In the Laboratory
Bruker SMART X2S Benchtop System: A Means To Making X-ray Crystallography More Mainstream in the Undergraduate Laboratory Ilia A. Guzei,* Nicholas J. Hill, and Uzma I. Zakai Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706 *
[email protected] The benefits of incorporating chemical crystallography into an undergraduate science curriculum have been discussed previously in this Journal (1-4). X-ray crystallography is a powerful and increasingly common tool for routine structural characterization and has underpinned many fundamental advances in science (5); however, it remains poorly represented at the undergraduate level. In contrast, techniques such as NMR, GC-MS, and computational molecular modeling are now commonplace in laboratory courses (6-8). Several strategies have been adopted to bring X-ray crystallography into the mainstream undergraduate experience (9), including using an overhead projector to simulate X-ray diffraction experiments (10)! Several universities have formed alliances to economize equipment and to establish joint teaching and research projects. As pointed out by Szalay et al. (4), a lack of access to the required instrumentation, resources, and expertise appears to be a significant barrier to the teaching of practical chemical crystallography. A promising alternative to this approach is for undergraduate programs to acquire a diffractometer that produces publishable-quality data, is relatively inexpensive to run, and requires very low maintenance and no dedicated crystallographer. Thus, the introduction of the Bruker SMART X2S (11), a single crystal X-ray diffractometer designed for institutions lacking crystallographic infrastructure, is encouraging for the instructors wishing to include chemical crystallography in an undergraduate course. We recently had an opportunity to evaluate this instrument. Background about the Instrument The Bruker X2S system, Figure 1, is quarter-portable (∼150 kg), compact (64 97 47 cm), and requires a single 110 V power supply. Installation takes approximately 20 min, including initial cooldown of the detector. For an X-ray diffractometer to require no (re)alignment upon delivery is remarkable, although our department is only an 8 mi drive away from the Bruker AXS American headquarters. The goniometer, radiation source (Mo KR), and CCD detector are internally housed and protected by metal casing. Samples are affixed to a prealigned holder by a UV-curable adhesive, placed in a plastic cap, and loaded directly onto the goniometer. This removes the need for manual mounting and centering of the sample, allowing the student to “get on with it”. A touch-screen is used to enter sample data (ID, formula, sample dimensions). Data are collected at room temperature; however, it is possible to use a special low-temperature device. Information on the progress of the experiment is provided in real time. An automated structure-solution package processes the data and solves the structure, ultimately providing a fully worked-up structural model.
_
There are two other major manufacturers of X-ray crystallographic equipment: Rigaku (Japan) has two benchtop systems, SCXmini and XtaLABmini, both of which use conventional X-ray tubes, whereas Oxford Diffraction (United Kingdom) has neither a similar product nor imminent plans to introduce one. As of December 2009, the Bruker AXS and Rigaku benchtop instruments are priced in the range between $100,000 and $200,000 (for exact price quotes the reader should contact the manufacturers directly). Testing the Instrument As with any instrument, data quality is a function of sample quality, and it should be expected that crystals generated by undergraduate students would likely be of low quality. With this in mind, 19 samples of varying quality were examined with the specific aim of testing the tolerance of the instrument. The X2S provides users with limited options during experiment setup and data collection. In many regards, this is ideal for a teachingoriented instrument, because students receive an accurate picture of what an X-ray diffraction experiment entails without sorting through a myriad of options. However, from the instructor viewpoint, the inability to control key experimental parameters such as collection time, exposure time, number of frames, and so forth renders the data collection aspect of the X2S a true “black-box” process. A degree of control over collection parameters would be welcome, and Bruker is currently incorporating an “expert” instrument control mode. In addition, the newly available realtime display of the experimental diffraction pattern facilitates a discussion of the data collection process. Upon collection of all reflections, the instrument automatically processes the data and solves the structure using an expansive automation layer. A semi-interactive 3D representation of the molecule is displayed on the touch-screen and a full report of the experiment and structure solution is generated and burned to a CD. The automated data processing routine is useful for a process-oriented environment, but a major attraction of the instrument from a teaching viewpoint is the ability to reprocess the students' data in a stand-alone X-ray crystallography software package supplied with the instrument. Thus, instructive comparison can be drawn between results generated automatically and those produced manually by a student under instructor's guidance. Furthermore, the students can analyze their data in a stepwise manner and reach key milestones along the path to full data refinement. This system has been successfully tested at the American Crystallographic Association 2009 summer school and sold to at
_
r 2010 American Chemical Society and Division of Chemical Education, Inc. pubs.acs.org/jchemeduc Vol. 87 No. 11 November 2010 10.1021/ed100014a Published on Web 08/30/2010
_
Journal of Chemical Education
1257
In the Laboratory
take advantage of it. We conclude that the instrument hardware is robust and well suited for routine crystallographic characterization of both stable organic and organometallic compounds. Six articles (15-20) based on the data acquired have been published in the crystallographic journal Acta Crystallographica E, which rigorously checks crystal data and structure quality. Summary
Figure 1. The Bruker SMART X2S portable benchtop diffractometer.
least three chemistry sites in the United States. The informal reviews were good and several articles containing structural results based on SMART X2S data have been published by others (12-14) and by us (15-20). Results The instrument was tested with 19 organic crystals of various habits. In all cases, the instrument tried to assess the crystal quality and proceeded to acquire a data set even when it established that the crystal was not very promising. This strategy proved to be fruitful, because subsequent manual processing of the data could be performed if desired. Out of the 19 crystals, 2 were not good. The remaining 17 data acquisitions resulted in solved structures. In 14 cases, the data were of publishable or near-publishable quality. Among these, 7 structures were solved automatically by program Autostructure and 2 structures required expert help to resolve incorrect atom assignments. Two of the 14 structures were twinned but could be processed and solved manually. Importantly, the number of publishable-quality structures is not a characteristic of the instrument, but rather a function of the quality (or lack thereof) of mounted crystals. The X2S collected publishable-quality data when the specimens were good, but it would be naive to expect perfect data from subpar crystals. The same is true for the initial automatic crystal evaluation; often experience was required to extract the best possible information postfactum from low-quality diffraction data. The manually processed data were surprisingly good (a testament to the high software quality), taking into consideration imperfect (automatic) crystal centering, the relatively low power of the X-ray tube, and air-cooled detector. Undoubtedly, the success rate with the automated routines would have been higher had we exclusively mounted large good-quality crystals. The X2S acquired excellent data and we illustrate this with the following example. A crystal of 2-(morpholinium-4-yl)ethanesulfonate was selected from its Aldrich bottle and mounted as usual. Program Autostructure did not correctly solve the structure. After reprocessing the data, it became clear that the composition differed from the one on the bottle; the compound was 2-(morpholinium-4-yl)ethanesulfonate monohydrate, with the water molecule disordered over two positions. After the disorder was modeled, the structure refined to an R factor of 3.62%. This structure had been reported in the literature twice; once at room temperature with an R factor of 7.3% (21) and once based on a synchrotron source study (22) at 100 K with an R factor of 4.5%. Thus, given a good crystal, the performance of the X2S system is outstanding, if a knowledgeable person can 1258
Journal of Chemical Education
_
Vol. 87 No. 11 November 2010
_
Several well-tested Bruker programs (such as SAINT, SADABS, and XL) are used with the instrument and run smoothly in a behind-the-scene mode within an automation layer. A relatively new program, Autostructure, is supplied to automatically solve and refine X-ray crystal structures. Whereas the instrument is capable of yielding the accurate structure, all structures solved automatically should be carefully examined, and chemical and basic crystallographic knowledge is required to verify the correctness of the result. Overall, the instrument competently does the technical job it was designed to do, acquire publishable quality data, and is enthusiastically recommended. However, it is absolutely critical that users of the instrument possess good crystallographic and chemical knowledge. Departments without in-house crystallographers may consider inviting outside experts to teach an X-ray crystallography course to undergraduate students and conduct a workshop on crystallographic data processing and structural refinement. The benchtop SMART X2S diffractometer is easy to install, robust, and consistently generates publishable quality data without a strict requirement for perfect samples. The automated structure solution software generally performs well; however, from a teaching viewpoint, students will receive greater benefit by using a stand-alone X-ray data software package. The Bruker SMART X2S diffractometer represents an important advance in chemical crystallography and should be seriously considered as a tool for teaching practical X-ray crystallography at the undergraduate level. Acknowledgment We thank Bruker AXS (Madison, WI) for loan of the SMART X2S instrument. Literature Cited 1. Crundwell, G.; Phan, J.; Kantardjieff, K. A. J. Chem. Educ. 1999, 76, 1242–1245. 2. Geremia, S.; Demitri, N. J. Chem. Educ. 2005, 82, 460–465. 3. Hoggard, P. E. J. Chem. Educ. 2002, 79, 420–421. 4. Szalay, P. S.; Zeller, M.; Hunter, A. D. J. Chem. Educ. 2005, 82, 1555–1557. 5. Jensen, W. P.; Palenik, G. J.; Suh, I. J. Chem. Educ. 2003, 80, 753– 761. 6. Clauss, A. D.; Nelsen, S. F. J. Chem. Educ. 2009, 86, 955–958. 7. Hoffmann, M. M.; Caccamis, J. T.; Heitz, M. P.; Schlecht, K. D. J. Chem. Educ. 2008, 85, 1421–1423. 8. Lavoie, J.-M.; Chornet, E. J. Chem. Educ. 2008, 85, 1555–1557. 9. Bosse, S. A.; Loening, N. M. J. Chem. Educ. 2008, 85, 93–96. 10. Dragojlovic, V. J. Chem. Educ. 1999, 76, 1240–1241. 11. Ruf, M. Am. Lab. 2009, 41, 28–31. 12. Briggs, J. B.; Jazdzyk, M. D.; Miller, G. P. Acta Crystallogr. Sect. E: Struct. Rep. Online 2009, 65, p1171.
pubs.acs.org/jchemeduc
_
r 2010 American Chemical Society and Division of Chemical Education, Inc.
In the Laboratory 13. Chemistruck, V.; Chambers, D.; Brook, D. J. R. J. Org. Chem. 2009, 74, 1850–1857. 14. Heston, S. A.; Noll, B. C.; Helm, M. L. Acta Crystallogr., Sect. E: Struct. Rep. Online 2009, 65, m793. 15. Guzei, I. A.; Annamalai, S.; Zimmerman, H. E. Acta Crystallogr. Sect. E: Struct. Rep. Online 2010, 2010, o72. 16. Guzei, I. A.; Hill, N. J.; Van Hout, M. R. Acta Crystallogr. Sect. E: Struct. Rep. Online 2010, E66, o40–o41. 17. Guzei, I. A.; Spencer, L. C.; Hill, N. J. Acta Crystallogr., Sect. E: Struct. Rep. Online 2010, E66, o42–o43.
r 2010 American Chemical Society and Division of Chemical Education, Inc.
_
18. Guzei, I. A.; Spencer, L. C.; Zakai, U. I. Acta Crystallogr., Sect. E: Struct. Rep. Online 2010, E66, o219–o220. 19. Guzei, I. A.; Spencer, L. C.; Zakai, U. I.; Lynch, D. C. Acta Crystallogr., Sect. E: Struct. Rep. Online 2010, E66, o221–o222. 20. Guzei, I. A.; Spencer, L. C.; Zakai, U. I. Acta Crystallogr., Sect. E: Struct. Rep. Online 2010, E66, o223–o224. 21. Christensen, A. N.; Hazell, R. G.; Lehmann, M. S.; Nielsen, M. Acta Chem. Scand. 1993, 47, 753–756. 22. Kubicki, M.; Adamiak, D. A.; Rypniewski, W. R.; Olejniczak, A. Acta Crystallogr., Sect. E: Struct. Rep. Online 2007, E63, o2604–o2606.
pubs.acs.org/jchemeduc
_
Vol. 87 No. 11 November 2010
_
Journal of Chemical Education
1259
