Development Of Crystallography Research Articles

Glass and Liquid Chemistry of Coordination Polymers and MOFs

Abstract The chemistry of coordination polymers and metal-organic frameworks (MOFs) has progressed largely with the development of crystallography. The study of “disordered systems” such as the liquid and glassy states of coordination polymers and MOFs has been developed in recent years, and various methods have been recognised to produce glasses from crystals. The structures of the glass and liquid phases are studied using synchrotron radiation X-rays and spectroscopy. Many of them have the coordination bond-based network structure found in the crystal structures. This suggests that the structural design principles of coordination chemistry can be applied to glasses and liquids of coordination polymers and MOFs. The inherent properties of the disordered system, such as wide compositions and high internal degrees of freedom, high material formability and softness, contribute to the coupled physicochemical properties.

Creating a New Universe: The Story of the Crystal Discovered by the Duality of Light and Electron

The study of crystals is like the beginning of solid state physics. Crystallography was developed rapidly with the discovery of X-ray. Recently, the era of physics is enriching with the emergence of new material groups such as graphene, topological insulators, and TMD materials. In a way, it is very interesting to see that the providence of the universe and the philosophy of life are reflected in the small crystal structure. However, unfortunately, little is known about when and how crystal growth began. How did our ancestors in the beginning grow and study crystal? This article examines the history of early crystal growth, the development of crystallography, and the relationship between crystallography and physics.

Structural chemistry at McGill

A brief description of some of the key individuals at McGill University and their contributions to the development of crystallography is given. This is followed by examples of recent structure determinations, which include organic heterocycles, natural products, inorganic salts, and organometallic complexes. Specifically, the bispyridinium adduct of protoporphyrin, the piperidinyl adduct of 3,7-dichloroquinine, trisbenzylmethylthiol, sodium methylarsonium (V), potassium hydroxylamine sulfonate, Vaska’s complex adduct from the oxidative addition of p-tolylmercaptan, and a bis isocyanoiminotriphenylphosphorane adduct of rutheniumdichloridetristriphenylphosphine are described.

Notes on the development of crystallography in Germany with special respect to the use of neutrons

Notes on the development of crystallography in Germany with special respect to the use of neutrons

“Non-Conformist Crystallography”

Now, 25 years or so after the quasi-crystal affair, we can perhaps see the development of crystallography, as it turns into nanotechnology and molecular biology, in a still longer-term perspective as part of the struggle to understand the universe rationally in the face of competing theories and superstitions. We follow changes of paradigm in investigations of the structure of matter and in various dualities, in particular in the dialogue between materials and information. In a small way, the discovery of quasi-crystals exhibits the interactions between the different world representations, Platonic, mental and physical (here labelled P, Q, R) and between conceptions of Laws, Natural, Mathematical, Civil/Military and Divine.

New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences.

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 ‘small molecule’ crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography’s role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

100 years of X-ray crystallography.

The developments in crystallography, since it was first covered in Science Progress in 1917, following the formulation of the Bragg equation, are described. The advances in instrumentation and data analysis, coupled with the application of computational methods to data analysis, have enabled the solution of molecular structures from the simplest binary systems to the most complex of biological structures. These developments are shown to have had major impacts in the development of chemical bonding theory and in offering an increasing understanding of enzyme-substrate interactions. The advent of synchrotron radiation sources has opened a new chapter in this multi-disciplinary field of science.

Quasicrystals and Other Aperiodic Structures in Mineralogy

In this article, we first present and discuss eighteenth-century descriptions of minerals that contributed decisively to the development of crystallography. Remarkably, these old crystallographic descriptions included morphologies with symmetries incompatible with an internal periodic order of atoms, which, however, have been recognised to be characteristics of quasicrystals. Moreover, we also review a number of studies of minerals with aperiodic crystal structures, including recently reported natural quasicrystals of extra-terrestrial origin. Finally, we discuss the current investigations addressing the search for new quasicrystalline minerals in nature.

Structural modeling of G-protein coupled receptors: An overview on automatic web-servers

Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well.

Preface

Year 2014 was announced as a year of crystallography, in order to honor the 100th anniversary of the Nobel prize for William Lawrence and William Henry Braggs. This was a memorable opportunity to review a current developments in crystallography addressing materials science challenges posed by new materials. Progress along this line in mostly fed by experimental techniques – new possibilities emerge from new, intense, tunable and precisely focused X-ray beams as well as from high resolution, sensitive, energy dispersive detectors. The new experimental data called for new, deeper methodology of structural interpretation. Crystal structure is one of principal factors determining the material properties. X-ray, neutron and electron diffraction methods for crystal and defect structure investigation are continuously developing, leading to new opportunities in materials research. Diffraction methods have been developing rapidly during last decades. They can be used for solving a variety of problems including crystal structure solution, defect structure determination, understanding of thin film structure and quality, structure variation mapping, structure dynamic changes, chemical reactions. The Symposium “Crystallography in Materials Science: Novel Methods for Novel Materials” (EMRS-Fall Meeting Symposium N, Warsaw, Poland, Sept. 15th–19th, 2014) was a forum for presentation of such methods and their applications. It had 67 registered participants with lectures covering a wide variety of topics, including historical and methodological aspects of crystallography as well as application of experimental and computational methods of crystallography to specific classes of materials (biological, nanocrystalline, aperiodic, quasicrystals, …). The present issue includes a set of articles which were accepted, after a peer-review procedure, for the proceedings. It is noteworthy that a relatively large number of papers concerns nano- and low-dimension materials, reflecting an increased interest in this direction of materials science. Besides articles contributing to methodology and software applicable to structure solution itself, a substantial part of papers is interdisciplinary, like contemporary crystallography, and focuses on vital challenges of today science and technology, combining description of the structure of various materials, including nanocrystals, with their optical, electric and magnetic properties. The organizers are grateful to International Union of Crystallography for a financial support of a number of young participants.

Crystals: animal, vegetable or mineral?

The morphologies of biological materials, from body shapes to membranes within cells, are typically curvaceous and flexible, in contrast to the angular, facetted shapes of inorganic matter. An alternative dichotomy has it that biomolecules typically assemble into aperiodic structures in vivo, in contrast to inorganic crystals. This paper explores the evolution of our understanding of structures across the spectrum of materials, from living to inanimate, driven by those naive beliefs, with particular focus on the development of crystallography in materials science and biology. The idea that there is a clear distinction between these two classes of matter has waxed and waned in popularity through past centuries. Our current understanding, driven largely by detailed exploration of biomolecular structures at the sub-cellular level initiated by Bernal and Astbury in the 1930s, and more recent explorations of sterile soft matter, makes it clear that this is a false dichotomy. For example, liquid crystals and other soft materials are common to both living and inanimate materials. The older picture of disjoint universes of forms is better understood as a continuum of forms, with significant overlap and common features unifying biological and inorganic matter. In addition to the philosophical relevance of this perspective, there are important ramifications for science. For example, the debates surrounding extra-terrestrial life, the oldest terrestrial fossils and consequent dating of the emergence of life on the Earth rests to some degree on prejudices inferred from the supposed dichotomy between life-forms and the rest.

William Barlow and the Determination of Atomic Arrangement in Crystals

SummaryWilliam Barlow (1845–1934) was an important if unconventional scientist, known for having developed the ‘closest-packing’ atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the ‘success’ of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

Early developments in crystallography

It has been more than 100 years since the discovery of X-ray diffraction by crystals. The evolution of this technique has transformed our understanding of Nature very profoundly. In India, the early proponents of this area of research were Kedareshwar Banerjee, A R Verma, S Ramaseshan and G N Ramachandran, etc. In this article, contributions of some of them are highlighted.

Universality of crystallography

The work briefly considers the historical development of crystallography from a “servant of mineralogy” to a basis of the modern natural sciences, which became possible thanks to the discovery, in 1912, of the diffraction of X-rays by crystals and X-ray structural analysis with the subsequent rapid accumulation of structural knowledge in chemistry and other sciences.

The 100 Years History of Crystallography in Japan

A century ago, crystallogtaphy ushered in the era of modern science & technology in Japan. The beginning of modern crystallography in Japan dates back to 1913. Torahiko Terada (Tokyo Imperial University) demonstrated X-ray diffraction[1] and Shoji Nishikawa (Tokyo Imperial University) reported on X-ray patterns of fibrous, lamellar and granular substances[2]. In 1936, Ukichiro Nakaya (Hokkaido University) successfully classified natural snow crystals and made the first artificial snow crystals. In the last half-century, developments in crystallography helped form thriving manufacturing sectors such as the semiconductor industry, the iron and steel industries, the pharmaceutical industry, the electronics industry, the textile industry, and the polymer industry, as well as a wide array of academic research.

Japanese Science & Technology with Crystallography

Divers Japanese Science and Technology has advanced together with the progress of crystallography in biology, chemistry, physics, materials science, metallurgy, electronics, engineering, geoscience, etc. Based on the highly scientific and crystallographic technology, Japan has been a great contributor in developing of high-end X-ray generator, electron microscope as well as large scale Photon Science facilities, such as Photon Factory (SR), SPring-8 (SR), J-PARC (Neutron) and SACLA (XFEL). Under such background, we promote IYCr2014 with the partnership of 36 academic societies in the field of pure and applied sciences. In the last half-century, developments in crystallography have also helped thriving manufacturing sectors such as the semiconductor, the iron and steel, the pharmaceuticals, the electronics, the textile, and the chemical industries. Some of the recent impressive outcomes in Japan are fundamental findings of photosynthesis [1] and pristine asteroid [2]. Crystallography in Japan keeps promoting our nationwide projects grappling with global problems such as environment and food, and will contribute to realize a sustainable society.

ChemInform Abstract: Molecular Chirality in Chemistry and Biology: Historical Milestones

AbstractReview: <175 refs.

Molecular Chirality in Chemistry and Biology: Historical Milestones

AbstractBeginning early in the 19th century, developments in crystallography, optics, and chemistry in France set the stage for the discovery of molecular chirality by Louis Pasteur in 1848. He found that the crystallization of the sodium ammonium salt of ‘paratartaric acid’, a mysterious ‘isomer’ of natural (+)‐tartaric acid (TA), produced two different crystal types that were non‐superimposable mirror‐image forms of each other. He separated the two types and found their optical rotations in solution opposite in direction and equal in absolute magnitude. This led him to conclude that paratartaric acid is a combination of two mirror‐image molecule types of TA that are ‘dissymmetric’, an existing term he adapted to the connotation of today's ‘chiral’. In 1857, he found that the two enantiomers of TA were metabolized by a microorganism at drastically different rates, and thereby discovered biological enantioselectivity. In 1886, Italian chemist Arnaldo Piutti discovered D‐asparagine and found that it tasted intensely sweet, in contrast to the known L‐asparagine which had no taste. This was the discovery of stereoselectivity at biological receptors. As a result of advances in stereoselective synthesis and enantioselective chromatography during the last decades of the 20th century, in the 1990s the importance of molecular chirality in drug action and disposition began to receive serious attention from drug‐regulatory authorities and the pharmaceutical industry, the overall result of which has been the near‐complete disappearance of racemic drugs as newly introduced pharmaceuticals.

Diffraction Across the Length Scale

This JOM special topic concerns advances in neutron and x-ray diffraction directed toward the study of the structural properties of materials at different length scales. This year, the scientific community is celebrating 100 years since the discovery of x-ray diffraction by Laue, Bragg, and the first experimental diffraction pattern obtained from a crystal by Friedrich and Knipping. After their experiment, it was immediately understood that x-rays could become one of the most powerful tools for material characterization, medicine, etc. During the last century, the importance of diffraction methods utilizing x-rays and later electrons, neutrons, and Mossbauer photons increased enormously, while their area of applicability significantly broadened. For example, compare the first laboratory x-ray tubes of 100 years ago with the ultrabrilliant synchrotron x-ray sources of today that have opened fantastic possibilities for the analysis of structure in a broad spectrum of materials. In the first decades of x-ray science, the studies of regular Laue–Bragg reflections, specifically their positions and intensities, were the primary focus of research. This allowed the characterization of crystallographic structure starting from simple lattices and moving toward complicated organic structures. Diffraction studies became the basis for the development of crystallography, physics, chemistry, etc. Later, the focus of x-ray science moved to the understanding of both static and dynamic lattice defects. In real crystals, thermal vibrations and other defects disturb periodic atomic arrangements and alter the diffracted intensity. Diffraction lines and reflections may broaden, their intensity weakens, and sometimes the so-called diffuse scattering appears around and between the Bragg peaks. The character of the scattered intensity relates to the shortand long-range order, type, and symmetry of defects, the interaction energy between different atoms, the Fermi surface, and phonons, and critical fluctuations near phase transitions, etc. The selected manuscripts present a slice of several x-ray and neutron diffraction applications that are currently the focus of research in different laboratories worldwide. These manuscripts demonstrate the possibilities of materials studies utilizing small local probes providing information about submicron volumes in those materials and larger beams probing statistically averaged properties of those materials. First, three manuscripts titled ‘‘Microscopic Deformation in Individual Grains in an Advanced High-Strength Steel’’ by Zhenzhen Yu, Roziliya Barabash, Oleg Barabash, Wenjun Liu, and Zhili Feng, ‘‘Acquisition, Sharing and Processing of Large Datasets for Strain Imaging: An Example of an Indented Ni3Al/Mo Composite’’ by N.S. McIntyre, R.I. Barabash, J. Qin, M. Kunz, N. Tamura, and H. Bei and ‘‘In Situ Observation of the Dislocation Structure Evolution During a Strain Path Change in Copper’’ by Christian Wejdemann, Henning Friis Poulsen, Ulrich Lienert, and Wolfgang Pantleon present example applications of different versions of x-ray microdiffraction with a beamsize 0.5 lm for in-depth understanding of the mechanical behavior at the mesoscale. Several versions of microdiffraction were developed: Polychromatic x-ray microdiffraction (PXM) and differential aperture x-ray microscopy (DAXM) were developed by Oak Ridge National Laboratory at the microdiffraction beamline 34-IDE at the Advanced Photon Source at Argonne National Laboratory. This method is directly based on Laue diffraction experiments. Modernization of the beam line apparatus and the high brilliance of synchrotron emissions create unusual opportunities to extract the mesoscale information about the materials. A slightly different version of this technique is described by McIntyre et al. where it is employed at the microdiffraction beamline at the Advanced Light Source. The PXM technique utilizes both a monochromatic beam and a white (pink) beam with an energy range of 5–25 keV. It is best suited to study defects in polycrystalline or multiphase materials Rozaliya I. Barabash is the guest editor for the Mechanical Behavior of Materials Committee of the TMS Structural Materials Division, and coordinated the topic Diffraction Studies across the Length Scales in this issue. JOM, Vol. 65, No. 1, 2013

Structure/reactivity relationships and mechanism from X-ray data and spectroscopic kinetic analysis

The development in crystallography is nothing short of phenomenal, showing an ever increasing trend towards applications, such as in molecular biology. ‘Traditional’ small molecule chemical crystallography tends to, in many aspects, be considered as trivial due to the exponential growth in computing power and the parallel expansion in software. However, many dynamic processes (still) occur at the molecular level. Thus, the fundamental understanding of subtle nuances in structural behaviour, and the associated influence on other (kinetic) properties, is often trivialized when conclusions are simply made based on thermodynamic observations alone. This review aims to emphasize the importance of crystallography in small molecule chemistry by presenting detailed evaluations of two extended ‘case studies’, i.e. the first on structure and dynamics of the middle transition metal cyanide-oxido complexes, and the second on rhodium model homogeneous catalyst precursors. Both underline the fact of understanding the overarching principles of dynamics, i.e. time-resolved behaviour of processes, but considered from a structural perspective. The reference point is to focus on an integrated and overarching mechanistic approach, utilizing structural data, but in particular reaction kinetics, to obtain a more complete picture of processes or systems being evaluated.