Serial crystallography develops by leaps and bounds at the ESRF

Serial crystallography is a new way of studying macromolecular structures using synchrotron and X-FEL sources around the world.

The Structural Biology group at the ESRF is continuously developing new methods to advance the field. Two articles describing advances made are published today in Acta Crystallographica Section D.

“On the Structural Biology Group beamlines one of the ultimate aims is that users can define protocols for experiments, click ‘go’ and let the experiments run by themselves”, explains Gordon Leonard, head of the Structural Biology group at the ESRF. With this idea in mind and to get as much information as possible from the samples available, the team has already adopted serial crystallography, a technique which involves taking diffraction data from many, sometimes hundreds or thousands, of crystals in order to assemble a complete dataset, piece by piece. Indeed, the members of the group are constantly developing new ways to improve the method through collaboration involving scientists from the ESRF, DESY, the Hamburg Centre for Ultrafast Imaging, the European X-FEL and the University of Hamburg.

>Read more on the European Synchrotron website

Image: Daniele de Sanctis on the ID29 beamline.
Credit: S. Candé.

Scientists create “Swiss army knife” for electron beams

Pocket accelerator combines four functions in one device 

DESY scientists have created a miniature particle accelerator for electrons that can perform four different functions at the push of a button. The experimental device is driven by a Terahertz radiation source and can accelerate, compress, focus and analyse electron bunches in a beam. Its active structures measure just a few millimetres across. The developers from the Center for Free-Electron Laser Science (CFEL) present their “Segmented Terahertz Electron Accelerator and Manipulator” (STEAM) in the journal Nature Photonics. Terahertz radiation is located between microwaves and the infrared in the electromagnetic spectrum.

One of the central features of the device is its perfect timing with the electron beam. The scientists achieve this by using the same laser pulse to generate an electron bunch and to drive the device. “To do this, we take an infrared laser pulse and split it up,” explains first author Dongfang Zhang from the group of Franz Kärtner at CFEL. “Both parts are fed into nonlinear crystals that change the laser wavelength: For the generation of an electron bunch the wavelength is shifted into the ultraviolet and directed onto a photocathode where it releases a bunch of electrons. For STEAM the wavelength is shifted into the Terahertz regime. The relative timing of the two parts of the original laser pulse only depends on the length of the path they take and can be controlled very precisely.”

This way, the scientists can control with ultra-high precision, what part of the Terahertz wave an electron bunch hits when it enters the device. Depending on the arrival time of the electron bunch, STEAM performs its different functions. “For instance, a bunch that hits the negative part of the Terahertz electric field is accelerated,” explains Zhang. “Other parts of the wave lead to focusing or defocusing of the bunch or to a compression by a factor of ten or so.” While compression means the electron bunch gets shorter in the direction of flight, focusing means it shrinks perpendicular to the direction of flight.

>Read more on the PETRA III at DESY website

Image: The mini accelerator STEAM (centre) is driven by Terahertz radiation (yellow, coming from both sides). It can accelerator, compress, focus and analyse the incident electron bunches (blue).
Credit: DESY, Lucid Berlin

Edges and corners increase efficiency of catalytic converters

X-rays reveal oxide islands on noble metal nanoparticles

Catalytic converters for cleaning exhaust emissions are more efficient when they use nanoparticles with many edges. This is one of the findings of a study carried out at DESY’s X-ray source PETRA III. A team of scientists from the DESY NanoLab watched live as noxious carbon monoxide (CO) was converted into common carbon dioxide (CO2) on the surface of noble metal nanoparticles like those used in catalytic converters of cars. The scientists are presenting their findings in the journal Physical Review Letters. Their results suggest that having a large number of edges increases the efficiency of catalytic reactions, as the different facets of the nanoparticles are often covered by growing islands of a nano oxide, finally rendering these facets inactive. At the edges, the oxide islands cannot connect, leaving active sites for the catalytic reaction and an efficient oxygen supply.
Catalytic converters usually use nanoparticles because these have a far greater surface area for a given amount of the material, on which the catalytic reaction can take place. For the study presented here, the scientists at DESY’s NanoLab grew platinum-rhodium nanoparticles on a substrate in such a way that virtually all the particles were aligned in the same direction and had the same shape of truncated octahedrons (octahedrons resemble double pyramids). The scientists then studied the catalytic properties of this sample under the typical working conditions of an automotive catalytic converter, with different gaseous compositions in a reaction chamber that was exposed to intense X-rays from PETRA III on the P09 beamline.

>Read more on the PETRA III at DESY website

Image: With increasing oxygen (red) concentration, an oxide sandwich forms on the surface of the metallic nanoparticles, inhibiting the desired reaction of carbon monoxide to carbon dioxide. At the edges, however, the oxide sandwich brakes up, leaving free active sites for catalysis. The more edges the nanoparticles posses, the more efficient will the catalytic converter work.
Credit: DESY, Lucid Berlin

Scientists observe nanowires as they grow

X-ray experiments reveal exact details of self-catalysed growth for the first time

At DESY’s X-ray source PETRA III, scientists have followed the growth of tiny wires of gallium arsenide live. Their observations reveal exact details of the growth process responsible for the evolving shape and crystal structure of the crystalline nanowires. The findings also provide new approaches to tailoring nanowires with desired properties for specific applications. The scientists, headed by Philipp Schroth of the University of Siegen and the Karlsruhe Institute of Technology (KIT), present their findings in the journal Nano Letters. The semiconductor gallium arsenide (GaAs) is widely used, for instance in infrared remote controls, the high-frequency components of mobile phones and for converting electrical signals into light for fibre optical transmission, as well as in solar panels for deployment in spacecraft.

To fabricate the wires, the scientists employed a procedure known as the self-catalysed Vapour-Liquid-Solid (VLS) method, in which tiny droplets of liquid gallium are first deposited on a silicon crystal at a temperature of around 600 degrees Celsius. Beams of gallium atoms and arsenic molecules are then directed at the wafer, where they are adsorpted and dissolve in the gallium droplets. After some time, the crystalline nanowires begin to form below the droplets, whereby the droplets are gradually pushed upwards. In this process, the gallium droplets act as catalysts for the longitudinal growth of the wires. “Although this process is already quite well established, it has not been possible until now to specifically control the crystal structure of the nanowires produced by it. To achieve this, we first need to understand the details of how the wires grow,” emphasises co-author Ludwig Feigl from KIT.

>Read more on the FLASH and PETRA III at DESY website

Image: A single nanowire, crowned by a gallium droplet, as seen with the scanning electron microscope (SEM) of the DESY NanoLab.
Credit: DESY, Thomas Keller

Liquid crystal molecules form nano rings

Quantised self-assembly enables design of materials with novel properties

At DESY’s X-ray source PETRA III, scientists have investigated an intriguing form of self-assembly in liquid crystals: When the liquid crystals are filled into cylindrical nanopores and heated, their molecules form ordered rings as they cool – a condition that otherwise does not naturally occur in the material. This behavior allows nanomaterials with new optical and electrical properties, as the team led by Patrick Huber from Hamburg University of Technology (TUHH) reports in the journal Physical Review Letters.

The scientists had studied a special form of liquid crystals that are composed of disc-shaped molecules called discotic liquid crystals. In these materials, the disk molecules can form high, electrically conductive pillars by themselves, stacking up like coins. The researchers filled discotic liquid crystals in nanopores in a silicate glass. The cylindrical pores had a diameter of only 17 nanometers (millionths of a millimeter) and a depth of 0.36 millimeters.

There, the liquid crystals were heated to around 100 degrees Celsius and then cooled slowly. The initially disorganised disk molecules formed concentric rings arranged like round curved columns. Starting from the edge of the pore, one ring after the other gradually formed with decreasing temperature until at about 70 degrees Celsius the entire cross section of the pore was filled with concentric rings. Upon reheating, the rings gradually disappeared again.

>Read more on the PETRA III at Desy website

Image: Stepwise self-organisation of the cooling liquid crystals. (Extract, see the entire image here)
Credit: A. Zantop/M. Mazza/K. Sentker/P. Huber, Max-Planck Institut für Dynamik und Selbstorganisation/Technische Universität Hamburg; Quantized Self-Assembly of Discotic Rings in a Liquid Crystal Confined in Nanopores, Physical Review Letters, 2018; CC BY 4.


Record number of participants at User Meeting

Celebrating a year of glorious firsts and outlining future developments

“Welcome to the first European XFEL user meeting with actual users!” said Martin Meedom Nielsen, head of the European XFEL council as he opened the three day event on 24 January in front of a packed lecture hall on the DESY campus in Hamburg. With 1200 registered participants from ca. 100 institutions from 30 countries, this year’s joint European XFEL and DESY photon science users’ meeting, the first since operation began, was the biggest yet.

Meedom Nielsen and European XFEL Managing Director Robert Feidenhans’l started the meeting by summarizing the achievements and developments of the last year and thanking everyone who had contributed to the facility’s success. “It has been a fantastic year,” said Feidenhans’l looking back on his first year as director of the facility, “a tough year and we have worked really hard, but a fantastic year.” “2017 was a year of glorious firsts” said Meedom Nielsen, highlighting especially the facility’s inauguration in September and the beams of laser light that shone across the city to mark the occasion. “Hamburg was shining for European XFEL, and European XFEL was shining back” he said.

>Read more on the European XFEL website

 Photo Credit: European XFEL


1200 participants at annual users’ meeting

Record number of attendees at the joint DESY and European XFEL event

The joint meeting of users of DESY’s research light sources and the European XFEL X-ray laser once again drew a record number of attendees to Hamburg. Some 1200 participants from nearly 100 institutions from around 30 countries have registered for the three-day event (24-26 January) held at DESY, more than ever before. A particular highlight this year is the beginning of scientific user operation at the European XFEL, from which first results were presented.

“The users’ meeting in Hamburg is the largest in the world for research with X-ray light sources, and we are very proud of that,” emphasised DESY Director Helmut Dosch. “The tremendous interest reflects the importance of these unique research tools for all natural sciences and beyond.” DESY’s research director for photon science, Edgar Weckert, added: “With the X-ray lasers FLASH and European XFEL and the storage-ring-based X-ray source PETRA III, the metropolitan region offers a worldwide unique combination of high-intensity research light sources that serve a wide range of disciplines, from biology and medicine to energy, material and earth science to physics, chemistry and even art history.”

Image: DESY, Axel Heimken

Scientists decipher key principle behind reaction of metalloenzymes

So-called pre-distorted states accelerate photochemical reactions too

What enables electrons to be transferred swiftly, for example during photosynthesis? An interdisciplinary team of researchers has worked out the details of how important bioinorganic electron transfer systems operate. Using a combination of very different, time-resolved measurement methods at DESY’s X-ray source PETRA III and other facilities, the scientists were able to show that so-called pre-distorted states can speed up photochemical reactions or make them possible in the first place. The group headed by Sonja Herres-Pawlis from the RWTH Aachen University  Michael Rübhausen from the University of Hamburg and Wolfgang Zinth from Munich’s Ludwig Maximilian University, is presenting its findings in the journal Nature Chemistry.

The scientists had studied the pre-distorted, “entatic” state using a model system. An entatic state is the term used by chemists to refer to the configuration of a molecule in which the normal arrangement of the atoms is modified by external binding partners such that the energy threshold for the desired reaction is lowered, resulting in a higher speed of reaction. One example of this is the metalloprotein plastocyanin, which has a copper atom at its centre and is responsible for important steps in the transfer of electrons during photosynthesis. Depending on its oxidation state, the copper atom either prefers a planar configuration, in which all the surrounding atoms are arranged in the same plane (planar geometry), or a tetrahedral arrangement of the neighbouring ligands. However the binding partner in the protein forces the copper atom to adopt a sort of intermediate arrangement. This highly distorted tetrahedron allows a very rapid shift between the two oxidation states of the copper atom.

>Read more on the PETRA III website

Image Caption: Entatic state model complexes optimize the energies of starting and final configuration to enable fast reaction rates (illustrated by the hilly ground). The work demonstrates that the entatic state principle can be used to tune the photochemistry of copper complexes.
Credit: RWTH Aachen, Sonja Herres-Pawlis

A mixtape for drug discovery

New method enables automated fast investigation of enzymatic processes

Scientists at DESY have developed a new method that enables automated and fast screening of promising drug candidates. This novel technique, called mix-and-diffuse serial synchrotron crystallography, can image the interaction of potential drug targets with drug candidates or other molecules. The concept has the potential to take structure and fragment based drug design to a new level, as the researchers write in the Journal of the International Union of Crystallography (IUCrJ).

>Read More on the PETRA III website

Image: Principle of the mix-and-diffuse serial synchrotron crystallography: protein crystals are mixed with a solution of a drug candidate and X-rayed on a tape running through the X-ray beam.
Credit: Beyerlein et al., IUCrJ 

Spectrally broad X-ray pulses can be “sharpened” by purely mechanical means

Abrupt motion sharpens X-ray pulses

A team of theoretical and experimental physicists, including scientists from DESY, lead by the Max Planck Institute for Nuclear Physics (MPIK in Heidelberg, Germany) has developed and realized a method to “sharpen” spectrally broad X-ray pulses by purely mechanical means. It is based on fast motions, precisely synchronized with the pulses, of a target interacting with the X-ray light. Thereby, photons are redistributed within the X-ray pulse to the desired spectral region, as the scientists demonstrated at DESYs X-ray source PETRA III and the European Synchrotron Radiation Facility ESRF (Grenoble, France). The researchers present their work in the journal “Science”.

The novel method can intensify the spectrally broad X-ray pulses in a narrow spectral region. Such X-ray pulses are desired for a number of fundamental physics experiments or are a prerequisite for some precision experiments. The key roles are played by a piezoelectric transducer which performs precise motions upon electric signals and by a thin iron foil. Precisely synchronized motions redistribute the photons within the X-ray pulse to a narrow wavelength region. “Our method doesn’t waste photons like a monochromator that only cuts off the undesired wavelengths”, explains Jörg Evers from the division of Christoph Keitel at MPIK. “On the other hand, we don’t need to increase the overall energy of the X-ray pulse.”

>Read More

X-ray experiments reveal two different types of water

The strangest liquid of all is even more unusual than we thought

Liquid water exists in two different forms – at least at very low temperatures. This is the conclusion drawn from X-ray experiments carried out at DESY and at the Argonne National Laboratory in the US. An international team of researchers headed by the University of Stockholm now reports its findings in the Proceedings of the National Academy of Sciences (PNAS).

The scientists led by Anders Nilsson had been studying so-called amorphous ice. This glass-like form of frozen water has been known for decades. It is quite rare on earth and does not occur in everyday life; however, most water ice in the solar system actually exists in this amorphous form. Instead of forming a solid crystal – as in an ice cube taken from the freezer – the ice takes on the form of disordered chains of molecules, more akin to the internal structure of glass. Amorphous ice can be produced, for example, by cooling liquid water so rapidly that the molecules do not have enough time to form a crystal lattice.

>Read More

Picture: Liquid water has two variants: High Density Liquid (HDL) and Low Density Liquid (LDL) which have now been observed at extremely low temperatures, but can not be bottled. Photo: Gesine Born, DESY

High-pressure experiments solve meteorite mystery

X-ray analysis reveals unexpected behaviour of silica minerals

With high-pressure experiments at DESY’s X-ray light source PETRA III and other facilities, a research team around Leonid Dubrovinsky from the University of Bayreuth has solved a long standing riddle in the analysis of meteorites from Moon and Mars. The study, published in the journal Nature Communications, can explain why different versions of silica can coexist in meteorites, although they normally require vastly different conditions to form. The results also mean that previous assessments of conditions at which meteorites have been formed have to be carefully re-considered.

The scientists investigated a silicon dioxide (SiO2) mineral that is called cristobalite. „This mineral is of particular interest when studying planetary samples, such as meteorites, because this is the predominant silica mineral in extra-terrestrial materials,“ explains first author Ana Černok from Bayerisches Geoinstitut (BGI) at University Bayreuth, who is now based at the Open University in the UK. „Cristobalite has the same chemical composition as quartz, but the structure is significantly different,“ adds co-author Razvan Caracas from CNRS, ENS de Lyon.

>Read More

Picture: Credit: NASA/JPL/University of Arizona [Source]