synchrotrons and X-ray free electron lasers (XFELs) takes multiple diffraction patterns of crystal replicas in random orientations. The common requirement of changing / multiple orientations is imposed by the need to swipe through the 3D reciprocal space...
With the advent of next generation modelling methods, such as AlphaFold2, structural biologists are increasingly using predicted structures to obtain structure solutions via Molecular Replacement (MR) or model fitting in Cryo Electron Microscopy (Cryo-EM). Inaccuracy in domain-domain orientations is often a key limitation when using predicted models. Slice’N’Dice is a software package designed...
The electron configuration of the transition metals in the coordination compounds can be switched by changes in temperature, pressure or light irradiation with a specific wavelength (Light-Induced Excited Spin-State Trapping, i.e. LIESST effect) [1]. The new spin state, obtained in this way, has an influence on the alterations of the magnetic, optical and structural properties. Changing the...
The human cytomegalovirus (HCMV) persists indefinitely despite vigorous humoral and cellular immune reactions. This virus poses a substantial threat to the well-being and survival of immunocompromised persons, including transplant recipients and individuals with HIV, as well as those affected by congenital infection. Therefore, a vaccine against HCMV is considered to be the highest priority,...
Radiometal-based radiopharmaceuticals offer a unique opportunity to diagnose, treat, and monitor many diseases, including cancer. While only a few radioactive metals have been used in recent decades due to difficulties in their production and purification, a wide variety of non-standard radionuclides are available today, offering a great choice in terms of decay energy and properties, and thus...
Two isostructural at room temperature complexes of Bi(III) with halogens and, 1-phenylethyl-N-ethylthiosemicarbazide have been investigated in order to scrutinize the solid-to-solid phase transitions induced by temperature in analogous structures.
The experiments allowed establishing the structures of chloride and bromide (2) complexes of general formula (µ2-X) (BiX2L2)2 where X is Cl or Br,...
Typically for crystals of small size (<1000 μm3), powdered X-ray diffraction (PXRD) is a useful alternative to the single-crystal X-ray diffraction (SCXRD) technique. Nevertheless, single-crystal diffraction experiments remain preferable for obtaining highly detailed and accurate crystal structures. Over the past two decades, rapid progress has been made in 3D electron diffraction (3DED) and...
In the past, structure solution was unthinkable without profound expertise in space groups. One had to determine the Laue class given by the symmetry of the diffraction pattern and then to check the systematic absences. This led to one or more possible space groups and the structure solution needed to be tested in these space groups. Later programs like XPREP [1] facilitated the...
For many experimental techniques, sample morphology is a critical factor for success. For example, in the case of low energy diffraction experiments, a spherical crystal can mitigate and potentially remove the need for absorption corrections of the diffracted X-rays [1]. We have developed a laser system to shape crystals or other materials into spheres (Figure 1), or any shape required to...
The steroidal drug, spironolactone, is a well-established and widely-used diuretic and aldosterone antagonist. It forms numerous polymorphs and solvates, thus frequently featuring in studies within the crystallographic community. The first single-crystal data were available in 1972, with subsequent studies finding other polymorphs or solvates aiming at improving its solubility and,...
High pressure crystallography in the home lab has revolutionized the study of materials under extreme conditions. However, obtaining high-quality data for successful structure determination, especially for samples with low symmetry, poses a major challenge. Despite the powerful techniques available, the volume of reciprocal space accessible for X-ray examination is constrained by the shape and...
Marine cyanobacteria are main contributors to carbon and nitrogen fixation, yet they are limited by iron availability. The most abundant and smallest photosynthetic organism on Earth is the cyanobacterium Prochlorococcus that can thrive in low nutrient waters [1]. Interestingly, Prochlorococcus has a single FutA iron binding protein, in contrast to cyanobacteria that possess two FutA proteins...
Symmetry breaking is pivotal for controlling ferroic functions in materials, such as ferroelectric, ferromagnetic or ferroelastic,[1, 2] which enables applications in sensors, memories, transducers or actuators.[3] Commonly, ferroic phases emerge from descendant symmetry-breaking. Indeed, the laws of thermodynamics dictate that the ordered low entropy ferroic phase forms at low temperature,...
The α-phase of Pigment Orange 13 is a microcrystalline powder. No large crystals suitable for single-crystal X-ray diffraction could be grown. The X-ray powder diffractogram consists of only a few peaks, which could not be indexed reliably. Therefore, single-crystal 3D electron diffraction (3D ED) data were collected [1].
The electron diffraction space consists of sharp Bragg reflections and...
Here we describe the current state and recent advancements in diamond anvil (DAC) research capabilities at the Extreme Conditions Beamline (ECB, P02.2), PETRA III, Hamburg, Germany.[1,2] The ECB specialises in DAC experiments in the fields of high-pressure physics, geophysics, chemistry and materials science. The beamline provides a tightly focused X-ray beam at high energies and high...
The excitonic insulator (EI) is a coherent electronic phase which was predicted to be realized in narrow gap semiconductors and semimetals with small band overlap driven by poorly screened coulomb interaction between conduction band electrons and valence band holes [1, 2]. Ta2NiSe5 is one of the few promising candidates for an EI. The compound undergoes a second order structural phase...
Structural analysis of functional materials is the fundamental step towards the ability of tuning their physical properties as desired. For crystalline materials, 3D ED has been proven to be an effective TEM technique to perform ab initio structure solution and refinements of crystals with size well below 1µm [1]. As the crystal or domain size reduces, the capacity to collect 3D ED data with...
The interaction studies between antigens and antibodies is very crucial in controlling and preventing infectious diseases. Structural biology tools help to analyse clearly the interaction and binding interface between an antibody and its specific antibody in detail. In this study, we designed DNA constructs encoding various antigens, which are SARS-CoV-2 NP, SASRS-CoV-2 RBD, MERS-CoV NP and...
Cholesterol dependent cytolysins (CDCs) are pore forming toxins produced mostly by Gram positive bacteria and are responsible for bacterial pathogenesis. The CDCs are secreted as soluble monomers and upon interaction with cholesterol containing membrane; they undergo oligomerization to form large pores.
Fluorescence and mutagenic studies on perfringolysin (CDC of Clostridium perfringens)...
Structural and functional characterization of hyper-stable human serum albumin variants engineered in silico by the group of Sarel Fleishman (Weizmann Institute of Science). The Cryo-EM structure of hSA3 (generated from hSA wt and introducing 73 mutations) is here discussed. Besides,to explore all the possible applications of these unique hyper-stable hSA variants, a set of functional...
Due to different stereo-chemical activities of the lone electron pairs (LEPs) of 5s2 (Sb3+) and 6s2 (Pb2+) cations in metal oxides, PbSbMO4 (M = Fe, Cr, Mn) would be an excellent playgroup to understand how a mixed influence of LEP-containing cations on a given Wyckoff position play roles for the phases crystal-physico-chemical properties.
We present the synthesis and characterization...
The confirmed presence of hydrous sulfates on the surface of Mars has been a hotly debated topic for several decades (recently e.g., [1-3]). Especially Mg-sulfate hydrates, with the ability to change their hydration state based on local humidity and temperature, are regarded as one of the key minerals governing the water budget at equatorial latitudes on the ‘red planet’[4]. Under laboratory...
The family of Grainyhead/CP2 (Grh/CP2) transcription factors was originally discovered in Drosophila and subsequently found in a wide variety of multicellular organisms extending from insects to humans. In humans, one branch of the family is constituted by the Grainyhead-like proteins Grhl1, Grhl2 and Grhl3, and the CP2 branch comprises transcription factors Tfcp2, Tfcp2l1 and Ubp1. The CP2...
The widely used NanoLuc luciferase was engineered over ten years ago but the oxidative mechanism by which it generates blue photons remained unclear [1]. Here we decipher NanoLuc luciferase action through crystallographic, spectroscopic, and computational experiments. We show that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the...
In enterobacteria such as Escherichia coli, the general stress response is mediated by RpoS, the stationary phase dissociable promoter specificity subunit of RNA polymerase. RpoS is degraded by ClpXP during active growth in a process dependent on the RssB adaptor, which is thought to be stimulated by phosphorylation of a conserved aspartate in its N-terminal receiver domain and inhibited by...
Vibrio cholerae and enterotoxigenic Escherichia coli (ETEC) are two bacterial pathogens responsible for millions of diarrhea cases each year. These pathogens release two similar AB5 toxins that are directly responsible for the severe diarrhea: the cholera toxin (CT) and E. coli heat-labile enterotoxin (LT), respectively. They consist of a catalytically active A1 subunit, an A2 linker, and a...
Elettra Sincrotrone Trieste is a multidisciplinary research center, based on a third generation source, for materials and life sciences and includes 28 beamlines. Among those XRD2 is dedicated to high throughput macromolecular crystallography (MX) experiments; it has been in operation since 2018, and it caters to the structural biology community worldwide, operating in partnership with...
Structural Biology has significantly influenced drug discovery and development over the past few decades. The use of structural information to design and improve drug molecules trace back to the early 1980s, following the advent of macromolecular X-ray crystallography. In the 1990s significant advancements in computational power and algorithms greatly enhanced the capability of Structure...
Three-dimensional (3D) electron diffraction is an emerging technique that has shown great promise as a powerful tool for the structural characterization of materials. Compared to traditional single crystal X-ray diffraction (SCXRD), 3D electron diffraction can be used to analyze small crystalline samples and amorphous materials, providing valuable information about the atomic structures and...
Cryptosporidium parvum, an apicomplexan protozoan parasite, is the causative agent of cryptosporidiosis, one of the most common causes of diarrheal disease worldwide. Cryptosporidiosis is strongly related to early childhood mortality, with prevalence in tropical countries, and is also a potential life-threatening complication in individuals with poor health or weakened immune systems (HIV/AIDS...
Over the past decade, Bragg peak electron diffraction (3D ED / MicroED) has rightfully took its place in the arsenal of structure analysis methods [1]. It is only natural that the analysis of total electron scattering also finds its way into the line-up of structure characterization techniques [2].
Similar to X-rays, electrons can be used for atomic pair distribution function (PDF) analysis....
In this work, we review structural complexity in the family of Prussian Blue Analogues (PBAs). These porous framework materials are extensively studied for ion trapping, gas storage, gas purification, as well as for rare electronic and magnetic effects like charge transfer and humidity-sensitive magnetism [1,2]. Despite their simple cubic average structures, PBAs reveal rich complexity in the...
The self-assembly of fascinating coordination polymers (CPs) remains a topical research subject. Materials of interest in terms of applications in several fields, environment, storage, gas separation, catalysis, optoelectronics, etc [1-2]. They result from multifunctional organic ligands combined with metals by coordination bonds, sometimes associated to supramolecular interactions.
In this...
In a prebiotic context, supramolecular ordering, such as liquid crystal self-assembly, adsorption on solid surfaces and, finally, crystallization, is believed to promote selection and non-enzymatic polymerization of nucleotides, thus providing an effective pathway to the emergence of the RNA World on the primordial Earth [1-3]. Laboratory simulations of the prebiotic hot springs (wet-dry...
The present work reports the synthesis and structural design of a new Ni(II) complex [Ni(L)PPh3] with the S-benzyl-2-(2-hydroxyphenyl-ethylidene)dithiocarbazato (H2L) ligand. The metal complex was characterized by single-crystal X-ray diffraction, FT-IR, UV-Vis, and 1H nuclear magnetic resonance. Single crystal X-ray analysis revealed a mononuclear complex with distorted square planar geometry...
Photoreceptor proteins regulate adaptation of living organisms to light. A class recently discovered uses a vitamin B12 derivative to sense green light and regulate the biosynthesis of carotenoids, which protect against photo-oxidative damage. CarH is a prototype of this class. We provide a molecular description of CarH gene regulation mechanism in real time by using time resolved X-ray...
Poster abstract for European Crystallography Meeting 2024.
The poster concerns the structural effects from increasing the Fe/Mn ratio in layered transition metal oxides (NaTmO2) for Na-on batteries
Polymers play a central role in our modern society where they are used as base materials in the manufacture of countless everyday products or they find more sophisticated applications in medicine, diagnostics and fine chemistry. However, less than 1% of the 350 megatons/y of manufactured polymers are bio-based, with the vast majority still being of fossil origin. Environmental as well as...
Hydrated borates (e.g., borax, tincalconite, colemanite, kernite, ulexite) are the most common ore minerals of boron, an important geochemical marker, in pegmatitic and granitic systems, for petrogenetic processes and a strategic element in a series of technological applications. Hydrated borates have been listed as critical raw materials by the EU [1], and they could be used as aggregate in...
The cell wall of bacterial pathogens is a complex structure essential for survival and virulence. In Mycobacterium tuberculosis (Mtb), the D,L endopeptidase RipA has emerged as a major peptidoglycan (PG) hydrolase for cell separation in cytokinesis and, although defects in this protein have important implications for Mtb virulence, the precise mechanisms by which RipA mediates cell separation...
Polymorphic toxins are weapons of bacterial warfare which are being used to restrict competitors, aid kin selection and shape bacterial communities. Polymorphic toxin systems (PTS) are well studied in gram negative bacteria however there are limited studies from gram positive bacteria. In Bacillus subtilis, several members of toxin-immunity protein pairs including YeeF-YezG, YobL-Y, obK...
The chemistry of the XeF2–MF4 systems remains a topic of considerable interest due to the ongoing unresolved nature of the first noble gas compound, XePtF6, which may be a XeF2·PtF4 adduct [1]. To date, only a handful of structures of these compounds have been crystallographically characterized, displaying XeF2 coordination to...
The global transition away from dependence on fossil fuels necessitates the development of devices that can utilise alternative fuel sources such as hydrogen. Solid oxide fuel cells (SOFCs) are one technology that benefits from high energy conversion efficiencies and a lack of moving parts. Traditional materials used to form the oxide ion conducting electrolyte in SOFCs (e.g.,...
Rabies virus (RABV) is a lethal neurotropic virus which causes approximately 60,000 deaths annually. The trimeric glycoprotein (G) spikes of RABV are the only surface-exposed proteins on the virion and mediates receptor recognition and host cell entry. RABV-G displays several epitopes which are targeted by antibodies, including neutralizing monoclonal antibodies (mAb) that have been proposed...
Light chain amyloidosis (AL) represents a systemic and life-threatening condition characterized by the accumulation of misfolded immunoglobulin light chains (LCs) in multiple tissues and organs throughout the body. The deposited amyloid fibrils of misfolded LCs disrupt normal tissue structure and function and hence cause organ associated pathologies. The process by which an amyloidogenic...
Carbon capture and storage (CCS) strategies have emerged as reliable options for addressing the environmental issue of reducing CO2 concentration in the atmosphere and mitigating climate change worldwide [1]. Zeolites are a versatile class of porous materials that are thermally and chemically stable and can display selective CO2 adsorption behaviour, which makes them suitable for gas...
Urea is an incredibly intriguing molecule due to its extensive applications in various fields, including pharmacy, agriculture, and industry. From structural point of view it exhibits a significant versatility in forming a wide range of systems, from simple ones to highly complex compounds, including macrocycles. Arguably most interestingly, it has the ability to form channel clathrates with...
Urea, the first naturally occurring compound synthesized by F. Wöhler nearly 200 years ago, continues to attract considerable interest[1]. Its derivatives find applications in various fields, ranging from cosmetology[2] to the production of explosives[3]. Due to its low toxicity and wide availability, urea is widely utilized in organic synthesis. The ability of urea molecules to form hydrogen...
V. Napolitano, F. Squeglia, E. Kramarska, A. Ruggiero, M. Romano and R. Berisio
Antimicrobial resistance (AMR) is a worldwide health problem, which contributes to morbidity and mortality globally, and is aggravated by the lack of effective vaccines. Currently available antibiotics target essential pathways imposing selective pressure that favors resistance development, leading to the...
An intriguing new application of coordination compounds as proton-conducting materials in electrochemical devices, as key components for the safety and efficiency of fuel cells, has been found due to their great porosity, crystallinity, designability and adjustability of structure and properties. In addition, the development of proton conductors that respond to stimuli is of interest not only...
During development of the brain cortex, young neurons migrate to form cortical layers with distinct functions. Teneurin (Ten), a cell adhesion molecule, plays an important role in this process. As a canonical cell adhesion molecule, it interacts in homophilic fashion to produce adhesion between cells. It also interacts with other proteins, especially Latrophilins (Lphn). The molecular...
Nucleotide metabolism is intricately regulated by a variety of enzymatic reactions. In purine catabolism, the dephosphorylation of inosine monophosphate (IMP) produces inosine [1,2], the primary intermediate. The reaction is catalyzed by IMP-specific 5’-nucleotidase 1 (ISN1) which is present in many but not all eukaryotic organisms [3].
ISN1 plays a role in IMP catabolism in the metabolic...
Materials with phase transition phenomenon often lead to build switches, sensors, cantilever and so on. In this work, a novel ligand, 2-(2-(4- fluorobenzyl)-2H-tetrazol-5-yl) pyridine (2-PFBTP) was used to synthesize one-dimensional coordination polymers, Fe$^I$$^I$(2-PFBTP)$_2$(4,4’-bpy)$_2$．0.5 C$_2$H$_5$OH (1) and Fe$^I$$^I$(2-PFBTP)$_2$(bpea)$_2$ (2), hereinafter...
In the world of modern electronics and lighting technology, optical light-emitting diodes (LEDs) are a major innovation, offering energy-efficient, versatile and environmentally friendly solutions for various applications [1].
Among them, Thermally Activated Delayed Fluorescent (TADF) diodes stand out for overcoming limitations of conventional phosphorescent organic LEDs (OLEDs), particularly...
Ultrasmall nanoparticles of noble metals with chemical stability and high specific surface area represent a broad field for their application in heterogeneous catalysis, imaging and biomedicine [1]. With a diameter of 1-2 nm, such ultrasmall nanoparticles can be considered as a mixture of metal clusters containing 100-250 atoms for which the crystal structure might differ from the one of bulk,...
Many bacterial pathogens employ a type III secretion system (T3SS) to inject cytotoxic effector proteins into the cytoplasm of human host cells. A T3SS is a large multi-protein complex resembling a macromolecular syringe. T3SS assembly and function relies on the correctly timed selection of proteins for secretion. Secreted proteins usually require binding to a cognate chaperone that remains in...
In the context, of the contribution of cement industry to the greenhouse effect there is an increased interest for using clinkers containing polymorphs of the main phases which are formed at lower temperatures, as this results in reduced gas emissions. Thus, any study that helps to explore the structure relations of the polymorphs present in the clinker is of interest for both scientific and...
Lipase is an enzyme that catalyses the hydrolysis of fats, converting triacylglycerols into the glycerol and fatty acids. Lipases are widely used in processing of dietary lipids, production of biodiesel, and synthesis of bioactive esters. Substrate specificity of lipases often limits the application, so that enhanced selectivity and engineered catalytic sites are desired among food and...
The World Health Organisation has identified a diverse range of diseases which share a set of common features as neglected tropical diseases (NTDs). NTDs mainly occur in the (sub-)tropics, they afflict mainly the poorest part of the society and often lead to chronic, debilitating and stigmatising diseases. Among the NTDs, Leishmaniasis and Chagas disease are due to infections by protozoan...
Pets have been recognized as one of the major sources of indoor allergens posing a great risk for the development of IgE-mediated diseases such as rhinitis and asthma [1]. To date, the WHO/IUIS database reports eight cat allergens, among which the frequency of IgE recognition and allergen-specific IgE reactivity is found to be the highest for Fel d 1, Fel d 4 and Fel d 7 making them clinically...
Layered perovskite-related materials have garnered significant attention in recent years owing to their fascinating physical properties such as ferroelectricity, piezoelectricity, antiferroelectricity1-4 and technological applications.5 Dion-Jacobson (DJ) phases, a type of layered perovskite-related material, have emerged as an intriguing class of materials with crystal structure comprising of...
Cellulases are utilized by bioethanol production industries for converting complex cellulose into fermentable sugars. β-glucosidase, constituting the last enzyme of the cellulose degradation pathway, is inhibited by its product – glucose [1]. This inhibition becomes a bottleneck of the industrial cellulose hydrolysis process. Hence, engineering β-glucosidases with high glucose tolerance along...
M. Vrankić1, T. Nakagawa2, Y. Ding2, A. Moliterni3, J. Popović1, K. Bu2, X. Lü2, H. Liu2
1Division of Materials Physics, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia, 2Center for High-Pressure Sci-ence & Technology Advanced Research, 100094 Beijing, P.R. China, 3Institute of Crystallography (IC)-CNR, 70126 Bari, Italy
mvrankic@irb.hr
Hybrid organic-inorganic...
An in-depth understanding of the structure – property relationships is essential for the successful discovery and development of new functional materials capable of overcoming the limitations of the currently used ones. As the materials’ complexity increases, characterisation using a range of scattering-based techniques and complementary methods, as well as state-of-the-art data analysis...
A. Bistrović1, S. Raić-Malić1, M. Cetina2
1University of Zagreb Faculty of Chemical Engineering and Technology, Marulićev trg 20, HR-10000 Zagreb, Croatia, 2University of Zagreb Faculty of Textile Technology, Prilaz baruna Filipovića 28a, HR-10000 Zagreb, Croatia
mario.cetina@ttf.unizg.hr
Cyclin-dependent kinases (CDKs) belong to the serine/threonine kinases with fundamental role in...
Bacilli and mycobacteria have both unique low-molecular-weight (LMW) thiols that play critical roles in the defense system to buffer the intracellular redox environment and counteract oxidative stress encountered by human neutrophils during infections. Bacilli species like the pathogen Staphylococcus aureus use the LMW thiol bacillithiol (BSH), while mycobacteria like *Mycobacterium...
Understanding the structural insight and diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. Our experience on virus-like particles (VLPs) of grouper nervous necrosis virus (GNNV) [1] and shrimp nodavirus [2] has led us to determine structures of T=4 and T=3 capsids of honeybee-infecting Lake Sinai...
Structural insights into the photoactivated adenylate cyclases can be used to develop new ways of controlling cellular cyclic adenosine monophosphate (cAMP) levels for optogenetic applications. OaPAC is a recently discovered blue-light using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate...
Quantum materials have attracted lots of attention in condensed matter physics because of their exotic and fascinating physical properties, such as topological insulators/superconductors, geometrical spin/charge frustrations, or Dirac and Weyl semimetals. It has been demonstrated that the different coupling strengths of electronic ordering with spins, orbital, and lattice are responsible for...
Quantum materials have attracted lots of attention in condensed matter physics because of their exotic and fascinating physical properties, such as topological insulators/superconductors, geometrical spin/charge frustrations, or Dirac and Weyl semimetals. It has been demonstrated that the different coupling strengths of electronic ordering with spins, orbital, and lattice are responsible for...
Research on coordination complexes dates back to the end of the 19th century and has not lost interest to this day, on the contrary. The main reason for its growing popularity is the structural diversity of such compounds, varying from mononuclear to polymeric structures, as well as their potential applications. For example, coordination polymers can be used in catalysis, ion exchange, gas...
In the quest to overcome the resistance of mycobacterium (MMTB) species against isoniazid (INH), a combination of INH and INH-derivatives with different moieties have been explored and are of continuous investigation [1]. Isoniazid is a drug that has long been used in the treatment of pulmonary and extra-pulmonary TB infections caused specifically by M. tuberculosis, M. bovis and M. kansasii...
Surface and epitaxial stresses play a paramount role in the atomic structure of nanoscale object and thereof in their use, such as in the catalytic properties of metal particles. They are suspected to drive transitions of shape [1], of atomic structure and of epitaxy when size is reduced. Nevertheless, x-ray diffraction intrinsically struggles to faithfully characterize small clusters.
In...
Previous studies showed that cations with polarizing properties can lead to B−H bond activation of hydroborates, as evidenced by a shift of the B−H stretching vibration band in the Raman spectra$^\mathrm{[1]}$. In extreme cases, this bond activation results in a substitution reaction, as the reaction between Bi$^{3+}$ cations and [B$_{12}$H$_{12}$]$^{2−}$ anions to the neutral molecule...
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Crystal structure prediction (CSP) remains a pivotal challenge in the field of material science,[1-3] with strong implications that span diverse domains from pharmaceuticals to advanced materials engineering. Despite the strong efforts and the significant progress achieved in the last years, the accurate prediction of the most thermodynamically stable polymorphs remains and intricate...
In 2009, the first natural icosahedral quasicrystal (icosahedrite: Al63Cu24Fe13) was found in nature [1], thus showing that these materials could form also in a natural environment beside those produced in laboratory experiments. To shed light on the formation process and stability of this natural quasicrystals, we measured a full diffraction pattern containing both Bragg and diffuse...
The content provided is a detailed description of research concerning Schiff bases derived from 2,6-diacetylpyridine, focusing on their coordination chemistry and the synthesis of a specific nickel(II) complex. It begins by highlighting the versatility of coordination modes exhibited by these Schiff bases, supported by findings from the Cambridge Structural Database, which contains data on...
Rare-earth aluminates RE3Al5O12 with the cubic garnet structure are an important class of optical materials with a range of technological applications. When formed under typical reaction conditions as ceramics or single crystals, these materials do not tolerate large deviations from ideal RE3Al5O12 stoichiometry, and exhibit well-characterised luminescence responses based on the identity of...
We report the synthesis of four copper(II) and cobalt complexes Cu2(PAA)4(DMSO)2, [Cu(PAA)2 (DMPA)2N3]n(2), [Cu2(PAA)4]n (3)[1] and Co2(PAA)4(DMPA)2[2] (PAA: phenylacetic anion, DMSO = dimethyl sulfoxide and DMAP = 4-(dimethylamino)pyridine). We characterize the compounds structurally using X-ray diffraction, thermal analysis and magnetic properties....
Lithium-ion batteries (LIBs) have become essential in today’s world and are seen as a potential strategy to lower CO2 emissions [1]. Layered lithium metal oxides, such as lithium cobalt oxide (LCO) and lithium nickel manganese cobalt oxide (NMC), have been a popular choice of cathode due to their high energy density and good performance [2]. However, they contain elements with low abundance...
Heterocyclic compounds such as benzoglyoxalines or benzimidazoles, better known as benzimidazoles, exhibit a wide range of physical properties [1] and pharmacological activities [2], making them useful for therapeutic purposes [3-5]. In the context of our research work, we synthesized the dichloride of 2-(2-aminophenyl)-1H-benzimidazol-3-ium, a hybrid compound derived from benzimidazoles. This...
In recent years, there has been a significant surge in the exploration of metal complexes containing biologically active ligands, with a focus on both their biological applications and structural intricacies. Notably, complexes incorporating 1,10-phenanthroline show promise in combating cancer through DNA intercalation [1], while synthetic nickel (II) complexes are being investigated for their...
1Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, UK
deepti@ebi.ac.uk
P The Protein Data Bank in Europe (PDBe) and the Protein Data Bank in Europe Knowledge Base (PDBe-KB) are crucial in structural biology. As part of the Worldwide Protein Data Bank (wwPDB), PDBe archives and provides global access to 3D structural data of biological macromolecules. It offers robust...
Halogen bonds (XB) have gained extensive interest over the last decades, especially from theoretical chemists and physicist but also from the crystal engineering community. XBs emerge from the interaction of an electron-deficient site of a (mostly heavy) halogen atom (called the XB donor) and a nucleophile, thus forming a halogen bonded adduct. The electron-poor site at the halogen has been...
Enterovirus D68 (EV-D68), a member of the Picornaviridae family, has emerged as a significant pathogen associated with severe respiratory illnesses and neurological complications, particularly in children. The virus has been linked to acute flaccid myelitis (AFM), affecting the gray matter of the spinal cord, and leading to polio-like neurological symptoms such as muscle weakness. The viral...
The protozoa are a large group of single-cell eukaryotes which include important human pathogens such as Toxoplasma gondii (the causative agent of Toxoplasmosis) and Plasmodium falciparum (which causes malaria). Often, these parasitic infections are asymptomatic, however, they become life threatening in critical conditions, such as pregnancy, or in immunocompromised patients. In fact, it is...
Crystallography is applied to many disciplines of natural sciences: materials research, solid state physics, structural biology, engineering – all use results obtained from crystallographic research as an essential part of their toolbox. A great number of excellent textbooks can be recommended [1]. The XXI century however gives us additional opportunities and challenges: a large amount of...
The minerals of the pearceite-polybasite group are well-known for their structural complexity, including the presence of twinning, different polytypes and modulated structures [1]. They have general formula [M$_6$T$_2$X$_7$][M$_{10}$X$_4$] with M = Ag and Cu, T = As and Sb, and X =S, Se and Te, giving rise to a wide range of compositions and eight different endmembers [2]. Pearceite and...
The isothiouronium salts are formed by S-alkylation of thiourea [1]. Various thiourea derivatives as well as various alkyl substituents can be used for fine tuning of resulting compound’s properties. As isothiouronium group usually possesses hydrogen atoms on positively charged nitrogen atoms, they tend to form strong charge assisted hydrogen bonds. These features led to their use in anion...
In recent years, the design strategy of binary cocrystals has been established by utilizing specific intermolecular interactions and using the knowledge of supramolecular synthons. However, the synthesis of higher-order cocrystals remains a challenging task, since balancing more components and controlling specific interactions in a crystal is difficult [1,2]. For the design of hydrogen-bonded...
Recently, a new deep-learning-based method (called PhAI) for solving the crystallographic phase problem was developed [1]. PhAI is a neural network that has been trained to predict all the given reflection phase values based on their amplitudes. Initially, it has been trained to solve structures with small unit cells in P21/c or its supergroups (for example, C2/c, Pbca and others). The initial...
The youth of the continent of Africa represent a large majority of the population. The UN predicts that the youth population in sub-Saharan Africa will have doubled by 2050. As the continent’s biggest resource, the African youth, with a special emphasis on the marginalized girl child, needs to be provided with the tools for the advancement of science, technology, engineering, and mathematics...
3D electron diffraction (3D ED) or microcrystal electron diffraction (MicroED), has become a complementary to X-ray diffraction technique for determining the routine crystal structure of compounds from sub-micron size crystals[1-3]. Moreover, electron diffraction can also provide high-resolution high-good quality data but charge density analysis of that data is still very challenging. On the...
Compared to X-ray crystallography and NMR spectroscopy, cryogenic electron microscopy (cryo-EM) is still an upcoming technology to resolve protein structures. One of the bottlenecks of cryo-EM is sample preparation. Conventionally, microliter sized samples are applied on a grid, of which >99% is removed by blotting. The blotting step has limited reproducibility and can damage the sample. Here,...
After being developed over hundreds of years, in 2024 crystallography is witnessing a growing crisis of paper mills and artificial tools that generate hundreds of papers [1]. The rebuttals [2,3] of the two Nature papers [4,5] illustrate the following common mistakes and problems in using black boxes. The first paper [4] reported the GNoME database of 384+ thousand ‘stable’ predicted structures...
The crystal structure of two Y2O3 and B2O3 containing pyroxenes occurring in glass ceramics used as solders in solid oxide fuel cells (SOFC) are described.
Y2O3, CaO, MgO and ZrO2 containing aluminoborosilicate glass powders were sintered at a temperature of 850°C for 100h and 1000h. XRD, 3D ED and TEM-EDX measurements were done to investigate the evolution of the crystalline phase...
The use of pozzolanic materials to trigger low-temperature hydraulic reactions in calcium-based inorganic binders has been the most relevant technological evolution in the field of construction materials since the beginning of pyrotechnology. After the first applications by ancient Mediterranean societies of the Second and First Millennium BCE, the potential of pozzolanic binders was fully...
Leucopterin (LCPT, Fig. 1), C6H5N5O3, member of the class of pteridines, is the white pigment in the wings of Pieris brassicae butterflies [1]. This is particularly interesting, since in nature as well as in industry, organic white pigments are rather scarce compared to inorganic white pigments, because (I) inorganic pigments such as CaCO3 or TiO2 are easy to synthesise industrially; also...
As a family of functional materials with ordered pores, including zeolites, metal–organic frameworks (MOFs) and covalent-organic frameworks (COFs), crystalline porous materials have presented a wide range of applications in adsorption/separation, electrochemistry and storage, etc [1-3]. The synthesis of novel crystalline porous materials with superior performance requires a comprehensive...
The ESRF’s large-volume press beamline, ID06LVP, has been in User operation for just over a decade [1]. It complements the ESRF’s already wide-ranging extreme conditions portfolio by offering, primarily, in situ angle-dispersive diffraction-based experimentation with a multi-anvil device that operates in one-and two-stage modes. Through use of independent anvils; both normal compression, with...
P. M. Rybicka1, M. Kulik1, M. L. Chodkiewicz1, P. M. Dominiak1
1Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw , ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland
p.rybicka@uw.edu.pl
In the MATTS data bank[1,2], the local coordinate system and symmetry are essential parts of an atom type definition, specified manually when adding a new atom type entry....
Research on organocatalysts has begun in recent decades, and their application in a growing number of new reaction pathways is expanding. Organocatalysts are not only being discovered for use in new areas but also offer a simplified operational scheme akin to enzymes. Crucially for industry, they provide an opportunity to move away from non-renewable heavy metals. Often, organocatalysts yield...
When subjected to high pressure, a crystal structure can undergo significant alterations [1]. These changes may involve modifications in molecular conformation, supramolecular assembly and overall molecular organisation of the crystals. A comparative study was carried out on a Quinine Catalyst, HOF and boron catalyst among other organocatalysts under both the ambient and high-pressure...
Srebrodolskite (CaFeO2.5) and brownmillerite (CaFeAlO2.5) are interesting minerals found in both natural occurrences and synthetic forms within industrial contexts such as slags and cements. These compounds exhibit a unique oxygen-deficient perovskite structure characterized by ordered vacancies, notably differing from the primitive perovskite aristotype in the local environments of Fe and Al...
One of the key players of cholesterol trafficking in mammal is Niemann-Pick type C1 (NPC1) protein. The cholesterol transport from lysosomal by NPC1 is closely coupled with another protein called NPC2 and malfunction of any of these protein leads to a disease called the Niemann-Pick type C (NPC) disease. After the full-length NPC1 structure was determined by cryo-EM experiment, much of the...
Sample displacement is one of the most significant aberrations that affect the results of X-ray powder diffraction (XRPD) experiments. It can lead to an incorrect determination of d-spacings and lattice parameters, or to wrong materials found in phase identification analysis. Modern laboratory diffractometers provide options for minimizing the displacement using accurate sample positioning and...
Respiratory Complex I (NADH: ubiquinone oxidoreductase) stands as the largest multi-subunit mitochondrial enzyme, pivotal for energy transduction within cells, essential for oxidative phosphorylation, and crucial in regulating NAD+/NADH pools as entry point of the electron respiratory chain. Recent advancements in electron cryogenic microscopy (cryo-EM) have unravelled the conserved...
In single-crystal structure determination, instrumentation and user-friendly software and tools for collecting data, then solving, model-building and refining crystal structures have advanced tremendously over the last 40 years; way beyond what one could have imagined back then. Utilising hardware or data to its full potential requires good software to go with it and good software requires...
The chemistry of mercury-containing oxides shows an interesting variety regarding the role of mercury. Mercury can serve either as mono- or di-atomic cation in Hg(+II)- and Hg$_2$(+I)-oxometalates, as oxomercurate(+II) anion or, as recently reported by us, as mercuride cluster anion [Hg$_8$]$^{6-}$ with a formal oxidation state of “-6/8” in the mercuride oxide double salt Cs$_{18}$Hg$_8$O$_6$....
High pressure single crystal X-ray diffraction is a well-established technique in chemical crystallography, used to examine the behaviour and response of compounds to pressures in the 10s of GPa range. This enables researchers to study the phase behaviour of materials, their compression dynamics and structural phase changes, and thus infer information about the intermolecular interactions....
Tsai and Bergman clusters represent distinct structural motifs found within icosahedral quasicrystals. The dominance of one cluster type over the other determines the classification of the quasicrystal. However, research has shown that structures ini-tially attributed to one cluster type can alternatively be interpreted in terms of the other. For instance, in 2008, the proposed structure...
Scattering mechanisms that are specific to electron diffraction (ED) have a noticeable effect on measured intensities, with no counterpart in other diffraction measurements such as X-ray and neutron diffraction where single scattering dominates. While this brings the opportunity to access information that is otherwise difficult to obtain, it also adds to the complexity of the analysis that is...
Co-crystals of covalently modified isoniazid were synthesized, using hydroxybenzoic acids as co-formers. During the co-crystallization of benzophenone derivatives of isoniazid, a small change in reaction or conditions played a large role in the outcome of the resulting supramolecular structure. The addition of either one or two methyl substituents to the benzophenone rings resulted in...
The Multipolar Atom Types from Theory and Statistical clustering (MATTS) databank [1, 2] is an advanced tool which applies Transferable Aspherical Atom Model (TAAM) [3] for crystal structures refinement. Such a method helps to describe the asphericity of atomic electron densities and helps to interpret diffraction data better than refinement approaches based on spherical atoms...
Zeolites with CHA framework-type are of interest because of their applications in a variety of technological and industrial processes. The versatility of the framework, and the fact that it is a small-pores zeolite, makes it one of the most exploited porous material in the field of gas separation and selective catalytic reduction of NOx [1-3]. Particular attention has been devoted to the Na-...
Andrew King1, Jean-Paul Itié1, Sebastian Schoeder1, Florence Pizzorni-Itié2 Luc Bachelot2 , Maria Gorea3 , Christian Chilli2
1 Synchrotron SOLEIL, L’Orme des Merisisers, 2 Musée des écritures Ampus, 3 Laboratoire Arscan UMR 7041
Andrew.king@synchrotron-soleil.fr
The magic scroll belongs to the collection of the future “Musée des Ecritures” in Ampus (Var, France). Some engraved...
I16 is a high flux, high resolution x-ray beamline based at the Diamond Light Source. The beamline operates in the 2.7-15 KeV range and it is a diffraction facility optimized for the study of resonant and magnetic scattering processes from single crystal samples [1]. Resonant elastic X-ray scattering is ideal to characterize electronic, magnetic, and structural properties of materials thanks...
The Versatile Macromolecular Crystallography Microfocus (VMXm) beamline is a micro/nanofocus beamline joining the suite of macromolecular crystallography beamlines at Diamond Light Source. The beamline is now accepting users and has been designed to enable rotation data collection from microcrystals down to 0.5 microns in size and took its first users in Autumn 2018. The beamline optics...
S-layers are crystalline arrays found on bacterial and archaeal cells (Fig. 1). Lactobacillus is a diverse family of bacteria known especially for potential gut health benefits. This study focuses on the S-layer proteins from Lactobacillus acidophilus and Lactobacillus amylovorus common in the mammalian gut. Atomic resolution structures of Lactobacillus S-layer proteins SlpA and SlpX...
Tuberculosis (TB) is the second leading killer pathogen after Covid -19. In 2022, WHO declared a total of 1,3 million deaths caused by its etiologic agent, M. tuberculosis. The currently available vaccine against TB, BCG, is not totally effective to prevent the disease. The urgency to find a new vaccine against TB due to the high mortality led us to approach structure vaccinology (SV) for...
The D7 neutron diffuse scattering instrument at the Institut Laue-Langevin [1] has been an important experimental tool in the study of disordered materials, making use of neutron polarization analysis to provide a clean and unambiguous separation of the magnetic, incoherent, and structural contributions to the scattering.
D7 has been disassembled, and the new D007 [2] starts its commissioning...
The newly constructed Debye beamline at the Swiss Light Source (SLS), available after the SLS upgrade mid-2025, is positioned to provide multimodal X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) analysis to investigate the chemical, geometrical and electronic structure of functional materials under operating conditions. Equipped with a 5 T superbend magnet source and utilizing...
Nearly three years on from the initial release of AlphaFold2, we have seen the community not only adopt it as a protein structure prediction tool, but also adapt it for new use cases in a variety of inventive ways. Here we would like to focus on the most recent update of AlphaFold, its expanded functionality, and the potential impact this update may have on the field of structural biology and...
It may be hard to believe, but it is a proven fact that the first objects that our ancestors collected, without any practical purpose, without any use, were crystals—quartz and calcite crystals a few centimeters in size. They did this for at least 770,000 years, probably before the appearance of our consciousness. Actually, this collection is considered the first evidence of symbolic thought...
Peptoids are N-substituted polyglycines with useful biological activities and interesting chemical properties both in solution and in the solid state. The lack of the amide proton prevents the formation of NH···CO hydrogen bonds and makes peptoids the ideal platform for evidencing the influence of CH···OC and CO···OC interactions in stabilizing molecular conformations and the solid state...
Powder Diffraction is a well-established method which allows to investigate long-range order structural properties of crystalline materials. On the other hand, Total Scattering measurements in combination with the Pair Distribution Function method is an expanding and powerful technique which allows to investigate the short-range and/or long-range order at the same time, making it possible not...
In the context of global health, tackling the critical issue of antimicrobial resistance (AMR) has become a top priority. A promising strategy in this effort involves harnessing the synergistic effects between safe metals and commonly used antibiotics or molecules with known antimicrobial properties. Our research on antibiotic coordination frameworks explores the innovative field of...
A modified version of the Hirshfeld partition of the electron density, exponential Hirshfeld, is introduced for use in Hirshfeld atom refinement (HAR)[1]. Its application in HAR (expHAR) sometimes significantly improves the accuracy of hydrogen atom parameters (Fig. 1).
It is demonstrated that reduced accuracy of ADPs of a hydrogen’s bonding neighbour may prevent an accurate determination of...
The real space approach to the atomic structure of Tsai-type quasicrystal
R. Strzalka, I. Buganski, J. Wolny
AGH University of Krakow, Faculty of Physics and Applied Computer Science, Krakow, Poland
strzalka@fis.agh.edu.pl
The great breakthrough in understanding the atomic structure of iQCs came with the model of binary Cd_5.7 Yb (Cd_85.1 Yb_14.9) phase [1] that provided a template...
Multicentric covalent bond (pancake bond), which is common in crystals of planar organic radicals, is a type of π-interaction that involves spin pairing and formation of covalent bond between radical rings. Energy of such interaction is comparable to the energy of strong hydrogen bond and it can be as high as −20 kcal mol-1.[1] Study of these interactions involves exploring the nature of the...
Mechanochemical technologies are transforming how we think about chemical reactivity, whilst offering new, sustainable routes for industrial manufacture. However, mechanochemistry’s true potential is limited by our lack in understanding of how these processes work. Mechanochemical reactions are preceded by an induction period, during which time no reaction is observed. We showed recently[1]...
Lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone) is a pigment extracted from the bark of Handroanthus heptaphyllus (Vell.) Mattos commonly known as pink trumpet tree or lapacho. The group of 1,4-naphthoquinones and its derivatives has attracted a lot of attention since these compounds exhibit a wide range of biological and pharmacological effects. In particular, lapachol has...
The Single Particle, Clusters and Biomolecules & Serial Femtosecond Crystallography (SPB/SFX) instrument [1] of the European X-Ray Free-Electron Laser (EuXFEL) is focused on time resolved research using diffraction and scattering methods with an emphasis towards life science. This instrument addresses the needs of the research communitiy for crystallography, single particle imaging communities...
Cholera is an acute life-threatening diarrheal infection caused by the bacterium Vibrio cholerae. Having brought about seven world pandemics, cholera is endemic in several countries. There has been an acute upsurge of the 7th cholera pandemic since 2021. In this regard, cholera has re-emerged in at least 30 countries, in areas that have been free of cholera for decades, with high mortality...
If it appears as a mineral, the ternary sulfide AgBiS2 can crystallize as schapbachite (cubic, space group: Fm3 ̅m, a = 564.8 pm, Z = 2) with a cation-disordered rock-salt structure (Ag+/Bi3+ at 4a, S at 4b) [1] or as an ordered trigonal variety (matildite). The latter was first considered as adopting the delafossite structure of α-NaFeO2 with layerwise ordering of the still octahedrally...
The YLID crystal (Fig. 1) has been shipped to users and employed as test crystal for adjusting and calibrating single-crystal X-ray diffractometers by the leading companies since 1969. Therefore, tens of thousands of YLID crystal structures must have been determined under various conditions and setups everywhere around the world over the past half a century. Guzei et al. have analysed lattice...
The knowledge of the interface between different components in composites is crucial to understanding and predicting all the exciting chemical and physical properties of these materials. However, the structural study of the interface regions within a MOF composite is extremely challenging, given the low volume of interaction and the consequent need for characterisation to be carried out at the...
1STOE & Cie GmbH, Hilpertstrasse 10, 64295 Darmstadt, Germany
folkers@stoe.com
„Die Sendung mit der Maus" (Maus) is an educational show on German public TV that has been airing weekly since 1971. Aimed at elementary school children, it features fun stories (Lachgeschichten) and educational segments (Sachgeschichten), teaching viewers about various topics such as lightbulbs, chewing gums,...
We report our recent theoretical and experimental investigations on Grazing-Incidence X-ray Back Diffraction (GIXBD) from a highly miscut ($\theta_m$ = 89.926°) Si (12 4 0) crystal. The unique optical characteristics of X-ray back diffraction, such as wide angular acceptance and high energy resolution, excited from a highly asymmetric-cut crystal demonstrate significant angular dispersion...
Crystal-chemical investigation of mineral phases is an essential step in Earth Sciences to shed light on genetic processes occurring in different geological environments. Single-crystal or powder X-ray diffraction and electron microprobe are generally applied to determine the structure and the chemical composition of crystalline phases. These analytical techniques are the best for providing...
We have developed several, on-demand, sample-efficient delivery and reaction initiation strategies that use room temperature microcrystal slurries and serial crystallography methods for time-resolved studies [1-3]. As illustrated in Fig. 1 and 2, our drop-on-drop on tape strategy produces high spatial resolution over a wide range time points and can be applied at synchrotrons or at XFELs....
Whenever it is possible, for any small-molecule crystalline specimen scientist by default prefer to use the X-ray diffraction experiments for combined substance identification and structure analysis as it is a much cheaper, more convenient and much more established technique than any other diffraction method. However, some substances tend not to form crystals of sufficient size for X-ray...
Topological crystalline insulators (TCIs) with hourglass fermion surface states enable exploration of remarkable topological phases and are further enriched by crystalline symmetries and magnetic order. However, hourglass fermion surface states are hard to verify for the drawbacks including the air sensitivity, miscellaneous band dispersions crossing Fermi level, and challenging of cleavage in...
MgO, promoted with NaNO3, is a class of CO2 sorbents that shows great promise for industrial applications in pre- and post-combustion CO2 capture processes. These sorbents offer a high theoretical gravimetric CO2 capacity of 1.09 g CO2 per g viz. MgO, MgO+CO2→MgCO3 ΔH300K = –106.05 kJ mol–1, are...
see file
Predicting a protein's 3D structure from its amino acid sequence remains a fundamental challenge in structural biology, with wide-ranging applications in drug discovery and disease understanding. An impressive milestone has been reached in protein research, with the structures of around 100,000 unique proteins now determined [1] through a substantial experimental effort [2, 3]. This...
Marta S. Semrau1, Theo Battista1^, Viktorja Sidarovich2, Rachele Ortolan1, Andrea Dalle Vedove3, Ivana Manini4, Daniela Cesselli4,5, Valentina Adami2, Graziano Lolli6, Paola Storici1
1Protein Targets for Drug Discovery Lab, Structural Biology, Elettra, Sincrotrone Trieste S.C.p.A, SS 14 Km 163.5 in AREA Science Park, Basovizza, 34149 - Trieste, Italy, 2HTS and Validation Core Facility,...
The Cambridge Structural Database (CSD) and the Crystallography Open Database (COD) contain thousands of structures. Large portions of these databases overlap, often because their entries originate from the same publication. Constructing a list of CSD-COD cross entries is difficult because data can be reformatted in the curation process, many data points do not reliably distinguish or identify...
Modern ultrafast laser technologies have opened new perspectives in controlling bistable photo-active materials, where light can be used to switch between different phases and thus different properties down to ultrashort timescales [1]. In this context, Prussian Blue Analogues (PBAs) represent attractive photo-active materials as they exhibit wide bistability regimes. The electronic charge...
Mammalian rhodopsin is our receptor for vision. It belongs to the highly druggable G protein-coupled receptor family. Upon light illumination, the photoreceptor binds and activates the intracellular G protein transducin, triggering a cascade of signalling events to the brain via the optic nerve within milliseconds. However, the intramolecular initial events transforming the rhodopsin resting...
Prussian blue analogues (PBAs) are versatile metal–cyanide framework materials with a broad range of potential applications. Besides mass transport and mass-storage applications enabled by their microporosity, many PBAs also experience electronic and magnetic bistability [2]. This bistability allows an optical and magnetic switching of PBAs between two distinct states by external stimuli, such...
Porous crystalline materials are now regularly designed and studied for use in capturing or storing harmful gases as a means to addressing some of the problems of the climate crisis. This work is using the family of Zeolitic Imidazolate Frameworks (ZIFs) to develop approaches to studying the structural properties of these materials whilst they perform these functions. The process of Carbon...
In thin film research, understanding the origin of order parameters and learning how to manipulate them has always been one of the core objectives. The materials often display delicate interactions among spin, orbital, and lattice order parameters. With the development of thin film deposition techniques, one can even introduce various emergent phenomena by artificially engineering...
Ladderanes are highly unusual fatty acids and -alcohols found in the lipids of anaerobic ammonium-oxidizing bacteria [1] (Fig. 1) They have five or three cyclobutane rings fused to one another making them sterically very strained [2], giving them a high energy content that makes them interesting as biofuels. How enzymes overcome the energetic barrier to produce molecules with such...
Artemisinin (ART) is widely known for treating malaria and it is well-tolerated within patients. However, it belongs to the BCS (Biopharmaceutics Classification System) class II drug meaning it has low solubility and bioavailability. Transitions between polymorphs which can be generated with pressure can affect bioavailability. Therefore, studying the mechanical properties using high pressure...
A halogen bond (XB) is a supramolecular interaction that involves a region of positive electrostatic potential (σ hole) [1] on the halogen
donor atom and a nucleophilic acceptor atom or functional group. The use of XB therefore provides an opportunity to utilize heavy
elements, such as bromine and iodine, which are not readily amenable to forming hydrogen bonds, in the construction of...
Copy of submitted Abstract file
Retinoic acid (RA) is one of the active metabolite forms of Vitamin A and functions as a key signalling molecule in the control of many developmental processes including differentiation, proliferation and apoptosis. Intracellular RA interacts with a range of cellular binding proteins and nuclear receptors as part of its key modulatory role in the regulation...
Since its inception, X-ray diffraction (XRD) has become a pivotal method for material structure characterization. Advancements in theory, experimentation, and technology have led to remarkably accurate diffraction patterns. Extracting comprehensive information from these patterns requires models that account for both electron density and thermal motion. While electron density modelling has...
The term hydrogen bonding has an over 100-year history, and research on this phenomenon is of enduring interest. Hydrogen bonds (HBs) are the driving force for organocatalytic reactions, the formation of transition metal complexes, drug…protein interactions, and the assembly of biological structures as proteins and the DNA duplex. Since studies revealed a mixed nature of hydrogen bonding where...
We will present recent advancements in the field of modulated molecular ferroelectric crystals, focusing on the intricate connec-tions between incommensurability, intermolecular interactions, and the ferroelectric properties of these materials. Highlighting the significance of understanding the modulated structure for comprehending crystal chemistry and functional properties.
Supramolecular...
Lipases (E.C. 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism,...
Plant-type (Class 2 in new classification) L-asparaginases are a group of the Ntn-hydrolases, which mature via autoproteolytic cleavage into subunits α and β, and are further divided into potassium-dependent and potassium-independent enzymes. Ntn-hydrolases utilize an N-terminal nucleophile (Thr in this case) in their catalytic mechanism and share the same αββα sandwich fold....
Understanding the structural properties is crucial before exploring into the mechanistic aspects of dehydration of pharmaceutical hydrates and polymorphic transformations, such as solid-solid phase transitions. While various techniques exist for determining crystal structures, X-ray diffraction—encompassing powder and single crystal structure determination—stands out as the most commonly used...
The so-called hydrogen economy [1] refers to the use of molecular hydrogen as a clean energy vector. This issue has recently returned to the scene, urged by the need of ensuring access to clean and affordable energy to all, as stated, e.g., by Goal 7 of the 17 Sustainable Development Goals promoted by the United Nations [2]. Two of the challenges of the hydrogen economy are the safe storage...
The gastrointestinal tract is home to a complex ecosystem of commensal bacteria, profoundly influencing human health. Under conditions of low-fiber diet, certain commensal bacteria adapt by utilizing host mucin O-glycoproteins as alternative substrates [1,2]. Among these, Bacteroides caccae has been implicated in degrading the colonic mucous layer, thereby heightening susceptibility to...
3D-electron diffraction (3D-ED) is one of the fastest growing areas of crystallography [1] due to its ability to yield structure solutions from crystals two to three orders of magnitude smaller than is generally possible with X-rays. In previous work we have shown that it is a very useful tool for investigating polymorph evolution during crystal growth of glycine [2] and carbamazepine [3],...
3D electron diffraction (3D ED) has emerged as an alternative to x-ray diffraction for structure elucidation of crystals in the sub-micrometer range [1]. With scattering cross-sections typically 104 times larger than x-rays, data can be routinely collected from nano-sized grains. Experiments performed in transmission electron microscopes or electron diffractometers allow to focus electron...
1The Cambridge Crystallographic Data Centre - Cambridge (United Kingdom)
hello@ccdc.cam.ac.uk
The Cambridge Structural Database (CSD) [1] is the crystallographic database for organic and metal-organic molecules and it contains over 1.25 million crystal structures. In this session we will explore how teachers can leverage the database and associated software for teaching STEM subjects in...
The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, especially where the experimental data are of limited resolution. We have previously established a novel protein structure validation approach...
The utilisation of structural flexibility in materials is a common strategy to enhance their properties. The intentional introduction of disorder locally disrupts the long-range order. Often disorder on a local scale is not random, and certain preferred local atomic configurations may significantly impact material properties [1]. In a diffraction these local ordering principles are manifested...
The increasing focus on safety in battery technology has directed much of the research towards batteries with aqueous electrolytes or electrolytes with water added. The salt concentration level in the electrolyte system is crucial to modifying the solvated structure of lithium cation due to the inactivation of water molecules. While water-in-salt electrolytes show promise, it's important to...
Electron diffraction (MicroED/3DED) can provide the three-dimensional atomic structures of molecules from previously unamenable samples1. Despite its transformative potential, MicroED is subject to the crystallographic phase problem. For macromolecules, MR solution has been considerably simplified by the availability of accurate and complete predictions. Especially for some types of versatile...
It is not practicable to write a meaningful “flow chart” for experimental crystallography. That is to say that each step on the way to determining a crystal structure, starting with crystal growth and ending with publication, has so many variables that any attempt to define a workflow chart would rapidly result in something with multiple overlapping options. It would be of no use at all. ...
„Die Sendung mit der Maus“ (Maus) is an educational show on German public TV which has been running weekly since 1971. It targets elementary school children and features fun stories (Lachgeschichten) as well as educational stories (Sachgeschichten), which taught us what happens to waste water, how batteries are recycled and much more about how the world works. In German speaking countries, you...
Negative linear compressibility (NLC) is an unusual and counterintuitive behaviour of crystals in response to increased pressure, where crystal expands along one of principal axis. Although, at first it seems this phenomenon contradicts laws of thermodynamics they can be satisfied as long the volume of crystal decreases due to adequate positive linear compressibility (PLC) along two remaining...
The availability of highly accurate protein structure predictions from AlphaFold 2 (AF2) and similar tools has hugely expanded the applicability of Molecular Replacement (MR) for crystal structure solution. Many structures solve routinely using raw models, structures processed to remove unreliable parts or model split into distinct structural units, providing a clear route to automation. There...
During the process of translation, ribosomes produce proteins decoding the information stored in messenger RNAs (mRNAs). The linear nature of the message to decode requires the correct identification of the reading frame on the mRNAs. The identification of the first triplet (the mRNA start codon) and the delivery of the first aminoacyl-tRNA to this codon is an essential milestone to achieve...
Finding the right space group for a crystal structure is always a crucial step in structure solution. But sometimes, it can indeed cause a great difficulty for the crystallographer especially in the case of inorganic compounds with high crystal symmetry. High symmetry, supercell structures, crystal mosaicity, twinning and disorder all can make the determination of the space group...
The development of X-ray radiation sources, mainly the availability of the X-ray free electron lasers and the 4th generation synchrotrons, leads to increased interest in serial macromolecular crystallography. This method facilitates e.g. time-resolved studies, collection of data not affected by radiation damage, and pump and probe experiments, all at physiologically relevant room temperature....
Over a decade ago, the 1,2,4-triazole-3-thione scaffold was discovered to directly bind the active site zinc cations of metallo-b-lactamases (MBLs). Since then, extensive research has been conducted on this molecular scaffold's potential as a source of MBL inhibitors through comprehensive screenings of analogs with diverse lateral substituents. Analysis of their binding mode via X-ray...
With the ever-increasing demand for new and improved battery materials, efficient characterization methods to obtain precise insights into both raw materials and fully assembled batteries are more important than ever. Since most modern battery materials are crystalline, and the crystallinity and crystal structure can have a significant influence on a material’s performance, X-ray diffraction...
Reactions between 1,2-di(tetrazol-2-yl)ethane (ebtz), 1,6-di(tetrazol-2-yl)hexane (hbtz) or 1,1’-di(tetrazol-1-yl)methane (1ditz) and Fe(BF4)2 in presence of adiponitrile (AND), glutaronitrile (GLN) or suberonitrile (SUN) resulted in the formation of coordination polymers [Fe(μ-ebtz)2(μ-ADN)] (BF4)2 (1), [Fe(μ-hbtz)2(μ-ADN)] (BF4)2 (2), [Fe(μ-1ditz)2(GLN)2] (BF4)2·GLN (3) and...
The study of neolithic schematic rock art, which is presence over a vast geographical area from the Iberian Peninsula to Italy and documented by more than 140 sites in southern France, constitutes an efficient way of approaching Neolithic societies. Material characterization is an essential step to study this kind of paintings, understand the provenance, chronology, know-hows, and graphic...
Domain walls, which separate regions of differing polarisation in ferroic materials, are not only mobile but often exhibit properties different to that of the domains themselves. This includes phenomena such as increased conductivity at the domain walls or displaying polar domain walls in otherwise non-polar materials, which may find applications in nanoelectronics and memristive technologies....
