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2020 | Buch

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21st Century Challenges in Chemical Crystallography I

History and Technical Developments

herausgegeben von: Prof. D. Michael P. Mingos, Paul R. Raithby

Verlag: Springer International Publishing

Buchreihe : Structure and Bonding

Enthalten in: Springer Professional "Wirtschaft+Technik" , Springer Professional "Technik" , Springer Professional "Wirtschaft"

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Über dieses Buch

This volume summarises recent developments and possible future directions for small molecule X-ray crystallography. It reviews specific areas of crystallography which are rapidly developing and places them in a historical context. The interdisciplinary nature of the technique is emphasised throughout. It introduces and describes the chemical crystallographic and synchrotron facilities which have been at the cutting edge of the subject in recent decades. The introduction of new computer-based algorithms has proved to be very influential and stimulated and accelerated the growth of new areas of science. The challenges which will arise from the acquisition of ever larger databases are considered and the potential impact of artificial intelligence techniques stressed. Recent advances in the refinement and analysis of X-ray crystal structures are highlighted.

In addition the recent developments in time resolved single crystal X-ray crystallography are discussed. Recent years have demonstrated how this technique has provided important mechanistic information on solid-state reactions and complements information from traditional spectroscopic measurements. The volume highlights how the prospect of being able to routinely “watch” chemical processes as they occur provides an exciting possibility for the future. Recent advances in X-ray sources and detectors that have also contributed to the possibility of dynamic single-crystal X-ray diffraction methods are presented. The coupling of crystallography and quantum chemical calculations provides detailed information about electron distributions in crystals and has resulted in a more detailed understanding of chemical bonding.

The volume will be of interest to chemists and crystallographers with an interest in the synthesis, characterisation and physical and catalytic properties of solid-state materials. Postgraduate students entering the field will benefit from a historical introduction to the subject and a description of those techniques which are currently used. Since X-ray crystallography is used so widely in modern chemistry it will serve to alert senior chemists to those developments which will become routine in coming decades. It will also be of interest to the broad community of computational chemists who study chemical systems.

Inhaltsverzeichnis

Frontmatter

Early History of X-Ray Crystallography

Abstract

The discovery of the optical microscope played an important role in the scientific revolution of the seventeenth century because it enabled one to directly view objects which were invisible to the naked eye. In 1667 Robert Hooke improved the microscope invented in the previous century in Holland and used it to examine the “microscopic” appearance of snowflakes and plants. Others were able to view for themselves the presence of very small objects and the structures of plants, hair, skin, bones etc. The development of X-ray crystallography at the beginning of the twentieth century by von Laue and the Braggs played an equally important role in the scientific revolution which has shaped our lives. The technique they discovered did not enable scientists to look at the molecular world by looking through a more powerful microscope, but it provided data which when processed enabled scientists to calculate the structures of molecules and appreciate their three-dimensional structures. It provided the zeitgeist of our time that the knowledge of the structure would lead to a more profound understanding of the function and properties of that class of molecule.

This chapter recounts the early history of the development of this important technique and describes how the early technical problems were overcome. It is a fascinating technique because unlike the optical microscope it required the development of a deeper understanding of the way in which the X-rays interact with the electron density in the planes of the crystal and the development of models in order to model this electron density satisfactorily. This chapter traces how these problems were overcome. In the early days, the structures of even simple organic molecules would take a PhD student several months or even years to solve the structure. In time and particularly since the 1950s, the development of more sophisticated equipment and the massive rise in computing power made it possible to solve the three-dimensional structure of an organic molecule within a few minutes with the latest detectors on a laboratory instrument. This successful trajectory has resulted in the ability to study ever more complex molecules and use smaller and smaller crystals. The structures of over a million organic and organometallic compounds are now archived in the most commonly used database, and this wealth of information creates a new set of problems for future generations of scientists.

D. Michael P. Mingos

Recent Developments in the Refinement and Analysis of Crystal Structures

Abstract

Crystal structure refinement and analysis is a powerful method for determination of crystal structures and finds widespread application in determination of structures of crystals of small molecules and frameworks at atomic resolution. The independent atom model is used to describe atomic scattering for routine use, while more accurate aspherical scattering factors are increasingly available. The structure factor is presented as the Fourier transform of convolutions of scattering and probability densities in the crystal structure to clarify how aspherical scattering factors and alternative displacement probabilities can be introduced into refinement methods. Non-linear least squares fitting of the crystal structure parameters in the structure factor equations is described using matrix algebra notation which enables simple derivation of the extensions required for discussion of crystallographic restraints and leverage analysis. Finally, combined analysis of multiple single-crystal experiments is discussed highlighting the potential of refinement tools to extract useful information from joint X-ray and neutron data and from mixed ground-state and excited-state X-ray data from pump-probe experiments.

Richard I. Cooper

Leading Edge Chemical Crystallography Service Provision and Its Impact on Crystallographic Data Science in the Twenty-First Century

Abstract

National facilities provide state-of-the-art crystallographic instrumentation and processes and tend to act as an indicator for the direction of a community in the medium term. There has been a significant step up in terms of instrumentation and approach in the last 10 years which has driven data generation. This has had a significant impact on databases – in turn we observe a substantial change in the use of the Cambridge Structural Database (CSD) from relatively basic search/retrieve to gaining deep understanding about factors that govern the solid state. Databases are now able to drive new science in areas such as crystal engineering. Looking forward, we will see more automated pipelining of the data generation process, and this will require better integration with databases. Databases will provide more predictive power – and this will inform the science/crystallography that should be done.

Simon J. Coles, David R. Allan, Christine M. Beavers, Simon J. Teat, Stephen J. W. Holgate, Clare A. Tovee

Crystallography Under High Pressures

Abstract

This chapter highlights the area of crystallography of molecular systems under high-pressure conditions. It is an area of crystallography that has seen a rapid expansion over the last two decades. Advances in technology and data processing have facilitated the discovery of new materials, polymorphs and chemistries under extreme conditions. We discuss these advances using examples of organic and metal-organic materials as well as providing guidance to the pitfalls to be avoided conducting these studies.

Stephen A. Moggach, Iain D. H. Oswald

Watching Photochemistry Happen: Recent Developments in Dynamic Single-Crystal X-Ray Diffraction Studies

Abstract

Photoresponsive materials are an important contemporary research area with applications in, for example, energy and catalysis. Mechanistic information on solid-state photochemical reactions has traditionally come from spectroscopy and modelling, with crystallography limited to snapshots of endpoints and long-lived intermediates. Recent advances in X-ray sources and detectors have made it possible to follow solid-state reactions in situ with dynamic single-crystal X-ray diffraction (SCXRD) methods, allowing a full set of atomic positions to be determined over the course of the reaction. These experiments provide valuable structural information that can be used to interpret spectroscopic measurements and to inform materials design and optimisation.

Solid-state linkage isomers, where small-molecule ligands such as NO, NO₂⁻, N₂ and SO₂ show photo-induced changes in binding to a transition metal centre, have played a leading role in the development of dynamic SCXRD methodology, since the movement of whole atoms and the predictable temperature dependence of the excited-state lifetimes make them ideal test systems. The field of “photocrystallography”, pioneered by Coppens in the late 1990s, has developed alongside advances in instrumentation and computing and can now provide the 3D structures of species with lifetimes down to femtoseconds.

In this chapter, we will review the development of photocrystallography experiments against linkage isomer systems, from the early identification of metastable species under continuous illumination, through measuring kinetics at low temperature, to recent experiments studying species with sub-second lifetimes. We will discuss the advances in X-ray sources and instrumentation that have made dynamic SCXRD experiments possible, and we will highlight the role of kinetic modelling and complementary spectroscopy in designing experiments. Finally, we will discuss possible directions for future development and identify some of the outstanding challenges that remain to be addressed.

Lauren E. Hatcher, Mark R. Warren, Anuradha R. Pallipurath, Lucy K. Saunders, Jonathan M. Skelton

Time-Resolved Single-Crystal X-Ray Crystallography

Abstract

In this chapter the development of time-resolved crystallography is traced from its beginnings more than 30 years ago. The importance of being able to “watch” chemical processes as they occur rather than just being limited to three-dimensional pictures of the reactant and final product is emphasised, and time-resolved crystallography provides the opportunity to bring the dimension of time into the crystallographic experiment. The technique has evolved in time with developments in technology: synchrotron radiation, cryoscopic techniques, tuneable lasers, increased computing power and vastly improved X-ray detectors. The shorter the lifetime of the species being studied, the more complex is the experiment. The chapter focusses on the results of solid-state reactions that are activated by light, since this process does not require the addition of a reagent to the crystalline material and the single-crystalline nature of the solid may be preserved. Because of this photoactivation, time-resolved crystallography is often described as “photocrystallography”.

The initial photocrystallographic studies were carried out on molecular complexes that either underwent irreversible photoactivated processes where the conversion took hours or days. Structural snapshots were taken during the process. Materials that achieved a metastable state under photoactivation and the excited (metastable) state had a long enough lifetime for the data from the crystal to be collected and the structure solved. For systems with shorter lifetimes, the first time-resolved results were obtained for macromolecular structures, where pulsed lasers were used to pump up the short lifetime excited state species and their structures were probed by using synchronised X-ray pulses from a high-intensity source. Developments in molecular crystallography soon followed, initially with monochromatic X-ray radiation, and pump-probe techniques were used to establish the structures of photoactivated molecules with lifetimes in the micro- to millisecond range. For molecules with even shorter lifetimes in the sub-microsecond range, Laue diffraction methods (rather than using monochromatic radiation) were employed to speed up the data collections and reduce crystal damage. Future developments in time-resolved crystallography are likely to involve the use of XFELs to complete “single-shot” time-resolved diffraction studies that are already proving successful in the macromolecular crystallographic field.

Paul R. Raithby

Backmatter

Titel: 21st Century Challenges in Chemical Crystallography I
herausgegeben von: Prof. D. Michael P. Mingos
Paul R. Raithby
Verlag: Springer International Publishing
Electronic ISBN: 978-3-030-64743-8
Print ISBN: 978-3-030-64742-1
DOI: https://doi.org/10.1007/978-3-030-64743-8

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