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X-ray Facility Adds Two New Instruments


Writer(s): Steve Scherer, Matthias Zeller


Two new single crystal X-ray diffractometers were installed in the X-ray Crystallography Facility during December. These instruments add improved capabilities, including: much higher sensitivity/read-out time; improved throughput data collection; and more intuitive data collection software.

Crystallography Manager Matthias Zeller answered a few questions about the recent changes in his lab:

What are the two new instruments and how will they add to the quality of your lab?

The new instruments are both manufactured by Bruker AXS of Madison, WI. They differ in the wavelength they are using, and in the size of the X-ray beam.

The first instrument is a Bruker D8 Quest with a Mo sealed tube and a Triumph curved monochromator with a 10 cm x 10 cm Photon-100 detector and fixed chi angle. It is equipped with an Oxford Cryostream 800 plus variable temperature device with a temperature range of 80-500K. This instrument is ideal for fast, high throughput data collection of well to weakly diffracting samples, and for heavily absorbing samples. Typical samples will include metal-organic complexes, metals, ceramics, and well diffracting organic crystals.

The second instrument is a Bruker D8 Quest with a Cu microsource, laterally graded X-ray optics (Goebel mirror) and kappa geometry, equipped with a Photon-II detector (10 cm x 14 cm). It is equipped with an Oxford Cryostream 800 variable temperature device (80-400K). Copper radiation is intrinsically better diffracted than the harder molybdenum radiation, which makes this instrument ideal for samples that are very weakly diffracting and for very small crystals (< 0.1 mm). This comes at the expense of data collection time as diffraction spots are spread further apart, which requires collection of more raw diffraction images, but allows to collect usable data for samples with not enough signal to noise when using harder X-rays. Copper radiation is also ideal for the determination of absolute structure of organic compounds (no atoms heavier than fluorine), a feature that is very important for chemists working in natural product synthesis.

How will they speed up sample analysis?

The main advantage of the new instruments are their much improved capabilities, compared to our old instruments. (The laboratory already has a new powder XRD instrument, installed mid-2016) The new single crystal diffractometers feature new generation X-ray detectors with much higher sensitivity and essentially zero read-out time. They are also substantially larger than previous detector models. The X-ray sources are substantially more intense, ca. 2-4 orders of magnitude (the exact numbers depend one which of the new instruments you compare to which of the old ones). Thanks to improved optics less of the X-ray intensity is “lost” on the way, and the X-ray beam is of higher quality (more parallel, more homogeneous). These three features combined, X-ray source, detector and optics, will allow us to measure “normal” samples much faster and with better quality results than previously. It will also allow us to analyze samples that before were way beyond our capabilities, such as e.g. much smaller crystals. These latter samples may still require several days to complete, but previously they were simply impossible, especially for samples that are too sensitive for transport to e.g. a synchrotron beam line.

Depending on the types of samples we expect that we can cut down the average data collection time by one half to two third. Expectations are that we will be able to analyze two to three crystals per day on both new machines, or 600 to 1000 samples per year, thus roughly tripling the throughput of the laboratory and (hopefully) eliminating long wait times and sample backlogs once and for all (this depends a bit on the quality of the crystals grown. Too many marginal samples might thwart our plans).

What are their new capabilities?

The new machines will have built in software capabilities for handling of twinned samples. Many crystals, even if nicely single, are “twins” or “triplets”, and often even the most proficient crystal grower (i.e., student) will not be able to obtain untwinned samples. The new instruments will simplify the analysis of twinned samples tremendously and make it straightforward and routine.

We will also be able to analyze what is called “incommensurately modulated” materials. In normal crystalline materials there is a small unit that repeats itself over and over again (that is what makes them crystalline rather than amorphous or glassy). In incommensurately modulated compounds this smallest unit repeats itself not in three dimensions, but in four, five or six (the repeating unit itself is modulated along one, two or three axes that are independent of the crystal axes). With the new instruments, we will be able to analyze these kinds of materials.

The machines also have built in powder-XRD capabilities (but these are not that important for our laboratory as we have an excellent dedicated powder diffractometer), and they will be able to handle heavily absorbing samples much better than our previous instruments.

The new data collection software is quite intuitive and much easier to learn than with the previous machines. I have used similar instruments previously extensively with undergraduates and even high school interns. Its basic use is quite easy, even for novice users with little science background. The results, three dimensional structures of molecules, can be readily visualized. You can “look at them” and see what you have made or analyzed. No detailed analysis with dozens of graphs or tables is needed. 

What instruments were removed?

There had been two single crystal instruments in the laboratory. A Nonius Kappa CCD diffratometer with a short wavelength molybdenum X-ray source, and a Rigaku R-axis curved image plate diffractometer with longer copper wavelength radiation. The Nonius instrument had been installed in 1997 and had been one of the first area detector X-ray diffractometers on the market. It had been an excellent instrument in its time, but its dated technology made it obsolete and unsuitable for our current needs. Spare parts were difficult to get and upkeep was getting more difficult every year. The R-axis image plate diffractometer was about half the Nonius instrument’s age, but also obsolete technology that had been mostly abandoned by the instrument manufacturers as a dead end direction. It was functional, but its capabilities were very limited, data collections were very time consuming and the quality of data one could obtain was seriously lacking. The software was not that easy to use, with many work-arounds necessary for collecting sufficiently good data. It did not lend itself very well to independent use by students.

What existing instruments remain?

Both single crystal diffractometers have been replaced, but the facility features a newly installed powder XRD instrument, recently purchased by the University to support research efforts in the laboratories of Drs. Christina Li, Corey Thompson and other materials chemists in the Department. The instrument is extensively used for powder X-ray analysis of metals, ceramics, pharmaceuticals, and other materials. Single crystal XRD is primarily used to determine a previously unknown structure. Powder XRD, on the other hand, is used for identification of materials with known structure, for determining the amounts of different crystalline materials in a sample, to determine the crystal size of a material or the stress or strain it was exposed to, the orientation of crystal grains, and other material’s properties that are of interest. For these purposes, our instrument has several special features, such as a hot stage for analysis at varying temperatures (up to 2000 °C), a five axis cradle for analysis of thin films and reflectivity measurements, a capillary adapter, inert gas capabilities, to mention a few.

Who funded the purchase of the new instruments?

The instruments are funded jointly by the National Science Foundation, NSF, and Purdue University through a Major Research Instrumentation grant from NSF’s division of physical sciences. These grants are quite competitive, universities are limited to two grant submissions annually and success rates are usually around 20%. The Principal Investigator, PI, on our proposal is Dr. Ren. Dr. Bart and I are co-PIs, and several dozen faculty from Chemistry are senior personnel or their projects part of the submitted proposal. The official award number and title are “CHE-1625543, MRI: Acquisition of an X-ray Diffractometer at Purdue University”.  Total amount of the award is, $312,104. $218,473 form NSF, and $93,631 provided as match from Purdue.

Who can use your facility?

The Purdue X-ray facility is currently primarily used by Purdue graduate/PhD students conducting research in all fields of chemistry, pharmaceutical sciences, etc. Students who would like to use the instruments have to be trained, and they have to pass Purdue’s Office of Radiological and Environmental Management’s (REM) quiz on Analytical X-ray Producing Equipment (nobody ever failed so far). Training on the instruments use can be one-on-one, or as part of 12650 - CHM 69600-004, the hands-on single crystal X-ray class, taught once a year (by me).

I expect that we will be opening up the facility for use by undergraduate students. The lengthy training required and the clumsy software used on the older instruments was a major hurdle for use by undergrads. With the purchase of the new instruments use of the machines will be much more straight forward, and it will lend itself to use in laboratory sections of undergraduate classes (e.g. some inorganic or physical chemistry classes). Independent use by undergraduates engaged in research projects will also be possible with the new instruments in place.

For students or faculty with only an occasional sample who prefer to not run their own analysis the lab runs their samples as a service (at no additional cost). In 2016 the lab has analyzed around 300 samples for sixteen Purdue research groups. 

The lab also runs samples for outside users, both from other universities and colleges as well as about half a dozen companies. About one third of samples run over the last twelve months were from non-Purdue researchers. Over the last year we have analyzed samples from places as close as Lafayette, from all over the US, and as far away as Hong Kong or Thailand.

The laboratory is one of Purdue University’s recharge centers. I.e., some of the costs of keeping the facility running have to be recovered by user fees. The current rate is $100 for a full single crystal data collection for Purdue users. Non-Purdue academic and non-profit users pay a slightly higher rate (the overhead rate of 55% is added), and commercial users pay the full unsubsidized rate.

The X-ray facility is open from 9 to 5 Mon-Fri, and trained users have access 24/7.

Purdue Chemistry X-ray Lab 2017January 2016

Lab view Dec 2016December 2016