scholarly journals A Strong Link Between Organic Chemistry and Chemical Crystallography Started a Century Ago

2019 ◽  
Vol 92 (2) ◽  
pp. 315-321
Author(s):  
Biserka Kojić-Prodić ◽  
Krešimir Molčanov
Keyword(s):  
Organic Chemistry ◽  
Crystal Engineering ◽  
Materials Science ◽  
Structural Data ◽  
Intermolecular Forces ◽  
Molecular Structures ◽  
X Rays ◽  
Molecular Architecture ◽  
X Ray ◽  
Chemical Crystallography

The article sheds light on some historical crossings of organic chemistry and chemical crystallography. It connects past and present bringing into the focus Prof. Kata Mlinarić-Majerski’s research. An impact of structural chemistry on organic synthesis and reactivity is shown. X-ray structure analysis was established as a unique method to determine the composition and architecture of synthetic and natural organic molecules, already in the second decade of the last century; some of historical and scientific milestones are shown. Numerous controversies were solved, when intriguing molecular structures had been determined and the nature of chemical bond was clarified. An absolute structure (chirality) determination using an anomalous dispersion of X-rays was an important step forward, particularly in pharmaceutical industry. Structural data provided by X-ray crystallography, stored by Cambridge Structural Data Centre have been of great impact on many areas of science. They are closely related to intra- and intermolecular forces and structure/function correlations directing us to synthesis of compounds with designed properties. The developments of supramolecular chemistry, crystal engineering, materials science, and most of all of molecular machines have been assisted by chemical crystallography. The essay does not aim to review the complete scientific opus of Prof. K. Mlinarić-Majerski but it is focused on some of the highlights of her research. The interdisciplinary approach in her research is related to the use of X-ray structural analysis to define molecular architecture, conformational chirality, conformational isomerism, and get insight into reaction paths, interactions governing molecular assembling, and to recognise chemical properties of new compounds. In these researches the X-ray crystallographers were involved.

scholarly journals Hydrogen atoms can be located accurately and precisely by x-ray crystallography

2016 ◽  
Vol 2 (5) ◽  
pp. e1600192 ◽  
Author(s):  
Magdalena Woińska ◽  
Simon Grabowsky ◽  
Paulina M. Dominiak ◽  
Krzysztof Woźniak ◽  
Dylan Jayatilaka
Keyword(s):  
Neutron Diffraction ◽  
Crystal Engineering ◽  
Large Scale ◽  
Materials Science ◽  
Structural Information ◽  
Inorganic Compounds ◽  
X Rays ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Recent Developments In Monochromatic Microprobe X-Ray Fluorescence (MMXRF)

1998 ◽  
Vol 4 (S2) ◽  
pp. 378-379
Author(s):  
Z. W. Chen ◽  
D. B. Wittry
Keyword(s):  
Materials Science ◽  
High Vacuum ◽  
Three Dimensional ◽  
High Sensitivity ◽  
X Rays ◽  
Fluorescence Excitation ◽  
X Ray ◽  
Quantitative Microanalysis ◽  
Recent Developments ◽  
Fifth Order

A monochromatic x-ray microprobe based on a laboratory source has recently been developed in our laboratory and used for fluorescence excitation. This technique provides high sensitivity (ppm to ppb), nondestructive, quantitative microanalysis with minimum sample preparation and does not require a high vacuum specimen chamber. It is expected that this technique (MMXRF) will have important applications in materials science, geological sciences and biological science.Three-dimensional focusing of x-rays can be obtained by using diffraction from doubly curved crystals. In our MMXRF setup, a small x-ray source was produced by the bombardment of a selected target with a focused electron beam and a toroidal mica diffractor with Johann pointfocusing geometry was used to focus characteristic x-rays from the source. In the previous work ∼ 108 photons/s were obtained in a Cu Kα probe of 75 μm × 43 μm in the specimen plane using the fifth order reflection of the (002) planes of mica.

The XFM beamline at the Australian Synchrotron

2020 ◽  
Vol 27 (5) ◽  
pp. 1447-1458 ◽  
Author(s):  
Daryl L. Howard ◽  
Martin D. de Jonge ◽  
Nader Afshar ◽  
Chris G. Ryan ◽  
Robin Kirkham ◽  
...  
Keyword(s):  
Materials Science ◽  
Energy Detection ◽  
Array Detector ◽  
X Rays ◽  
X Ray Diffraction ◽  
High Definition ◽  
Large Area ◽  
X Ray ◽  
Diffraction Microscopy ◽  
System Time

The X-ray fluorescence microscopy (XFM) beamline is an in-vacuum undulator-based X-ray fluorescence (XRF) microprobe beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the 4–27 keV energy range, permitting K emission to Cd and L and M emission for all other heavier elements. With a practical low-energy detection cut-off of approximately 1.5 keV, low-Z detection is constrained to Si, with Al detectable under favourable circumstances. The beamline has two scanning stations: a Kirkpatrick–Baez mirror microprobe, which produces a focal spot of 2 µm × 2 µm FWHM, and a large-area scanning `milliprobe', which has the beam size defined by slits. Energy-dispersive detector systems include the Maia 384, Vortex-EM and Vortex-ME3 for XRF measurement, and the EIGER2 X 1 Mpixel array detector for scanning X-ray diffraction microscopy measurements. The beamline uses event-mode data acquisition that eliminates detector system time overheads, and motion control overheads are significantly reduced through the application of an efficient raster scanning algorithm. The minimal overheads, in conjunction with short dwell times per pixel, have allowed XFM to establish techniques such as full spectroscopic XANES fluorescence imaging, XRF tomography, fly scanning ptychography and high-definition XRF imaging over large areas. XFM provides diverse analysis capabilities in the fields of medicine, biology, geology, materials science and cultural heritage. This paper discusses the beamline status, scientific showcases and future upgrades.

Digital Design of Molecular Sculptures and Abstractions

Leonardo ◽  
2011 ◽  
Vol 44 (1) ◽  
pp. 22-28 ◽  
Author(s):  
Edgar F. Meyer
Keyword(s):  
Molecular Structures ◽  
Digital Design ◽  
Milling Machine ◽  
Molecular Architecture ◽  
Cnc Milling ◽  
X Ray ◽  
Cnc Milling Machine ◽  
Computer Numerically Controlled ◽  
Modeling Software ◽  
The Aesthetic

While tactile models have been used to describe molecular structures for over a century, the sculpting of structural models is a recent phenomenon. Following X-ray coordinate selection, the author uses modeling software and a computer numerically controlled (CNC) milling machine to create precisely scaled, tactile molecular sculptures. The challenge is to inspire the general public to appreciate the aesthetic aspects of molecular architecture and to reveal the magnificence of nature on the molecular scale.

scholarly journals Photoreduction and validation of haem–ligand intermediate states in protein crystals byin situsingle-crystal spectroscopy and diffraction

IUCrJ ◽  
2017 ◽  
Vol 4 (3) ◽  
pp. 263-270 ◽  
Author(s):  
Demet Kekilli ◽  
Tadeo Moreno-Chicano ◽  
Amanda K. Chaplin ◽  
Sam Horrell ◽  
Florian S. N. Dworkowski ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Structural Data ◽  
X Rays ◽  
Solvated Electrons ◽  
X Ray ◽  
Redox States ◽  
Density Maps ◽  
Correct Assignment ◽  
Wide Range

Powerful synergies are available from the combination of multiple methods to study proteins in the crystalline form. Spectroscopies which probe the same region of the crystal from which X-ray crystal structures are determined can give insights into redox, ligand and spin states to complement the information gained from the electron-density maps. The correct assignment of crystal structures to the correct protein redox and ligand states is essential to avoid the misinterpretation of structural data. This is a particular concern for haem proteins, which can occupy a wide range of redox states and are exquisitely sensitive to becoming reduced by solvated electrons generated from interactions of X-rays with water molecules in the crystal. Here, single-crystal spectroscopic fingerprinting has been applied to investigate the laser photoreduction of ferric haem in cytochromec′. Furthermore,in situX-ray-driven generation of haem intermediates in crystals of the dye-decolourizing-type peroxidase A (DtpA) fromStreptomyces lividansis described.

The young hard active Sun: soft X-ray irradiation of tryptophan in water solutions

2010 ◽  
Vol 10 (1) ◽  
pp. 67-75
Author(s):  
A. Ciaravella ◽  
D. Bongiorno ◽  
C. Cecchi-Pestellini ◽  
M.L. Testa ◽  
S. Indelicato ◽  
...  
Keyword(s):  
Aqueous Solutions ◽  
Significant Role ◽  
Irradiation Dose ◽  
Room Temperature ◽  
Energy Deposition ◽  
Molecular Structures ◽  
X Rays ◽  
X Ray ◽  
Water Solutions ◽  
Isotopic Effects

AbstractThe X-ray emission of the young Sun was much harder and intense than today and might have played a significant role in the evolution of complex organics in protoplanetary environments. We investigate the effects of soft X-rays on tryptophan molecules in aqueous solutions at room temperature. As results of the irradiation experiments we detect several light species indicative of fragmentation, together with large molecular structures such as tryptophan dipeptide and tripeptide. Complexification is more evident in H2O solution than in D2O, probably due to isotopic effects. The abundances of peptides depend on the irradiation dose and decrease with increasing energy deposition. Radicals such as D, OD, H and OH, induced by the X-ray interaction with solvents, play a major role in determining the final products.

scholarly journals New Ag(I) Coordination Complexes Based on Bis(1-isoquinolinecarboxamide)ethane.

2014 ◽  
Vol 70 (a1) ◽  
pp. C665-C665
Author(s):  
Nicole Parra ◽  
Julio Belmar ◽  
Claudio Jiménez ◽  
Jorge Pasán ◽  
Catalina Ruiz-Pérez
Keyword(s):  
Crystal Engineering ◽  
Rational Design ◽  
Crystal Packing ◽  
Functional Materials ◽  
Coordination Complexes ◽  
Intermolecular Forces ◽  
Research Area ◽  
Molecular Structures ◽  
Gauche Conformation ◽  
Design And Synthesis

Crystal Engineering is an interdisciplinary research area that involves chemists, physicists, biologists and materials scientists.1It is an important field inside Supramolecular Chemistry which has been considered as a new form of synthesis, named Supramolecular Synthesis.2It is known that important properties in molecular solids are closely related with the way that molecules are aggregated in the condensed phase. Consequently, the ability to control the molecular association in the crystal packing could offer control over specific properties and potential applications. Because of that, the main goal of Crystal Engineering is the rational design and synthesis of functional materials using the nature of the intermolecular forces as a toolkit. Our strategy is the systematic study of non-covalent forces in homologous series.3In this work our interest is focused on the study of crystal packing of two homologous ligands N,N'-bis(1-isoquinolinecarboxamide)-1,2-ethane (1) and N,N'-dimethyl-N,N'-bis(1-isoquinolinecarboxamide)-1,2-ethane (2) and their Ag(I) coordination complexes. The compound 1 consists of two isoquinoline rings and one ethylene bridge linked by amide functional groups. Compound 2 is the result of the N-methylation of 1. The main difference in the molecular structures is that while 1 present a gauche conformation in the 1,2-ethanediamine bridge (600) 2 present a staggered conformation (1800). Curiously, in spite of this fact, the Ag(I) complexes in both cases present a small torsion angle of 4501-Ag(I) and 6502-Ag(I). These orientations allow the torsion of the isoquinoline moiety and the formation of homonuclear 0D coordination complexes, over the 1D coordination polymer expected. The main intermolecular interaction in 1 is the amide-to-amide hydrogen bond that is replaced by a weak CH··O interaction in 2 On the other hand, both Ag(I) complexes use the nitrate counteranion to build a chain using NH··O(nitrate) in 1 and CH(quinoline)··O(nitrate) in 2.Acknowledgment: Grant DIUC 212.023.049-1.0

X-Ray Diffraction – The Magic Wand

2020 ◽  
Vol 42 (3) ◽  
pp. 317-317
Author(s):  
Iqra Zubair Awan Iqra Zubair Awan
Keyword(s):  
Materials Science ◽  
Review Paper ◽  
Medical Community ◽  
X Rays ◽  
X Ray Diffraction ◽  
Medical Sciences ◽  
X Ray ◽  
Magic Wand ◽  
History Of ◽  
Engineering Materials

This review paper covers one of the most important discoveries of the last century, viz. X-ray diffraction. It has made enormous contribution to chemistry, physics, engineering, materials science, crystallography and above all medical sciences. The review covers the history of X-rays detection and production, its uses/ applications. The scientific and medical community will forever be indebted to Rand#246;ntgen for this invaluable discovery and to those who perfected its application.

The Use of X-Ray Photoelectron Spectroscopy in Materials Science

1991 ◽  
Vol 35 (B) ◽  
pp. 869-882 ◽  
Author(s):  
James Castle
Keyword(s):  
Surface Analysis ◽  
Photoelectron Spectroscopy ◽  
Materials Science ◽  
Polymer Surface ◽  
Surface Region ◽  
Binding Energies ◽  
Particulate Composites ◽  
X Rays ◽  
Additional Advantage ◽  
X Ray

AbstractThis review will attempt to show how XPS now makes an important contribution to Materials Science and to highlight the developments which have brought it to this position. XPS is now a mature technique for surface analysis but it has in addition a major role as a specialised tool, being essential to studies in which derivitization methods are used to tag surface groups.The requirements of users in this field have led to the development of X-ray sources which were not envisaged in the early development of the spectroscopy. The usual sources of aluminium Kα and magnesium Kα have limitations for those elements beyond magnesium in the periodic table which would have the Is lino as the principal peak - aluminium, silicon, oulphur and phosphorus for example. Higher energy sources such as silicon Kα or zirconium and silver Lα have made it possible to utilise the Is lines up to chlorine and have the additional advantage that a strong and well resolved series of Auger lines also becomes available. The higher energy radiations are thus particularly suited to the determination of relaxation energies in materials by use of relative shifts between the photo- and Auger lines of the spectrum. Such has been the utility of such relaxation energies that use is often made of Auger lines derived from the Bremmstrahlung component of the normal x-ray sources to make a similar measurement. This measurement is used in the study of insulating ceramics in which electrostatic charging makes measurement of binding energies uncertain.Modern materials technology is particularly concerned with the manufacture of composites; particulate, fibre and laminate composites are all well known and the key to their success often lies within the interface between the phases. Transfer of load across the interface places particular requirements on adhesion at the phase boundary and an understanding of the locus of failure during destructive testing is crucial to the development of satisfactory bonding processes. In coated and laminated products there is no problem in the use of XPS, with its excellent chemical sensitivity but there is a problem of increasing magnitude in fibre and particulate composites as the substructures become finer. This stems, of course, from the difficulty of providing a focused source of X-rays of sufficient magnitude. Imaging XPS is slowly becoming a reality with several systems having a capability of 10μm now available, and one of the markets for such instruments is that of composite materials.There are important areas of Materials Science in which XPS has been displaced by other techniques such as SIMS. One such area is that of polymer surface analysis. The selectivity of XPS for substituent groups in the surface region is not good. Derivitization methods have made an impact, enabling acidic or basic groups to be determined, but SIMS, which has the ability to detach molecular clusters, has obvious advantages which will become increasingly exploited aa the problems of charging become solved. Until then however XPS will continue to find a role in polymer research and development.

scholarly journals Recent advances in ultrafast X-ray sources

2019 ◽  
Vol 377 (2145) ◽  
pp. 20180384 ◽  
Author(s):  
Robert Schoenlein ◽  
Thomas Elsaesser ◽  
Karsten Holldack ◽  
Zhirong Huang ◽  
Henry Kapteyn ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Materials Science ◽  
X Rays ◽  
X Ray ◽  
High Order Harmonic ◽  
Recent Advances ◽  
Electronic Motion ◽  
Femtosecond Regime ◽  
Indispensable Tool ◽  
And Function

Over more than a century, X-rays have transformed our understanding of the fundamental structure of matter and have been an indispensable tool for chemistry, physics, biology, materials science and related fields. Recent advances in ultrafast X-ray sources operating in the femtosecond to attosecond regimes have opened an important new frontier in X-ray science. These advances now enable: (i) sensitive probing of structural dynamics in matter on the fundamental timescales of atomic motion, (ii) element-specific probing of electronic structure and charge dynamics on fundamental timescales of electronic motion, and (iii) powerful new approaches for unravelling the coupling between electronic and atomic structural dynamics that underpin the properties and function of matter. Most notable is the recent realization of X-ray free-electron lasers (XFELs) with numerous new XFEL facilities in operation or under development worldwide. Advances in XFELs are complemented by advances in synchrotron-based and table-top laser-plasma X-ray sources now operating in the femtosecond regime, and laser-based high-order harmonic XUV sources operating in the attosecond regime. This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.

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