This month, we have a special treat. Joe Reibenspies of Texas A&M University has provided a report on the 2nd PVAMU/TAMU Crystallographic Workshop, which was held in April and supported by Rigaku. I did not get to go, but I understand those who did have a great time.
This month we highlight the application laboratory at our headquarters in Tokyo. Jakub Wojciechowski provides some insight into background computations for powder analysis from single crystal datasets. AI applied to structure prediction made the news again in April and May; you’ll find the citations for RoseTTAFold2 and AlphaFold 3 below. Finally, Jeanette reviews Burn Book by Kara Swisher.
The summer meeting season starts soon. I look forward to seeing many of you at ACA, TPS, and DXC.
Look up (from your devices) and be safe,
Joe Ferrara
TOPIQ Webinar
Explore the diverse realm of sub-micron crystal structures through the lens of the XtaLAB Synergy-ED. This webinar delves into its applications across a wide spectrum of materials, including small molecules, MOFs, COFs, biological samples, minerals, and beyond. Highly beam-sensitive samples or measured under cryogenic conditions, the XtaLAB Synergy-ED offers exceptional capabilities for precise analysis. Discover how this instrument contributes to advancements in chemistry, materials science, and related fields.
The Second PVAMU/TAMU Crystallographic Workshop took place on April 12, 2024, bringing together thirty-eight students and faculty from Prairie View A&M (PVAMU) and Texas A&M University (TAMU). Rigaku provided the necessary instruments, while Lee Daniels and Eric Reinheimer (Rigaku) offered scientific support. The workshop featured crystallographers from both PVAMU and TAMU, who shared their expertise with the participants.
The workshop began with a round-robin activity in the morning, allowing students to engage in hands-on scientific experiments. They had the opportunity to explore powder diffraction, single crystal diffraction, and crystal growth/mounting activities. The participants were divided into four teams, each assigned to a specific station.
At the first station, under the guidance of Dr. Nattamai Bhuvanesh, students from PVAMU operated instruments at TAMU remotely, using powder diffractometers. This provided them with valuable experience in instrument operation.
Dr. Joseph Reibenspies led the second station, where students learned how to create saturated solutions of borax in hot water. They witnessed the rapid growth of Borax crystals from the cooled solutions and were taught how to mount them on nylon loops using microscopes. A brief presentation on crystal growth and the characteristics of a good single crystal specimen was also given.
The third station involved taking the samples to Lee Daniels from Rigaku. Here, the participants placed their samples on the goniometer of a benchtop Rigaku single crystal diffractometer (XtaLAB mini II) and collected data. Additionally, data for a crystal of Ni(cyclen)(NO₃) ₂ was collected for the purpose of publishing a co-authored paper related to the workshop.
The final station served as a break room, where students and faculty gathered to enjoy coffee and snacks while engaging in scientific discussions. Alison Altman (TAMU), Gina Chiarella, Harshica Fernando, Yunxiang Gao, Tony Grady, Tony D Green, Yingchun Li, Yuemin Liu, Matthew Minus, Gururaj Neelgund, Meryln Pulikkathara, Bright Adu, Josiah Armstead, and Uchechukwu Ariwodo from PVAMU interacted with the students on an individual basis, discussing both science and life at their respective universities.
A meal at Joe's Italian Restaurant in Hempstead, Texas marked the conclusion of the workshop, where both students and faculty gathered to dine. The group engaged in discussions about the day's events and the future of science at PVAMU and TAMU while enjoying a variety of dishes ranging from steaks to pasta.
The funding for the workshop was generously provided by the Deans of Arts and Sciences at TAMU and PVAMU. The students and faculty would like to express their sincere gratitude to PVAMU for providing the facilities and to Rigaku for lending the XtaLAB mini II and the expertise of their scientists, Dr. Lee Daniels and Eric Reinheimer.
Explore the diverse realm of sub-micron crystal structures through the lens of the XtaLAB Synergy-ED. This webinar delves into its applications across a wide spectrum of materials, including small molecules, MOFs, COFs, biological samples, minerals, and beyond. Highly beam-sensitive samples or measured under cryogenic conditions, the XtaLAB Synergy-ED offers exceptional capabilities for precise analysis. Discover how this instrument contributes to advancements in chemistry, materials science, and related fields.
shares information and fosters discussion about X-ray crystallography and SAXS topics. Connect with other research groups and receive updates on how they use these techniques in their own laboratories. You can also catch up on the latest newsletter or Rigaku Journal issue. We also hope that you will share information about your own research and laboratory groups.
At rigakuxrayforum.comyou can find discussions about software, general crystallography issues and more. It’s also the place to download the latest version of Rigaku Oxford Diffraction’sCrysAlisProsoftware for single crystal data processing.
Our Japanese applications lab is located at our headquarters in Tokyo and is staffed by four application scientists dedicated to single crystal diffraction.
We use a wide variety of analytical techniques to study not only crystalline samples such as single crystals and micro powders, but also molecules in solution.
Our application team comprises individuals with diverse backgrounds, ranging from chemistry to protein science. This diversity translates into a wide array of expertise, covering various analytical techniques such as single crystal studies, electron diffraction, crystal sponges, and solution scattering. While each technique demands specific skills, our team members excel in their respective areas, ensuring thorough analysis for every task.
Our newest addition to the Rigaku Tokyo Lab is Yoshiki Kiyota. Specializing in small molecules, he joined Rigaku after obtaining his master's degree. Prior to his current role in the lab, he was part of the sales group. Kiyota-san stands out as a member of the Application Team who possesses comprehensive knowledge of the products Rigaku offers.
Dr. Takashi Kikuchi received his degree in Engineering from the University of Tokyo being supervised by Prof. Makoto Fujita in 2011. After that, he worked with Prof. J. Fraser Stoddart, Northwestern University, as a JSPS research fellow from 2011-2012, and with Prof. Susumu Kitagawa, Kyoto University, from 2012 to 2015. Since 2015, he has worked at Rigaku Corporation as an application scientist specializing in single-crystal X-ray analysis, crystalline sponge method, and microcrystal electron diffraction (MicroED).
Dr. Hiroyasu Sato received his degree in Science from Kitasato University being supervised by Prof. Gaku Yamamoto in 2006. After that, he worked with Prof. Takuzo Aida at the University of Tokyo as a JST research fellow from 2006 to 2008. Since 2009, he has worked at Rigaku Corporation as an application scientist specializing in single crystal X-ray analysis and microcrystal electron diffraction (MicroED).
Dr. Takashi Matsumoto studied structural biology at Tokushima University and Himeji Institute of Technology, and then researched membrane proteins as a postdoctoral fellow at the Institute of Physical and Chemical Research and Osaka University. Currently, he manages the team as a group manager and analyzes protein dynamics using the MAXS method. Matsumoto-san has extensive knowledge of the analysis of molecules in crystals to molecules in solution.
Crystals in the News
April 19, 2024
While not directly related to crystallography, David Baker and scientists from the Republic of Korea, the UK, and the US have extended the functionality of RoseTTAFold2 to include generalized biomolecular modeling and design.
April 25, 2024
Researchers from the University of Minnesota have synthesized and characterized a previously inaccessible five-membered ring with a triple bond using Ni(COD)2.
May 8, 2024
Researchers from the UK have released AlphaFold 3, a better, faster AlphaFold that provides joint structure prediction of complexes, including proteins, nucleic acids, small molecules, ions, and modified residues.
May 8, 2024
Scientists from China and Germany have synthesized and characterized
Background computations for powder analysis from single crystals datasets
CrysAlisPro allows the generation of powder diagrams from micro-powder and single-crystal datasets by applying simple frame accumulation and signal extraction from sum-up images. This is a helpful tool for quickly comparing experimental patterns, even before final crystal structure model refinement.
In the case of high background datasets and powder experiments collected from a cluster of single crystals using the Gandolfi method, simple frame accumulation may lead to high noise and a significant background hump on extracted 1D diffraction pattern. In the case of a very weak dataset, the background accumulation can even hide the sample signal completely, as shown in the figure below.
In such cases, it is recommended that the background computations be made in batches and their substructions made before final signal accumulation. The powder diagram extraction and calculations require more time, but the resulting diagram is much clearer.
To enable Gandolfi background treatment, access the Advanced powered extraction option window by selecting the option (1) button in the Powder Graph tool in CrysAlisPro. Locate and select the Gandolfi (for single crystal frames) option (2), confirm it with the OK(3) button, and repeat the analysis by hitting the Reprocess button (4). The simplified workflow is shown in the figure below.
A 25° range is recommended as default for all background treatments in CrysAlisPro. However, it can be adjusted from 5° to the length of the scan. The shorter the range, the better background and signal separation are expected, at the cost of longer computations.
This background treatment is essential for signal extraction from 3DED datasets, as shown in the figure below.
More information and examples can be found in the CrysAlisPro help system at the ITS 81.
Kara Swisher's new memoir Burn Book: A Tech Love Story is a wild ride through the last three decades of Swisher's career as a journalist covering the technology beat at numerous publications. The title Burn Book evokes Tina Fey's cult classic movie Mean Girls (now a musical and movie musical based on both the movie and the musical, confusingly), in which the titular clique writes cruel and nasty and mostly untrue claims about their fellow high schoolers. But as the subtitle A Tech Love Story suggests, Swisher's burn book is a little more complex than that of Fey's fictional Plastics. It will be interesting to see if Swisher's burn book spawns more in the tech industry to publish, not unlike how Fey's fictional concept became real for many high schoolers across the country after the movie came out in 2004. But that's a digression.
Calling Burn Book a memoir also opens a lot of doors for what Swisher can and cannot say within the realm of journalistic integrity and ethics. Swisher includes the typical author's notes and acknowledgments at the end of Burn Book, but in lieu of an index, Swisher has a single page letting the reader know there is no real index—if you want to know what she has to say about any given tech leader or tech topic, you'll have to actually do the hard work and read her book (or, at least, skim it).
This is not a reference book or a well-researched history of the Silicon Valley tech bubble. Swisher doesn't want you to think that it is. The cover—with Swisher's face in black and white, superimposed with fake flames on the lenses of her sunglasses and the title, subtitle, and her name all in red, orange, and yellow (further evoking fire)—seems a clear parody of the cover of Walter Isaacson's two big tech leader authorized biographies of Steve Jobs and, more recently, Elon Musk. This book feels like an unauthorized biography of Silicon Valley.
Swisher drops a lot of names—she's been a leading tech journalist for 30 years, and she's interviewed all the major players—if not once, then twice, thrice, more times than that. She had the privilege of interviewing both Steve Jobs and Bill Gates—longtime tech industry corporate leader rivals, both in public image and product perception—at the same time. Apparently, the famous interview with Jobs and Gates almost didn't happen because Jobs effectively called Gates Satan in an interview earlier and Gates took it personally. Burn Book is rife with behind-the-scenes anecdotes like this.
Swisher doesn't hold back and doesn't take potshots or low blows—she seems to call it as she sees it in this memoir. There is certainly a lot of editorializing and opinion— but again, this is a memoir, not a history book. And because Swisher never claims it is anything more or less than a memoir, it's good. Burn Book is intriguing, entertaining, and a bit concerning at times, as all content related to tech inherently is.
