An Introduction to Synchrotron Radiation E-Book

Philip Willmott

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 994

Veröffentlichungsjahr: 2019

Beschreibung

The updated guide to the fundamental concepts, techniques and applications of synchrotron radiation and its applications in this rapidly developing field 

Synchrotron light is recognized as an invaluable research tool by a broad spectrum of scientists, ranging from physicists to biologists and archaeologists. The comprehensively revised second edition of An Introduction to Synchrotron Radiation offers a guide to the basic concepts of the generation and manipulation of synchrotron light, its interaction with matter and the application of synchrotron light in x-ray scattering, spectroscopy, and imaging.

The author, a noted expert in the field, reviews the fundamentals of important experimental methods, and explores the most recent technological advances in both the latest generation of x-ray sources and x-ray instrumentation. Designed to be an accessible resource, the book contains full-colour illustrations of the underlying physics and experimental applications, as well as the most commonly-used synchrotron techniques. In particular, the updated second edition now includes:

• In-depth descriptions of the latest x-ray-source technologies, notably diffraction-limited storage rings and x-ray free-electron lasers
• The latest advances in instrumentation, x-ray optics, and experimental methods in synchrotron radiation
• The most recent developments in macromolecular crystallography, time-resolved studies, and imaging techniques
• A comprehensive set of problems for each chapter, plus their ideal solutions in the appendices.

Written for undergraduate and postgraduate students from all areas of the natural and physical sciences, An Introduction to Synchrotron Radiation, Second Edition is an invaluable up-to-date reference source in this highly multidisciplinary field. 

PowerPoint slides of all the figures within the text are available for download, for instructors and users of this book, at http://booksupport.wiley.com

Leseprobe

An Introduction to Synchrotron Radiation

Techniques and Applications

Second Edition

PHILIP WILLMOTT

This edition first published 2019© 2019 John Wiley & Sons Ltd

Edition HistoryAn Introduction to Synchrotron Radiation: Techniques and Applications First edition, Wiley 2011

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The right of Philip Willmott to be identified as the author of this work has been asserted in accordance with law.

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Library of Congress Cataloging-in-Publication Data

Names: Willmott, Philip (Phil R.), author.Title: An introduction to synchrotron radiation : techniques and applications/Philip Willmott, Swiss Light Source, Villigen, Switzerland.Description: Second edition. | Hoboken, New Jersey : John Wiley & Sons, Inc., [2019] | Includes bibliographical references and index. |Identifiers: LCCN 2018054068 (print) | LCCN 2018060648 (ebook) | ISBN 9781119280378 (Adobe PDF) | ISBN 9781119280385 (ePub) | ISBN 9781119280392(pbk.)Subjects: LCSH: Synchrotron radiation. | X-ray optics.Classification: LCC QC793.5.E627 (ebook) | LCC QC793.5.E627 W55 2019 (print) | DDC 539.7/35–dc23LC record available at https://lccn.loc.gov/2018054068

Cover Design: WileyCover Images: Image courtesy of the Author using image from the RCSB PDB (www.rcsb.org) of 1PRC (Deisenhofer, J., Epp, O., Sinning, I., Michel, H. (1995) Crystalline refinement at 2.3 angstroms resolution and refined model of the photosynthetic reaction center from rhodopseudomonas viridis J Mol Biol 246 429–457 created with QtMG.

To Ella, Jo, Nyah, and Hanah.

Preface

In the seven years since the first edition of this book, there have been critical advances in both x-ray-source technology and experimental methods, leading to previously unimagined vistas of scientific discovery. In particular, two developments in x-ray sources are revolutionizing x-ray science and techniques. First, the emergence of high-gain, hard x-ray free-electron lasers (XFELs) has resulted in, among other things, the birth of new fields in macromolecular crystallography and time-resolved surface and catalytic chemistry. Even more recently, advances in vacuum and computer-numerical-control machining technologies have facilitated the realization of novel magnetic storage-ring components that substantially improve the electron-beam quality, in so-called diffraction-limited storage rings (DLSRs). The greenfield facilities of MAX-IV at Lund, Sweden, and Sirius in Campinas, Brazil, are the first of these fourth-generation synchrotrons, closely followed by several upgrades of third-generation facilities to DLSRs. They promise an increase in brilliance of up to two orders of magnitude compared to the state-of-the-art synchrotrons available at the time of writing the first edition of this book.

This rapid evolutionary phase is reflected in a certain readjustment of the emphasis of some chapters in this second edition. In particular, Chapter 3 has been significantly expanded to include a more thorough description of DLSR science and technology, which in turn has an impact on beamline design (Chapter 5) and experimental techniques, not least in macromolecular crystallography (Section 6.11) and x-ray imaging (Chapter 8). XFELs now command a chapter of their own. All the figures in this second edition are available online at Wiley as PowerPoint slides.

In addition to up-to-date examples of applications of various x-ray techniques, each chapter in this new edition contains problem sets, plus comprehensive solutions in the Appendices. Some of the problems are a straightforward plugging-in of numbers to equations presented in the main text – they are not intended to constitute an intellectual challenge, but rather to provide the student with an opportunity to appreciate the magnitudes of things, and their potential impact on other considerations, both practical and fundamental. Other problems, however, require some thought and a deeper understanding of the background science. It is hoped that, as such, these problems will provide an adjunct to the main text and furnish additional insights into the fascinating, multidisciplinary, and ever-expanding field of x-ray science.

Philip Willmott, Zürich, 2018

Acknowledgements

I am greatly indebted to many colleagues for their patience and tolerance in the face of my repeated questioning (some might say badgering), and for their critical reviewal of the manuscript and suggestions for improvements for this, the second edition.

In particular, I would like to thank Michael Böge, Anne Bonnin, Oliver Bunk, Marco Calvi, Nicola Casati, Ana Diaz, Uwe Flechsig, Ronald Frahm, Daniel Grolimund, Jerry Hastings, Gerhard Ingold, Juraj Krempasky, Federica Marone, Andreas Menzel, Chris Milne, Craig Morrison, Frithjof Nolting, Vincent Olieric, Bruce Patterson, Eduard Prat, Christian Schlepütz, Thomas Schmidt, Marco Stampanoni, Jörg Standfuss, Andreas Streun, Meitian Wang, Ben Watts, Tobias Weinert, Qing Wu, and the editorial team at Wiley, for their insights into all the aspects that hopefully make this edition a more rounded product than its predecessor.

About the Companion Website

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PPTs of all the figures

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http://booksupport.wiley.com

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1Introduction

How does nature create a living thing from simple chemical components? How is a complete human being constructed nine months after the unique mixing of its parents' genetic material contained in a single fertilized egg?

When I was a young child, these questions were only just beginning to be answered. Indeed, just five months before my own birth, the Nobel Committee announced that the 1962 Prize in Physiology or Medicine would be awarded to James Watson, Francis Crick, and Maurice Wilkins1 for their elucidation of the structure of deoxyribonucleic acid (DNA) [1] ‘and its significance for information transfer in living material’.

DNA resides permanently within the nucleus of a living cell. How then is its information conveyed to the rest of the cell and elsewhere in the organism; how is new living material subsequently synthesized; and how do initial (‘stem’) cells in the blastocyst differentiate into specialized cells as diverse as ganglions, muscle cells, or skin? Major steps towards answering these questions were made in research that would result in Nobel Prizes in Chemistry in 2006 and 2009.

The first step in carrying out the commands encoded in DNA is its transcription into so‐called messenger‐RNA (mRNA), which then leaves the confines of the nucleus to the protein‐producing parts of the cell. How mRNA is synthesized and carries the genetic information with high fidelity, via a very special macromolecule called RNA‐polymerase, was reported by Roger Kornberg and co‐workers in 2001 [2], for which he received the 2006 Nobel Prize in Chemistry.

The following step, protein synthesis, uses the blueprint of the mRNA, plus raw material in the form of amino acids attached to small transfer‐RNA (tRNA) molecules in a chemical factory called the ribosome. The detailed description of the mechanisms by which this highly complex biomolecular process occurs won Ada Yonath, Thomas Steitz, and Venkatraman Ramakrishnan the Nobel Prize in Chemistry in 2009 [3, 4].

Figure 1.1 The three central biostructures associated with the ‘Nobel trilogy of life’. Left: a DNA dodecamer; centre: the yeast RNA polymerase subunit; right: the 80S ribosome from Tetrahymena cerevisiae. Rendered from the pdb files 1bna, 1i3q, and (4v5o + 4v8p), respectively.

As should be apparent from its title, this textbook is not a treatise on molecular biology. It is, however, concerned with diverse aspects of a tool now considered indispensable to molecular biologists – synchrotron radiation. The thematic link between the above trilogy of Nobel Prizes is that of structure, and its inherent importance in determining biomolecular activity. Although the structure of DNA was determined to a large extent by a combination of model building, biochemical know‐how (including the application of Chargaff's rules), and some guesswork, it was x‐ray diffraction data which provided the last key information in solving the puzzle2. The latter two discoveries of the ‘Nobel life trilogy’ depended intimately on x‐ray diffraction (see Figure 1.1 and Table 1.1).

Table 1.1 Nobel Prizes awarded in the field of x‐ray research.

Year

Recipient(s)

Research discipline

1901

W. C. Röntgen

Physics; discovery of x‐rays

1914

M. von Laue

Physics; x‐ray diffraction from crystals

1915

W. H. Bragg and W. L. Bragg

Physics; crystal structure derived from x‐ray diffraction

1917

C. G. Barkla

Physics; characteristic radiation of elements

1924

K. M. G. Siegbahn

Physics; x‐ray spectroscopy

1927

A. H. Compton

Physics; scattering of x‐rays by electrons

1936

P. Debye

Chemistry; diffraction of x‐rays and electrons in gases

1946

H. J. Muller

Medicine; discovery of x‐ray‐induced mutations

1962

M. Perutz and J. Kendrew

Chemistry; structures of myoglobin and haemoglobin

1962

J. Watson, M. Wilkins, and F. Crick

Medicine; structure of DNA

1964

D. Crowfoot‐Hodgkin

Chemistry; structure of penicillin

1976

W. N. Lipscomb

Chemistry; x‐ray studies on the structure of boranes

1979

A. McLeod Cormack and G. Newbold Hounsfield

Medicine; computed axial tomography

1981

K. M. Siegbahn

Physics; high‐resolution electron spectroscopy

1985

H. Hauptman and J. Karle

Chemistry; direct methods to determine x‐ray structures

1988

J. Deisenhofer, R. Huber, and H. Michel

Chemistry; determining the structure of proteins crucial to photosynthesis

1997

P. D. Boyer and J. E. Walker

Chemistry; mechanism of adenosine triphosphate synthesis

†

2003

R. MacKinnon and P. Agre

Chemistry; structure and operation of ion channels

†

2006

R. D. Kornberg

Chemistry; atomic description of DNA transcription

†

2009

V. Ramakrishnan, T. A. Steitz, and A. E. Yonath

Chemistry; structure and function of the ribosome

†

2012

R. J. Lefkowitz and B. K. Kobilka

Chemistry; studies of G‐protein‐coupled receptors

†

2018

F. H. Arnold

Chemistry; the directed evolution of enzymes

†

†Work using synchrotron radiation as a primary tool.

The relevance of these studies goes well beyond pure academic understanding – the detailed description of DNA transcription and the difference in this process between eukaryotic organisms (with intracellular nucleus) and prokaryotic organisms (without intracellular nucleus), as well as a knowledge of the biochemical function of the ribosome, are already having a huge impact on the design of novel antibiotic substances and other drugs, and provide a deeper understanding of how some cancers arise and how they might be tackled.

Figure 1.2 Left: the cathepsin B structure determined using XFEL radiation. This is a potential target in the quest to develop new drugs against sleeping sickness, a disease caused by the parasite Trypanosoma brucei, which uses cathepsin to break down proteins within the host cell. Rendered from the pdb file 3mor. Right: a typical nanocrystal used in the XFEL ‘diffraction‐before‐destruction’ experiment grown in vivo in insect cells. The scale bar is 1  m.

Reprinted from [5] with permission from the American Association for the Advancement of Science.

The year that Yonath, Ramakrishnan, and Steitz were awarded their Nobel Prize also saw first light at the pioneering hard x‐ray free‐electron laser (XFEL), the Linac Coherent Light Source (LCLS) at the SLAC facility in California. The first report of a new biological structure (to a resolution of 2.1 Å) determined using the LCLS was reported a little over three years later [5] (see Figure 1.2). XFELs provide x‐ray beams with unique properties regarding pulse duration, peak pulse intensity, and beam cross‐section. Using a technique coined ‘diffraction‐before‐destruction’, crystals with sizes orders of magnitude smaller in volume than hitherto possible can be investigated. As the growth of sufficiently large and well‐ordered crystals has to date been the major bottleneck in biomolecular‐structure studies using x‐rays from synchrotrons, the application of this technique at XFELs represents a sea change in this field of research.

Figure 1.3 Synchrotron users by discipline. Estimated by the author from user data between 2013 and 2016 at the SLS, SSRL, APS, and ESRF.

The above examples beautifully illustrate that, since their discovery in late 1895 by Wilhelm Röntgen, x‐rays have played a pivotal rôle in society, particularly in medicine, pharmacy, physics, and chemistry. Whereas research using x‐rays was originally the dominion of physicists, x‐rays are now a ubiquitous tool for research in almost all branches of scientific endeavour (see Figure 1.3). They allow us, among many other things, to determine the internal architecture of cells and other biological structures; to identify the chemical composition, fabrication techniques, and provenance of archaeological artefacts; and even to examine the previously hidden earlier artistic efforts of one of the foremost influential post‐impressionist painters.

Figure 1.4 Publications which explicitly mention ‘synchrotron’ or ‘synchrotron radiation’ (blue data), and ‘XFEL’, ‘x‐ray free‐electron laser’, or ‘X‐FEL’ (yellow data, all entries case insensitive) in the field ‘topic’ in the Web of Science database, since the first paper by McMillan in 1945 [7]. Papers relating to astronomy, particle fields, and nuclear physics were excluded. Note also that many publications that contain data recorded at synchrotrons and/or XFELs do not include these keywords and that the actual total number of reports relying at least partly on them is substantially higher.

This broad range of applications of x‐rays has manifested itself since the turn of this century in the diversity of disciplines served and in the broad palette of techniques now available at synchrotron facilities, which represents one of the principal examples of multidisciplinary research [6]. Today, there are more than seventy facilities in operation, or under construction, worldwide, providing services for well over one hundred thousand users from virtually every discipline of the natural sciences. Each year, several thousand articles are published which explicitly mention synchrotrons (see Figure 1.4). Since 1945, in total almost papers relating to synchrotrons and synchrotron radiation have been published and have been cited almost times.

Why are