Volume 15, No. 09, November 2023
Introduction
For the first time in a few years, we held our annual European Users' Meeting in the UK. We had a strong turnout and an interesting program with a lot of innovative techniques and topics packed in. The meeting was organized in collaboration with the National Electron Diffraction Facility (NEDF) and co-sponsored by JEOL. The NEDF is a new facility offering data collection and structure determination using electron diffraction in a similar way to that in which the National Crystallography Service (NCS) has been offering X-ray services for many years.
The first day of our meeting was based around electron diffraction, with talks from invited speakers and NEDF staff to introduce the facility itself and the capabilities of electron diffraction in general. Speakers on the first day included Simon Coles and David Walker (NEDF), Simon Parsons (Edinburgh), Jere Tidey and Daniel Rainer (NEDF), David Waterman (STFC), Seb Pike (Warwick), Andrea Laybourn (Nottingham) and Kasper Pederson (DTU). These talks all drove home the point that electron diffraction has arrived and is enabling scientists to break new ground and reach new targets.
After the coffee break, we took our guests to see the facilities in Warwick, both their existing XtaLAB Synergy X-ray diffractometers and their brand-new electron diffractometer, the XtaLAB Synergy-ED. We also had a session hosted by Mathias Meyer in which he spent some time explaining the history of our collaboration with JEOL.
Despite the fantastic evening meal, merriment, and an unwelcome fire alarm at around 1:30 am everyone still managed to get back to the meeting room for 9 am the next day, where we had talks from our staff and more invited speakers. Second-day speakers included, Mike Probert (Newcastle), Mathias Meyer, Christian Schürmann, Khai Nghi Truong and Jakub Wojciechowski (all Rigaku), Lauren Hatcher (Cardiff), Michael Bodensteiner (Olexsys/Regensburg), Tom Turner (Leeds) and Tom Fellowes (Liverpool).
Thanks to our speakers, and attendees for making this meeting possible and making it such a fun event. We are fortunate to have a community of fantastic users.
By popular demand, we have decided to run another Rigaku School for Practical Crystallography in January 2024. The dates are January 15-19 and January 22-26. A syllabus and registration information will appear at Rigaku.com shortly.
We are changing things up this month. Instead of the Instrument in the Spotlight and the Researcher in the Spotlight we will highlight a technique and provide a useful tip. This month we highlight the FlowXI developed by Tom Turner at Leeds, which provides state-of-the-art analysis of crystallization processes in situ using X-ray diffraction and Raman. Our tip of the month is provided by Fraser White, who explains how to generate precession images. Please let us know what you think of these changes.
This month Jeanette reviews an important book titled Not Just for the Boys: Why We Need More Women in Science. We also have the usual features: Crystallography in the News and Useful Links.
Fraser White and Joe Ferrara
Technique in the spotlight
Flow crystallography
Flow crystallography is a technique where crystallization processes can be studied in situ by passing a crystallization mixture through an X-ray beam and detecting diffraction from crystals and crystallites.
FlowXl is a new research facility at the University of Leeds that enables state-of-the-art analysis of crystallization processes in-situ through combined Raman spectroscopy and powder X-ray diffraction.
The facility integrates a number of flow devices for studying crystallization processes, including a slurry recirculation loop for process reactors, droplet microfluidic devices, acoustic droplet levitator, variable humidity chamber and continuous flow crystallization devices. The goal of the facility is to provide researchers from industry and academia with an environment in which to design, develop, test and apply in-situ sample environments to the study of nucleation and growth of functional materials under fluid-flow or liquid environments. This facilitates new scientific discoveries and enables users to establish which experiments conducted initially at FlowXl require beamtime at synchrotron sources such as Diamond. Current case studies at the facility include probing the structural evolution of an active pharmaceutical ingredient (API) hydrate species during a solution mediated phase transformation to its anhydrate, tracking the solution supersaturation and solid state phase changes during evaporative crystallization of an inorganic salt in levitated droplets, and measuring the impact the of process conditions on the polymorphic selection of an API in continuous flow crystallization reactors.
FlowXl Facility inside the X-ray enclosure probing the crystallization of Na2SO4 inside a 10 μl acoustically levitated droplet using combined Raman spectroscopy and X-ray diffraction, the sample is in the center of the image where the laser of the Raman can be seen hitting the droplet.
The facility has a state-of-the-art Rigaku XtaLAB Synergy Custom X-ray diffractometer with an ultrahigh-brightness source, optimized towards data collection from the weakest of diffracting samples. This, paired with a detector with high dynamic range, fast readout speed and extremely low noise, allows for in-situ ;diffraction studies of samples in flow. Additionally, the set-up has a Raman spectrometer, a Labram HR Evolution from HORIBA Jobin Yvon, with both green (532 nm) and red (785 nm) lasers with respective ultralow frequency (ULF) modules allowing measurements in the sub-100 cm-1 region, with measurements down to 10 cm-1 routinely available. Two SuperHead fiber optic probes also facilitate in-situ measurements at samples contained within the X-ray diffractometer enclosure. This combination allows the user to probe solution-state molecular detail through to structural phase identification and quantification of materials in liquid systems.
The diffraction data versus time for the levitated droplet experiment, highlighting the key structural changes during evaporative crystallization.
Researcher in the spotlight
Dr Thomas Turner is a post-doctoral research associate in instrument design and flow systems at the School of Chemistry, University of Leeds. He completed his doctoral studies at the University of Leeds, where his research interests were focused on crystallization and the characterization of organic and pharmaceutical materials, in particular the study of nucleation using in-situ synchrotron X-ray scattering. Currently his research focus is on the development of a new EPSRC funded national facility, FlowXl, which utilizes state of the art in-situ X-ray diffraction combined with Raman spectroscopy to probe nucleation and crystallization processes of materials in flow.
Thomas will be presenting a new TOPIQ webinar for us on November 15 at 4PM CEST entitled “Flow-Xl: A New UK Facility for the Analysis of Crystallisation in Flow Systems.”
Product in the spotlight
XtaLAB SynergyCustom
One of the advantages of Rigaku's rotating anode X-ray generators is the ability to utilize both ports of the generator simultaneously. This might involve having two single crystal goniometers mounted on the generator or it might involve having one goniometer with a sample changing robot on one port dedicated to protein crystallography and a second goniometer dedicated to chemical crystallography. In order to accommodate the various configurations that a researcher might envision, Rigaku offers the XtaLAB Synergy-Custom, a system that can be configured with either a MicroMax-007 HF microfocus rotating anode source or the highest-flux in-house X-ray source, the FR-X. Additionally, the XtaLAB Synergy-Custom comes in a specially designed enclosure with your choice of table size to accommodate accessory equipment, such as an ACTOR 2 robotic system or a microscope close to the goniometer. Thus, the versatility offered by the XtaLAB Synergy-Custom system provides the most flexibility possible for your structural chemistry program.
Tip of the month
Generating standard and integrative precession images
What are they?
Reconstructed precession images (also called unwarped images) allow you to create any plane of reciprocal space using all the relevant frames from the data collection. Integrative precession images allow you to take a larger slice of reciprocal space to better identify certain features.
Why should I use them?
Precession images are very useful for visualizing the crystallinity of your sample. They may help show weaker peaks due to twinning, superstructure or incommensurate behavior as well as diffuse scatter. Integrative layers can be particularly useful for studying diffuse scatter, as you can choose a thicker slice of reciprocal space with which to create a composite image.
How do I make them?
- Click on the Unwarping button on the Lattice Wizard window (Figure 1).
Figure 1. Unwarp access.
- Check the orientation matrix is correct and click “next.” If it is not, go back to the Lattice Wizard and find the correct cell
- Choose the runs to generate the images (the more, the better) and click “next.”
- Choose which layers to generate:
- To quickly generate multiple layers, click on “generate layers” and choose the order and the resolution. For example, typing “2 0.8” will generate the -2kl, -1kl, 0kl, 1kl, 2kl images out to 0.8 Å, as well as the corresponding images along the k and l directions.
- To generate a single layer, click on “New layer”, choose "One pixel layer" for a standard precession image then choose the origin (O) and the two vectors (L1 & L2), as well as the output name for the image. For example, to generate the h4l plane you would set O = 0 4 0, L1 = 1 0 0, and L2 = 0 0 1.
- For integrative layers, repeat the above, choosing "Integrative layer" instead. Instead of an origin, you must now enter start and end origin vectors (Os & Oe) to define the thickness of the layer and integration units (number of slices) along with L1 and L2 as before.
- In either case, if portions of a layer are missing, you can apply 2D symmetry averaging to generate a full image of the plane.
- In the next few windows you can choose to apply various corrections to the images (background, convolution etc.) and apply a scale factor to make sure weak features are visible (typically a value of 20 is used).
- Once generated, you use all standard image analysis tools, including the information (i) button to check peak indices, and you can also overlay the reciprocal lattice grid (drop-down arrow next to the RED button). The images are stored in the “unwarp” folder of the main experiment folder, and can be accessed via the Image list button.
Examples
Below are two examples of crystals that showed interesting diffuse scatter features.
In Figure 2 you can see a “honeycomb” diffuse pattern, while in Figure 3 you can see that there is no Bragg intensity present, only signal from diffuse scatter! Both images were hk3 planes, with Os = (0 0 2.8), Oe = (0 0 3.2), and integration unit = 3.
Figure 2. Honeycomb.
Figure 3. Diffuse rings.
Book review
Not Just for the Boys: Why We Need More Women in Science
By Athene Donald
ISBN 9780192893406
Athene Donald’s Not Just for the Boys: Why We Need More Women in Science is a concise but compelling read for anyone and everyone. It’s a book for women who have pursued a career in science, regardless of where they are in that career. It’s also a book for men in the same position. It’s for anyone who has a young girl or young woman in their life with an interest in science and math. But it’s also a book for anyone who has a young girl or young woman in their life who doesn’t have an interest in science or math. Indeed, although Donald is writing about the importance of women in science and detailing the historical, present, and future impediments that can keep them from reaching their desired position in their respective fields, much of Donald’s argument can be applied to any field in which men outnumber women.
As a Professor Emerita of Experimental Physics at the University of Cambridge, Donald certainly has her own breadth of experience navigating science and academia as a woman. While she does draw on that experience, much of Not Just for the Boys includes numerous anecdotes and personal stories from women across scientific disciplines, as well as explanations of research findings from studies designed to determine if gender gaps really do exist in the sciences, both at the professional and student level (spoiler alert: they do).
Donald begins with a chapter entitled “What’s the Problem?” in which she outlines and addresses the issues at hand—namely, after decades of initiatives to increase the number of women in science and the fact that the population of the world is roughly 50% women, women do not account for 50% of scientists. She then proceeds to delve into the issue as deeply as she can in a book of a little over 200 pages, starting with how scientists are perceived in society (mostly as men) and how that impacts young women’s perceptions of what they can be. She also digs into what can keep young women from pursuing roles in scientific careers even if they have a proven interest, and what obstacles women can face once they’ve already made their career in the sciences. At the end of the day, it’s still a man’s world, and science is no exception.
onald argues that science, like any field, benefits from the diversity of those pursuing it. She acknowledges that, as a white woman, she still garners certain privileges not afforded to colleagues of color, particularly women of color. But Donald also acknowledges that as a white woman, she is not the right person to be writing a book about intersectionality in the sciences. While Donald’s book will certainly resonate for any woman in the sciences, if you’re looking for a read about women of color in the sciences, Jasmine Brown’s Twice as Hard is an excellent choice.
Review by Jeanette S. Ferrara, MFA
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