In the Laboratory
The Incorporation of Single Crystal X-ray Diffraction into the Undergraduate Chemistry Curriculum Using Internet-Facilitated Remote Diffractometer Control
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P. S. Szalay* Department of Chemistry, Muskingum College, New Concord, OH 43762; *
[email protected] M. Zeller and A. D. Hunter Department of Chemistry, Youngstown State University, Youngstown, OH 44555
Previous articles have eloquently addressed the numerous benefits of integrating single crystal X-ray diffraction into the curricula of the disciplines of science such as chemistry, biology, biochemistry, physics, and geology (1–3). Despite this demonstrated pedagogical value, single crystal X-ray diffraction has not been widely incorporated into the undergraduate science curriculum. One of the biggest impediments has been a lack of access to the requisite instrumentation. The purchase costs of diffractometers are comparable to 400 MHz NMR systems and they are less expensive to operate and maintain. However, the budgets of most primarily undergraduate institutions, PUIs, are currently struggling to fund the instruments that are more widely considered essential (e.g., by ACS accrediting committees) and they lack the additional financial resources required to purchase and maintain a less widely held instrument such as a single crystal Xray diffractometer. A solution to this problem was identified at Youngstown State University and implemented through the formation of a Web Accessible Single Crystal X-ray facility, the Youngstown State University–Primarily Undergraduate Institution Undergraduate Diffraction Consortium (YSU–PUI UDC). The formation of this consortium was made possible by several grants from the National Science Foundation and the Ohio Board of Regents along with internal funding. It is dedicated to undergraduate instruction in both formal courses and research. The facility is fully accessible over the Web so that participating PUI faculty and their students are able to control the diffractometer remotely as well as access data bases located at YSU. Diffractometer time and the single crystal X-ray diffraction software are provided to consortium members free of charge. The distance operation aspects of the facility are especially valuable to faculty and students in geographically remote regions, to those from institutions having a smaller total or more sporadic demand for crystallography, to those from less well funded institutions, and to those whose disabilities make travel problematic. Utilizing this facility, a single crystal X-ray diffraction experiment was carried out in the laboratory portion of the advanced inorganic chemistry course at Muskingum College, a private four-year liberal arts institution, over the course of two three-hour laboratory periods. The motivation behind the experiment was to give a group of undergraduate students with virtually no knowledge of X-ray diffraction and little understanding of the nature of crystalline solids a better understanding of both. Clearly, one cannot make students into X-ray crystallographers based on one experiment. However, the students have the opportunity to develop an enwww.JCE.DivCHED.org
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hanced understanding of how the process works and how powerful of a tool it can be for compound characterization. To give the students some background related to the experiment, about two hours was spent in the lecture component of the course discussing relevant background topics such as the fundamentals of solid state symmetry, Bragg’s Law, and a basic schematic of an X-ray diffractometer. The experiment described herein also fits into organic synthesis and characterization, biochemistry, instrumental methods, and physical chemistry laboratory classes. The Experiment
Background The structure of the crystalline compound, (η 6-pfluoroaniline)chromium(tricarbonyl), was determined in this experiment (Figure 1). Although, this compound had been previously prepared (4) and structurally characterized (5) via single crystal X-ray diffraction, the crystallographic data were not available to the students. This crystal offered a couple of advantages that were thought to work well with this type of experiment. The compound is a molecular species with a fairly uncomplicated structure and gives high quality crystals. Further, its structure can be solved in a straightforward manner, which was thought to be best for students using crystallography for the first time. From an inorganic chemistry standpoint, the compound also proved to be a valuable example of several fundamental transition-metal inorganic chemistry concepts such the eighteen electron rule, hapticity, and types of metal-ligand bonding (4, 6). In their lab reports, the students had to consider the implications of the molecular structures they calculated to discuss these aspects of the bonding in this complex. Using arene carbonyl complexes in this way has been discussed previously in some detail (4).
Figure 1. A thermal ellipsoid plot of the structure of (η6-p-fluoroaniline)chromium(tricarbonyl).
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In the Laboratory
Procedure
List 1. Equipment and Supplies
The experiment consists of several different stages. The primary features of these stages will be summarized in this section (List 1). Expanded details of the various stages are included in the Supplemental Material.W The first stage involved identifying and mounting a suitable crystal. In the second stage, the crystal to be analyzed was centered in the path of the X-ray beam of the diffractometer at the YSU host site by a YSU student or faculty member. Beginning at this point all further experimental steps and manipulations were carried out at the Muskingum College remote site. The third stage consisted of evaluating the suitably of the crystal for analysis by single crystal X-ray diffraction. This was accomplished through collection of a rotational frame (Figure 2) and determination of a preliminary unit cell by collecting a subset of the full diffraction data. In the fourth stage, the program RLATT was used to check for concerns about twinning and to verify that the unit cell obtained was reasonable for the data collected thus far. In the fifth stage, the collection of the first several frames of data was monitored to observe what was happening in the data collection process (e.g., how the detector was moving through reciprocal space). At this point, one can either leave the diffractometer to collect a full research quality data set suitable for publication (6–18 hours), collect a fast data set suitable for most chemical purposes (1–3 hours), or terminate the data collection and use a full publication quality data set that had been collected at YSU earlier. The time constraints of the lab meeting only once a week for three hours led to the decision to carry out this experiment at Muskingum College by collecting a few frames of data, terminating the data collection, and then using a previously collected full data set. Copies of several such full data sets are available from YSU. The full data set for (η6-p-fluoroaniline)chromium (tricarbonyl) was transferred to Muskingum College via the Internet prior to the start of the experiment. Copies were then placed on all of the workstations in a convenient computer lab. If a third laboratory period were available or the students were able to come into lab outside of regular class hours, research quality data collection could have been continued overnight and the data processed the following week. Alternatively, a fast data set with less X-ray exposure time per frame of data (full reciprocal space coverage but lower signal-to-noise ratio in the data) could be collected over 1–3 hours while the students solved one or more practice structures (2). In all of these cases, the complete diffraction data set is sent from the diffractometer via the Internet or on a CD to the remote site. At this point, the remote aspect of the experiment was completed and the sixth and final stage of the experiment began. The students completed the rest of the experiment working individually at workstations equipped only with the raw diffraction data and the suite of Bruker AXS structure solution software, available free to YSU–PUI UDC members. This stage of the experiment consisted of integrating the data, confirming the correct Bravais lattice had been obtained, the correct space group had been determined, and then the structure was solved and refined to a publishable level. To aid the students in this task, an outline of the SAINT, SHELXTL, and SHELXS programs was prepared. The outline guided the 1556
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For crystal mounting at the remote site: stereomicroscope microscope slides silicone grease quick-drying epoxy brass pins capillary tubes Bunsen burner For X-ray diffractometer control, data collection, data transfer from the host site to the remote site, and structural solution and refinement: PC Anywhere Bruker AXS Single Crystal Diffraction suite of programs
Figure 2. A sample rotational frame indicating a crystal is suitable for single crystal X-ray diffraction analysis.
students through the functions of the programs and included instructive comments on what was being accomplished as these programs ran. This outline is included with the Supplemental Material.W The students were instructed to continue to refine their structures until they reached certain standard crystallographic conditions. Thus, all nonhydrogen atoms had to be refined anisotropically, all hydrogen atoms had to be either located in the electron density map or added in calculated positions and refined isotropically, and convergence of the data had to be obtained (i.e., no significant changes in atomic positions or displacement parameters upon refinement). The reports for the experiment had to include a discussion of the electronic structure and bonding of the compound as well as a geometric analysis of the structure. Generation of the tables and thermal ellipsoid plots needed for the publication of a structure and a thermal ellipsoid plot were also required. Hazards This experiment involved minimal hazards. All of the experimental work carried out by the instructor and the students involving the use of X-rays was done from a remote site.
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In the Laboratory
Results and Discussion
Literature Cited
The reports prepared by the students demonstrated that the objectives of the experiment were met. Again, it is important to emphasize that this experiment is not intended to transform students into X-ray crystallographers. The motivation behind the experiment was to give a group of undergraduate students with virtually no knowledge of X-ray diffraction and little understanding of the nature of crystalline solids a better understanding of both. All of the students, with the aid of the handouts and occasional instructor input were able to complete all report requirements as described above. Stereomicroscopes may not be available in all chemistry laboratories, but are commonly available in biology and geology laboratories. The brass pins were purchased from the Charles Supper Company. Glass fibers can be made by placing a capillary tube in a flame, waiting until it melts, and then pulling the ends in opposite directions. The long fibers can then be cut to fit the brass pins using a razor blade. Quick-drying epoxy can be used to secure the glass fibers in the brass pins. The remote control of the diffractometer was accomplished using the program PC Anywhere (7). This program was also used to transfer diffraction data from the YSU host site to the Muskingum College remote site. This software is inexpensive and commercially available through numerous sources. All aspects of the diffractometer operation and processing of the experimental diffraction data to ultimately solve and refine the crystal structure of the compound were carried out using the Bruker AXS Single Crystal XRD suite of programs (SHELXTL and XSHELL) (8). As mentioned previously, some specific information regarding the operation of these programs is presented within the Supplemental Material.W A detailed description of several of these programs was previously published and can be referenced for additional information (9). More detailed guides are also available (10). The Bruker AXS programs were obtained at no charge to Muskingum College through participation in the YSU–PUI UDC. Membership in this consortium is still open to PUI’s by contacting A. D. Hunter at YSU. Similar PUI diffraction consortia have been formed elsewhere (e.g., Central States X-ray Diffraction Consortium directed by M. R. Bond at Southeast Missouri State University or by K. Kantardjieff at California State University Fullerton) and may be open to new members.
1. (a) Bond, M. R.; Carrano, C. J. J. Chem. Educ. 1995, 72, 421. (b) Stoll, S. J. Chem. Educ. 1998, 75, 1372. (c) Hoggard, P. E. J. Chem. Educ. 2002, 79, 420. (d) Arthurs, M.; McKee, V.; Nelson, J.; Town, R. M. J. Chem. Educ. 2001, 78, 1269. 2. Hunter, A. D. J. Chem. Educ. 1998, 75, 1297–1299. 3. (a) Hunter, A. D. Pittsburgh Diffraction Society Annual Meeting, Nov 5, 1998. (b) Hunter, A. D. American Crystallographic Annual Meeting, May 25, 1999. (c) Hunter, A. D.; DiMuzio, S. J. American Chemical Society Division of Chemical Education, University of Michigan at Ann Arbor, Jul 30–Aug 3, 2000. (d) Hunter, A. D.; DiMuzio, S. J. European Crystallographic Meeting, Nancy, France, Aug 24–31, 2000. (e) Hunter, A. D. British Crystallography Association Annual Meeting, Reading University, Reading, England, Apr 8, 2001; CP-17. (f ) Hunter, A. D.; DiMuzio, S. J. 222nd American Chemical Society National Meeting, Chicago, IL, Aug 2001; #451, p 258. (g) Hunter, A. D.; DiMuzio, S. J.; Lowery-Bretz, S.; McSparrin, L.; Snyder, B. 223rd American Chemical Society National Meeting, Orlando, FL, Apr 2002. (h) Hunter, A. D.; DiMuzio, S. J.; McSparrin, L.; Snyder, W. The Fall 2002 American Chemical Society Conference, Boston, MA, Aug 2002. 4. (a) Hunter, A. D.; Bianconi, L. J.; DiMuzio, S. J.; Braho, D. L. J. Chem. Educ. 1998, 75, 891–893. (b) Hunter, A. D. Discovery Research with Arene Chromium Tricarbonyl Chemistry. In Inorganic Experiments; Woollins, J. D., Ed.; VCH: New York, 2003; pp 364–367. 5. Zeller, M.; Hunter, Allen D.; Regula, Jody L.; Szalay, Paul S. Acta Cryst. 2003, E59, m975. 6. (a) Hunter, A. D.; Shilliday, L.; Furey, W. S.; Zaworotko, M. J. Organometallics 1992, 11, 1550–1560. (b) Hunter, A. D.; Mozol, V.; Tsai, S. D. Organometallics 1992, 11, 2251– 2262. 7. PC Anywhere Version 10.5, Symantec Inc., 2001. http:// www.symantec.com/pcanywhere/Consumer/index_news_ arch.html (accessed Jul 2005). 8. XRD Single Crystal Windows Software, Bruker Advanced Xray Solutions, 1998. http://www.bruker-axs.de/ (accessed Jul 2005). 9. Crundwell, G.; Phan, J.; Kantardieff, K. A. J. Chem. Educ. 1999, 76, 1242. 10. Hunter, A. D. Allen Hunter’s Youngstown State University X-Ray Structure Analysis Lab Manual: A Beginner’s Introduction, Fall 1998 Version F98D1 1997, 1998, 275 pages. The manual has been released electronically as pdf files to approximately 200 individuals at over 150 universities around the world. Described in J. Chem. Educ. 1999, 76, 163 and in the ACA and IUCr Newsletters. For the Complete Manual, see: http://www.as.ysu.edu/~adhunter/YSUSC/ Manual/Manual.W99D1.pdf (accessed Jul 2005). For the Covers for the Complete Manual, see: http://www.as.ysu.edu/ ~adhunter/YSUSC/Manual/Manual.Covers.W99D1.pdf (accessed Jul 2005). For an Updated Version of Chapter XIV on Growing Single Crystals, see: http://www.as.ysu.edu/ ~adhunter/YSUSC/Manual/ChapterXIV.pdf (accessed Jul 2005).
Acknowledgments MZ was supported by NSF grant 0111511. The diffractometer was funded by NSF grant 0087210, by the Ohio Board of Regents grant CAP-491, and by YSU. Some of the crystallographic education materials were funded by NSF 9980921. WSupplemental
Material
Details of each of the experimental stages and alternative options, copies of the student handouts, and a presentation developed by A. D. Hunter that covers some of the basics of crystallography are available in this issue of JCE Online. www.JCE.DivCHED.org
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