X-ray free electron lasers : applications in materials, chemistry and biology

485 Pages·2017·29.905 MB·English

by  Uwe Bergmann, Uwe Bergmann, Vittal Yachandra, Junko Yano, Heinz Frei, Claudio Pellegrini, Nicholas Sauter, Abas Ourmazd, Tomas Ekeberg, John Spence, Peter Zwart, Daniel DePonte, Uwe Weierstall, Allen Orville, Kelly Gaffney, Hirohito Ogasawara, Philippe Wernet, Markus Guehr, Steve Johnson, Shin-Ichi Adachi, Simone Techert, Roberto Alonso-Mori, Richard Neutze, Keith Moffat, Robert Schoenlein, Nina Rohringer, Christoph Bostedt, Henry Chapman, Phil Bucksbaum, Lin X Chen, Nils Huse

X-Ray Free Electron Lasers
Applications in Materials, Chemistry and Biology
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X-Ray Free Electron Lasers
Applications in Materials, Chemistry and
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97- Preface
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0. On April 10, 2009, the Linac Coherent Light Source (LCLS) at SLAC National
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oi: Accelerator Laboratory achieved lasing at a wavelength of 1.5 Å.1 This day
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g | marked the birth of a revolutionary new source, an X-ray free electron laser
c.or (XFEL). An XFEL provides ultrafast X-ray pulses that are about ten billion
s
s.r times brighter than those obtained from a synchrotron source. Combining
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pu the unique properties of X-rays, namely to probe the atomic and electronic
p:// structure of matter, with the extreme brightness and femtosecond time res-
n htt olution of an XFEL, has opened a new window into the inner workings of
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7 many fundamental processes. This book consists of a collection of chapters
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20 written by some of the experts and first users of XFELs. It describes the prop-
ust erties, methods and applications of XFELs with special focus on biological
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A systems and chemical materials, many of them related to photochemistry.
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. n 1 Photochemistry is centrally important to life on Earth and human society
d o because, ultimately, almost all the energy the world uses (nuclear and geo-
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h thermal energy are exceptions) is provided one way or the other by the Sun.
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bli As the pressing challenges of climate change, energy and environment need
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to be addressed in the coming decades, it is the intelligent use of the energy
provided by the Sun that may hold the key to the future of our planet and the
thriving of human society. And this is actually possible. First, the Sun deliv-
ers more than enough energy to Earth by almost a factor of 10 000. (Approx-
imately 1017 W of Sun power reaches the Earth compared to ∼1.6 × 1013 W of
all the power currently used by mankind.) Second, we are making progress
in gaining an atomic and molecular level understanding of the mechanisms
that convert energy from sun light—directly or indirectly—into other forms
that we can control and use. It is the understanding of such processes that
will ultimately ensure a sustainable future for our energy and environmen-
tal challenges, and the ultrafast, ultra-bright X-ray pulses provided by XFELs
might play a critical role in providing such understanding.

Energy and Environment Series No. 18
X-Ray Free Electron Lasers: Applications in Materials, Chemistry and Biology
Edited by Uwe Bergmann, Vittal K. Yachandra and Junko Yano
© The Royal Society of Chemistry 2017
Published by the Royal Society of Chemistry, www.rsc.org
v
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vi Preface
X-Rays are a unique tool to characterize the atomic and electronic struc-
ture of many materials, including artificial and natural, and periodic/ordered
and non-periodic/disordered systems. While X-ray microscopy methods
provide structural information of complex non-periodic systems down to
about 10 nm resolution, X-ray diffraction and scattering methods provide
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7- tion. A wide variety of X-ray spectroscopy methods provide detailed insights
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0 into the local electronic and atomic structure and bonding energetics of the
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6 absorbing atom in an element-specific manner. For the last 40 years, it has
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7 been the development of ever more powerful and brighter synchrotron radi-
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7 ation (SR) sources that has pushed the limits in resolution and sensitivity of
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39/ these X-ray methods. Currently, there are about 50 SR facilities, often called
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0.1 Light Sources, operational worldwide, serving tens of thousands of scientists
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oi: annually (see, for example, www.lightsources.org). X-Rays beams created by
g | d a synchrotron consist of short pulses (∼100 ps) and are bright, monochro-
or matic, polarized and tunable in energy. While these unique properties of SR
c.
s.rs have pushed the elemental sensitivity and spectral, as well as spatial resolu-
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htt tal timescale for many atomic and molecular processes. Here, even shorter
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st limited because of the lack of sufficient photons per pulse.
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the atomic resolution of X-rays provides simultaneous spatial and tempo-
ral access to probing molecular systems during their various functions.
The ultrafast, ultra-bright pulses generated at an XFEL have exactly these
properties.
Before the first XFEL turned on, it was anticipated in the “LCLS First
Experiments” report4 that the ability to directly follow the evolution of
bond lengths and angles could have a profound impact on the field of femto-
chemistry. The authors speculated that such experiments would advance
fundamental understanding of many processes, including photochemically
induced bond breaking, photosynthetic processes and dynamics in nanopar-
ticles. The extremely bright, ultrashort X-ray pulses could potentially also
image important biological structures at atomic resolution, in some cases
without the need for crystallization. A critical question had to be addressed
for most studies using ultra-bright X-ray pulses: can matter be probed before
the onset of damage? Calculations were performed to understand the inten-
sity and timescale limits above which damage-induced changes in the sam-
ple would occur and compromise, for example, diffraction data.5 From these
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Preface vii
calculations and from numerous XFEL experiments performed over the last
7 years, we know now that the allowable dose limit with femtosecond X-ray
pulses exceeds the limit for conventional X-ray methods by several orders of
magnitude. Consequently, XFELs can not only access ultrafast timescales,
they also can probe systems, whose characterization with synchrotron X-rays
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0 is limited by radiation damage, or simply not practical at a realistic time-
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0 viruses, bacteria, proteins, metalloenzymes and synthesized/manufactured
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6 chemical materials, in particular if they have to be studied under ambient
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7 and functioning conditions in real time.
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7 While the use of an XFEL has the potential to provide unique new insights,
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39/ such experiments, as well as the XFEL operation itself, are very challenging
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0.1 and generally much more complex than, for example, SR-based work. These
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oi: challenges can be summarized in three points:
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or (1) The interaction of extremely intense X-ray pulses with matter can
c.
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htt second, intense X-ray pulses often destroy the sample, requiring a
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st vidually specialized methods of sample environment and delivery, is
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. n 11 (2) The stochastic nature of the self-amplified spontaneous emission
o (SASE) process that is generally used to create XFEL pulses causes a
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bli and temporal pulse profile, as well as significant shot-to-shot spatial,
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experiments are carried out in a pump-probe manner, where an ultra-
violet/visible/infrared (UV/visible/IR; or even X-ray, in some cases) laser
pulse is used to initiate a process or reaction, and the XFEL pulse sub-
sequently probes its temporal evolution. Consequently, each pump-
probe event is treated as its own separate experiment. This requires
shot-to-shot spatial and temporal pump-probe synchronization, spec-
tral and spatial beam diagnostics, detection, and data processing. The
data volume produced in this shot-to-shot approach, especially when
combined with large pixel detectors, can be extremely high.
(3) In storage rings used in SR facilities, electrons are repeatedly used in
insertion devices placed around the ring to create X-ray beams that
are fed into simultaneously used experimental stages. In contrast, an
XFEL uses a single pass of electrons from a linear accelerator through
a long undulator producing just one X-ray beam. Although there
are schemes to share the X-ray beam between multiple experiments
and new high repetition rate accelerators can feed several undula-
tors simultaneously, the available capacity in XFEL experiments is
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viii Preface
presently severely limited compared to SR facilities. Fortunately, by
the end of the decade there will be about ten independent XFELs oper-
ational worldwide (see Chapter 1) and this enhanced capacity will
allow the build-up and growth of more and more robust experimental
programs based on XFEL research. However, the capacity of SR facili-
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6 ing advances and applications in science are at a similar place that
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7 SR-based science was about 40 years ago, when SR sources were con-
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7 sidered rare and esoteric. We are optimistic that the explosive growth
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0.1 an indicator of what we can expect from XFEL-based research in the
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oi: near future.
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or These unique characteristics and challenges of XFEL-based research and
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s.rs the judicious approaches to exploit and address them will be the common
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p:// ful that many of the pioneers of XFEL science have agreed to contribute to
htt this book. We have grouped the chapters into six larger sections, namely
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7 o Properties of XFELs, Biological Structure Determination, Photochemistry in Bio-
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st Directions. While these sections are thought to give a loose structure and flow
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u to the book—starting with a historical perspective on XFELs and ending with
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. n 11 an outlook of soft X-ray science enabled by the future high repetition rate
o XFELs—the reader will find that, in fact, each chapter is its own stand-alone
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he paper. We find that this will make it easier for the reader to follow the discus-
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bli sions, although there are unavoidably some repetitions of methods, systems
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the range of topics these chapters cover.
In the first section Properties of XFELs a historical introduction to XFELs
is given and their physical principles and main characteristics are reviewed
in the very comprehensive Chapter 1 by Geloni, Huang and Pellegrini. Here,
the principles of the SASE process to produce ultra-bright, ultrafast X-ray
pulses, and the critical parameters of the injector, linear accelerator and
undulator that comprise an XFEL are described in detail. The chapter closes
with a description of the present status and some exciting new develop-
ments in XFEL-related accelerator research, in particular new compact XFEL
machines, which could dramatically reduce costs and widen the applications
of ultrafast X-ray pulses. The general reader, as well as the expert in acceler-
ator physics, will find in this chapter many useful parameters and physical
principles of XFELs and a beautifully illustrated layout and description of
each XFEL facility currently operating or under construction.
Applications of XFELs to biological systems have really thrived because
the “probe-before-destroy” concept of ultra-short pulses has opened the
door to studies under functional conditions, and we have dedicated the next
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Preface ix
two sections to this topic. The section on Biological Structure Determination
contains four chapters describing various X-ray methods that have been spe-
cifically developed for XFELs. We begin with Chapter 2 by Spence, who gives
a comprehensive overview of various XFEL-based methods for the study of
biological systems. The chapter builds a link between new sample deliv-
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0 of the unique properties of ultra-bright, ultra-short XFEL pulses in structural
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6 biology. The first 7 years of XFEL-based research in this field are reviewed
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7 and their historical context is provided. This chapter also gives a broad over-
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39/ machines under physiological conditions.
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oi: based protein crystallography to study the structure and dynamics of bio-
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g | logical macromolecules under physiological conditions. XFEL experiments
or face challenges as compared to synchrotron work due to many differences,
c.
s.rs including the nature of the exposures (still shots instead of rotational image
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p:// fied in order to achieve the ultimate goal, namely to produce the best possi-
htt ble electron density maps from the recorded data.
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0 ing of non-periodic biological objects is described. Specifically, the data anal-
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st ysis required to reconstruct an object in three-dimensions (3D) from many
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u single shot two-dimensional (2D) projections is discussed in detail. An under-
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. n 11 standing of these algorithms is critical for assessing the origin of spatial res-
o olution limits in single particle imaging. The authors discuss to what extent
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bli size and elemental composition, X-ray wavelength, pulse brightness, detec-
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guide the design parameters of XFEL machines and instrumentation, and is
critical for developing a strategy for XFEL-based single particle imaging.
The second section on the biological application of XFELs focuses specifi-
cally on Photochemistry in Biological Systems. The section starts with Chapter 5
by Moffat describing the study of biological systems in solution, driven far
from equilibrium by optical pulses, and the structural course of their return
to equilibrium. These changes can be monitored by dynamic, time-resolved
X-ray scattering in the femtosecond to nanosecond timescale, and the prin-
ciples of this technique and its application at SR and XFEL facilities is pre-
sented in the chapter.
This is followed by Chapter 6 by Dods and Neutze, where the study of ultra-
fast structural motions in photosynthetic reaction centers is described.
These ubiquitous and important proteins use sunlight to drive reactions
with remarkably high quantum yield and energy efficiency. The authors
describe how X-ray scattering techniques at XFELs can probe real-time, ultra-
fast structural changes in these biomolecules and their functional role in
photosynthesis.
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x Preface
The section closes with Chapter 7 by Alonso-Mori and Kern describing the
simultaneous use of X-ray spectroscopy and X-ray scattering/diffraction
for electronic and geometric structure determination in metalloproteins
using XFELs. The authors provide a review of recent experiments, with an
emphasis on the structure and function of photosystem II, targeted toward
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6 studies of Photochemistry in Materials. While these chapters also include the
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7 discussion of new X-ray methods, they are each centred on specific systems
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7 and related scientific questions. The section starts with Chapter 8 by Wolf
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39/ and Gühr, where experiments on ultrafast dynamics in isolated molecules
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0.1 are described. These gas phase photochemistry studies use element- and
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oi: site-specific soft X-ray K-edge spectroscopy on C, N and O in organic mole-
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g | cules. The authors review recent pioneering studies using “indirect” meth-
or ods, such as Auger spectroscopy, and point out future opportunities for
c.
s.rs studies employing “direct” methods, such as near-edge X-ray absorption fine
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u structure (NEXAFS) spectroscopy.
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p:// In Chapter 9 by Ogasawara, Perakis and Nilsson chemical dynamics studies
htt in liquid water and at catalytic surfaces based on X-ray scattering and soft
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st three chapters focus on 3d transition metal systems studied by various X-ray
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u spectroscopy techniques, including X-ray absorption spectroscopy (XAS),
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. n 11 X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering
o (RIXS), which is a combination of XAS and XES.
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he In Chapter 10 by Chen the study of ultrafast photochemical reaction trajec-
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bli tories in Ni compounds by transient XAS is discussed. The study is used as
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figurations for initial excited states before thermalization on the timescale of
100 fs or shorter. Such studies can help to capture intermediates of potential
photocatalytic significance. A slightly different approach, namely the use of
Kα and Kβ XES and X-ray diffuse scattering (XDS), is described in Chapter 11
by Kjaer and Gaffney. This work focuses on tracking excited state dynamics in
photo-excited transition metal molecular systems. Notably, the XES and XDS
techniques, which are uniquely sensitive to electronic and structural dynam-
ics, respectively, are applied simultaneously in these XFEL-based studies on
ultrafast dynamics.
An even more detailed look at electronic structure dynamics can be
obtained by transition metal L-edge RIXS using soft X-ray pulses. This is
described in Chapter 12 by Wernet, which focuses on the orbital-specific map-
ping of chemical interactions and dynamics of the photochemically activated
prototypical metal complex iron pentacarbonyl [Fe(CO) ] in solution. XFEL-
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based RIXS is sensitive to the frontier–orbital interactions and populations
in the system with atomic specificity and femtosecond temporal resolution.
The method enables the correlation of metal–ligand coordination with