In the laboratory. Number of words in the manuscript: Corresponding Author

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1 The Incorporation of Single Crystal X-ray Diffraction into the Undergraduate Chemistry Curriculum Using Internet Facilitated Remote Diffractometer Control In the laboratory Number of words in the manuscript: 1876 Corresponding Author Paul S. Szalay Department of Chemistry Muskingum College 163 Stormont St. New Concord, OH preferred phone: (740) fax: (740) Contributing Authors Allen D. Hunter Department of Chemistry Youngstown State University One University Plaza Youngstown, OH phone: (330) fax: (330) Matthias Zeller Department of Chemistry Youngstown State University One University Plaza Youngstown, OH phone: (330) fax: (330)

2 The Incorporation of Single Crystal X-ray Diffraction into the Undergraduate Chemistry Curriculum Using Internet Facilitated Remote Diffractometer Control Corresponding Author Paul S. Szalay Department of Chemistry Muskingum College 163 Stormont St. New Concord, OH Contributing Author Allen D. Hunter Matthias Zeller Department of Chemistry Department of Chemistry Youngstown State University Youngstown State University One University Plaza One University Plaza Youngstown, OH Youngstown, OH Abstract A laboratory experiment on single crystal X-ray diffraction has been developed and implemented in an inorganic chemistry course for undergraduate students via internet facilitated remote diffractometer control. The experiment was carried out from a remote location, a computer lab at Muskingum College, with the X-ray diffractometer being housed at Youngstown State University. In this experiment, the structure of (η 6 -parafluoroaniline)chromium(tricarbonyl) was determined as a representative example. Keywords X-ray Crystallography Internet/Web-based Remote Instrument Operation Laboratory Instruction Inorganic Chemistry 2

3 The Incorporation of Single Crystal X-ray Diffraction into the Undergraduate Chemistry Curriculum Using Internet Facilitated Remote Diffractometer Control P. S. Szalay Department of Chemistry, Muskingum College, New Concord, OH M. Zeller and A. D. Hunter Department of Chemistry, Youngstown State University, Youngstown, OH Lab Summary Background 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. 1,2,3 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 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 X-ray 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 3

4 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. 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 and/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 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 enhanced 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/characterization, biochemistry, instrumental methods, and physical chemistry laboratory classes. 4

5 The Experiment Introduction The structure of the crystalline compound, (η 6 -p-fluoroaniline)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 solves 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 Procedure The experiment can be described as consisting of several different stages. The primary features of these stages will be summarized in this section. Expanded details of the various stages are included in the lab documentation materials in the WEB supplement to this paper. 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 5

6 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 any 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 suitable for publication set (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 a 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. This was due to the time constraints of the laboratory meeting only once a week for three hours. Copies of several such full data sets are available from YSU and were transferred via the internet to Muskingum College with copies being 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 6

7 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, also 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 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 lab documentation materials for the experiment in the WEB supplement to this paper. The students were instructed to continue to refine their structures until they reached certain standard crystallographic conditions. Thus, all non-hydrogen 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 7

8 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. Student Results 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. Equipment and Supplies For crystal mounting at the remote site stereomicroscope microscope slides silicone grease brass pins capillary tubes Bunsen burner quick drying epoxy 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 (SHELXTL) 8

9 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 & XSHELL). 8 As mentioned previously, some specific information regarding the operation of these programs is presented within the lab documentation materials. 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 9

10 University or by K. Kantardjieff at California State University Fullerton) and may be open to new members. 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. Acknowledgements MZ was supported by NSF grant The diffractometer was funded by NSF grant , by the Ohio Board of Regents grant CAP-491, and by YSU. Some of the crystallographic education materials were funded by NSF References 1. (a) Bond, M. R.; Carrano, C. J. J. Chem. Educ., 1995, 72, 421 (b) Stoll, S. J. Chem. Educ., 1998, 75, (c) Hoggard, P. E. J. Chem. Educ., 1999, 79, 420. (d) Arthurs, M.; McKee, V.; Nelson, J.; Town, R. M. J. Chem. Educ., 2001, 78, Hunter, A. D. J. Chem. Educ., 1998, 75, (a) Hunter, A. D. Pittsburgh Diffraction Society Annual Meeting, November 5 th, (b) Hunter, A. D. American Crystallographic Annual Meeting, May 25 th, (c) Hunter, A. D. and DiMuzio, S. J. University of Michigan at Ann Arbor, American Chemical Society Division of Chemical Education, July 30 th - August 3 rd, (d) Hunter, A. D. and DiMuzio, S. J. European Crystallographic Meeting, Nancy, France, 10

11 August 24 th - 31 st, (e) Hunter, A. D. British Crystallography Association Annual Meeting, Reading University, Reading, England, April 8 th, 2001, CP-17. (f) Hunter, A. D., DiMuzio, S. J. 222 nd American Chemical Society National Meeting, Chicago, IL, August, 2001, #451,258. (g) Hunter, A. D., DiMuzio, S. J., Lowery-Bretz, S., McSparrin, L., Snyder, B. 223 rd American Chemical Society National Meeting, Orlando, FL, April, (h) Hunter, A. D. DiMuzio, S. J.; McSparrin, L.; Snyder, W. the Fall 2002 American Chemical Society conference, Boston, MA., August, (a) Hunter, A. D.; Bianconi, L. J.; DiMuzio, S. J.; Braho, D. L. J. Chem. Educ., 1998, 75, (b) Hunter, A. D.: Discovery Research with Arene Chromium Tricarbonyl Chemistry, in Inorganic Experiments, J. D. Woollins Ed., VCH, New York, 2003, Zeller, M.; Hunter, Allen D.; Regula, Jody L.; Szalay, Paul S. Acta Cryst. 2003, E59, m (a) Hunter, A. D.; Shilliday, L.; Furey, W. S.; Zaworotko, M. J. Organometallics, 1992, 11, (b) Hunter, A. D.; Mozol, V.; Tsai, S. D. Organometallics, 1992, 11, PC Anywhere Version 10.5, Symantec Inc., XRD Single Crystal Windows Software, Bruker Advanced X-ray Solutions, Crundwell, G.; Phan, J.; and Kantardjieff, K. A. J. Chem. Educ., 1999, 76, 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. Has been released electronically as.pdf files to approximately 200 individuals at over 150 Universities around the world. Described in the J. Chem. Educ., 11

12 1999, 76, 163 and in the ACA and IUCr Newsletters. For the Complete Manual, see: For the Covers for the Complete Manual, see: For an Updated Version of Chapter XIV on Growing Single Crystals, see: 12

13 Figure 1. A thermal ellipsoid plot of the structure of (η 6 -p-fluoroaniline)chromium(tricarbonyl). 13

14 Figure 2. A sample rotational frame indicating a crystal is suitable for single crystal X- ray diffraction analysis. 14

15 Lab Documentation Detailed Experimental Description and Procedure The experiment as carried out at Muskingum College can be described as consisting of several different stages. Details of each of these stages and alternative experimental options will be presented herein. Copies of the handouts given to students will follow the stage descriptions. A presentation developed by A.D. Hunter that covers some of the basics of crystallography is also included in pdf format. Crystal Selection and Mounting The first stage of the experiment was the only component that could be done entirely at the remote site (i.e. Muskingum College) or the diffractometer site (i.e. YSU). In either case, the crystal to be analyzed was mounted on a glass fiber that was previously set in a copper pin using a quick drying epoxy. The crystal can be mounted on the fiber using the same quick drying epoxy or silicone grease if low temperature data collection is used. If done at the remote site, the students select and mount their own crystals (ideally ones they have made in their labs). These can then be mailed or sent by courier to the diffractometer site. Alternatively, the diffractometer operator at YSU could either select and mount crystals received through the mail or use a standard prepared sample. The actual crystal mounted for the (η 6 -p-fluoroaniline)chromium(tricarbonyl) data collection was carried out on site at YSU using quick drying epoxy. The procedure of recognizing and mounting a single crystal suitable for X-ray analysis was done at Muskingum College using crystals of cobalt nitrate. The evaluation of crystal quality was based on visual inspection using a stereomicroscope. As mentioned, crystals of cobalt nitrate were used for this exercise, but any suitably crystalline substance could be 15

16 used. In the laboratory period prior to the diffraction experiment, the students worked with the instructor selecting a crystal from a batch with various sizes and qualities and mounted it on a glass fiber secured in a brass pin. Silicone grease was used to fix the crystal to the fiber. The advantage to using silicone grease in this exercise is that the crystal can easily be removed from the glass fiber after the student has successfully completed the mounting. The fiber and pin then can be passed to the next student. The same fiber and pin can be used continuously. Each student in turn had the opportunity to select and mount a crystal. Centering the Crystal in the X-ray Beam In the second stage, the crystal to be analyzed is centered in the path of the X-ray beam. This operation can only be carried out by a diffractometer operator at the YSU host site but takes only a few minutes. In this experiment, a suitable crystal of (η 6 -pfluoroaniline)chromium(tricarbonyl) was selected at YSU and mounted by the diffractometer operator on a glass fiber secured in a brass pin. The brass pin was then placed in a goniometer head, and this unit placed on the diffractometer. The crystal was then centered in the path of the X-ray beam. Alternatively a crystal could be grown and mounted on a glass fiber in a brass pin at a remote site and sent via mail or courier to YSU. This crystal once received could be mounted on the diffractometer by the instrument operator at the host site and centered in the X-ray beam. Evaluation of Crystal Quality From this point forward all experimental steps and manipulations were carried out remotely on campus at Muskingum College. A computer lab with 20 work stations, each equipped with the suite of Bruker Diffraction programs, and a central computer that was 16

17 connected to a multimedia projector and equipped with PC Anywhere as well as the Bruker programs was used for this purpose. In the third stage of the experiment, the quality of the crystal had to be evaluated before a decision could be made on whether or not to collect data. The diffractometer can, of course, only be controlled remotely by one computer at a time. This necessitated that the steps within this stage be carried out as one group using the central computer in the laboratory with all the screen images of the central computer being projected onto a large multimedia screen by the projector. All the steps within this stage were carried out using different features in the SMART program. The initial evaluation of the crystal was accomplished by collecting a rotational frame. The frame was then inspected to determine whether the quality of the crystal warranted further analysis. Poor crystallinity, cracks, or disorders within the crystal can cause inconsistencies in rotational frames. Indeed discussions of these frames are an excellent springboard to help the students develop an intuitive understanding of what single crystal means. It needs to be noted that a good rotational frame is only an indicator that a crystal is single and good X-ray quality. If the rotational frame indicates the crystal is of poor quality an instrument operator at YSU mounts another crystal. Crystals can also be screened ahead of time so the valuable laboratory time of the students is not wasted. Once a suitable crystal has been identified by its rotational frame a further check on its quality is carried out by determining the unit cell. The unit cell option in the SMART program collects diffraction data in three different areas of reciprocal space. The program then automatically selects suitable reflections from this data, draws vectors between them and determines a unit cell and Bravais Lattice. 17

18 In the fourth stage, the program RLATT was used to check for any concerns about twinning and to verify that the unit cell obtained was reasonable for the data collected so far. This program provides a three dimensional image of the diffraction data as small squares each of which represents a reflection. This image can greatly assist the students in visualizing the arrangement of the reflections in reciprocal space and how data are collected by sweeping the detector through areas of reciprocal space. A feature of the program also enables the user to draw vectors between any two reflections. In doing this the origin of the unit cell is more obvious and the unit cell obtained in SMART can be visually checked. Once it was verified that there were no problems with the unit cell, the class as a group proceeded through the rest of the instrument setup and data collection was then initiated. Data Collection 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. How the crystal is oriented and where the detector is moving can be monitored because the values of 2-Theta, omega, phi, and chi are listed on the computer screen during data collection. At this point, one can either leave the diffractometer to collect a full research quality data set (6-18 hours), collect a fast data set (1-3 hours), or terminate the data collection and use a full data set collected earlier. The decision was made to carry out this experiment by collecting a few frames of data, terminating the data collection, and then using a full set data set collected earlier. The decision to carry out this experiment without collecting a complete set of data on the crystal was made as a concession to the time constraints of the laboratory meeting only once a week for three hours. Carrying out the experiment in this 18

19 way was possible because the structure for this crystal had previously been determined in A.D. Hunter s laboratory so a complete set of raw diffraction data was available through the YSU Structure Center. Prior to beginning this experiment, the data were transferred via the internet to Muskingum College and copies placed on all the workstations in the computer lab where the experiment was being carried out. If a third laboratory period were available, research quality data collection could have been continued overnight and then 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 in 1-3 hours while the students watch either in an extended second laboratory period or during a third laboratory period. In any of these cases, the complete diffraction data set was sent from the diffractometer via the internet or on a CD to the remote site. Structure Solution and Refinement 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 programs. This stage of the experiment consists of integrating the data, confirming the correct Bravais lattice has been obtained, determining the correct space group, then solving and refining the structure to a publishable level. To aid the students in this task, an outline of the SAINT, SHELXTL, and SHELXS programs was prepared. This outline guides the students through the functions of the programs and includes instructive comments on what is being accomplished as these programs run. More detailed guides are also available

20 The students were instructed to continue to refine their structures until they reached certain standard crystallographic conditions. All non-hydrogen 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. not significant changes in atomic positions or displacement parameters). The reports for this 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 files generally needed for publication of a structure, and a thermal ellipsoid plot were also required. 20

21 Handout Given to the Students Experiment X: Single crystal X-ray diffraction Objective: Work in conjunction with your instructor and individually to determine the crystal structure of (η 6 -p-fluoroaniline)chromium(tricarbonyl). The goal of this experiment is to give you some experience with and a better understanding of single crystal X-ray diffraction and the role it can play as a powerful characterization tool in science. From this experiment, you should also be able to develop a more thorough understanding of the nature of crystalline solids. Anticipated Time Frame: 2 laboratory periods Procedure Notes: The first three steps of the procedure, as outlined in the Remote X-ray Diffractometer User s Guide that was distributed in lecture, will be carried out at Youngstown State University, but under our control via internet control of their single crystal CCD diffractometer using the software program PCAnywhere. We will begin by obtaining a rotational frame for the crystal to evaluate its quality (including whether or not it is a single crystal). If the crystal is of good quality, then the unit cell will be determined by collecting a small amount of diffraction data (diffracted X-rays). If a good unit cell can be obtained then data collection will be initiated, but not completed due to time constraints. The complete diffraction data has already been transferred from YSU here and placed on your computers in the following location. C:\frames\xxxxx At this point, you will take over and process the complete set of raw X-ray data and solve the structure of the compound. To carryout this task follow the procedures explained in the user s guide you were given in class. Your individual tasks begin with part 4 of the procedure described in the user s guide. Results and Discussion: Your structure must be completely solved (all atoms must be found) and refined until it reaches certain standard crystallographic conditions. All non-hydrogen atoms have to be refined anisotropically, all hydrogen atoms have to be added in calculated positions and refined isotropically, and a R1 value of less than 6% has to be obtained. The reports for this experiment also have 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 files generally needed for publication of a structure, and a thermal ellipsoid plot are also required. 21

22 Be sure to include the following standard crystallographic data in your report. The information you did not have access to because of the remote nature of the experiment has been provided for you. Empirical formula: Formula weight: Temperature: Wavelength: the X-ray wavelength when Molybdenum Kα radiation is used as the source Crystal system: Space group: Unit cell dimensions: a = Å, α = b = Å, β = c = Å, γ = Unit Cell Volume: Ǻ 3 Z: Density (calculated): Mg/m 3 Absorption coefficient: mm -1 F(000): the number of electrons in the unit cell Crystal size: mm Crystal shape, color: block, yellow Reflections collected: Goodness-of-fit on F 2 : Final R indices [I>2σ(I)]: R1 =, wr2 = R indices (all data): R1 =, wr2 = Extinction coefficient: Largest diff. peak and hole: and e Å -3 22

23 Handout Given to the Students General Procedure for Data Collection and Structural Solution Using Remote Controlled Single Crystal X-Ray Diffraction The following is a user s guide for remote operation of the SMART APEX CCD Diffractometer housed in the Structure and Chemical Instrumentation Center at Youngstown State University. Please note that all options within the symbols < > are responses to be selected. These instructions do not include directions for mounting or centering crystals. Part 1: Connection to the remote host (See instructor for PCAnywhere access) 1. Click on the PCAnywhere icon on the desktop. Among the options available will be YSU X-Ray. Click on that icon and the connection should be made automatically. Part 2: Identifying the Quality of the Crystal and Collecting Data 1. Open the SMART program. When the prompt comes up, click on yes to open the previous project. Answer all subsequent questions that come up with yes until you reach the type of measurement. Select <small molecule> measurements. 2. Go to <crystal> on the toolbar and select <New Project>. Fill in the following: Name: For uniformity use the year, your initials, and a sample number (e.g. 03pss01a) Temp: 25 Working directory: C:/frames/surname/filename/work e.g. C:/frames/szalay/03pss01a/work Data directory: C:/frames/surname/filename 3. Click on <OK> 4. Go to <crystal> on the toolbar and select <evaluate> and check that the following parameters are selected: temp = -42 (or -43) Service mode = off then hit <esc>. 5. Go to <crystal> on the toolbar and select <Evaluate> and type <u>. Check that the settings are 50 kv and 40 ma. 6. Go to <acquire> on the toolbar and select <rotation>. The value should be 1 minute for average size crystals ( mm on all sides) or longer (up to 5 minutes) for smaller crystals. Once the rotation photo appears it needs to be checked. The desired appearance is a symmetric arrangement of well defined bright spots. Rings of white 23

24 around the center of the photo indicate a lack of crystallinity in the sample and virtually guarantee that the sample is not single crystal X-ray quality and another crystal should be tried. 7. If the rotation photo looks good, go to <detector> on the toolbar and select <Dark Current>. Set the time per frame to between 10 (which is the default) and 30 seconds. The 30 second setting should be used for smaller more weakly diffracting crystals. Name the file to be generated with the convention outlined in step 2 in this section followed by the time per frame of the collection. e.g. 03pss01a10._DK. 8. At this point, you will collect a small amount of data that will be used to make sure the crystal is single not twinned, and if it is not, to identify the unit cell of the crystal. This part of the procedure usually takes about 15 to 30 minutes depending upon the time per frame necessary which depends upon the quality of your crystal. First, go to <edit> on the toolbar and select <configuration>. Make sure that the sample-detector distance is Go to <crystal> on the toolbar and select <Unit Cell> and check the settings. 6.2, 251.6, frames = 20 seconds/frame = whatever was used in collecting the dark current (default is 10) <OK> The instrument will now automatically collect data and try to determine the unit cell. The data collection involves moving the crystal in three directions in the X-ray beam while detecting diffracted X-rays in 20 different positions along the three directions. Of the collected data (diffracted X-rays which appear as white spots on the computer screen) 60% should be retained and processed by the program in determining the unit cell. If not, this is an indication of multiple crystals or twinning and the crystal should be considered potentially suspect. If a unit cell can be determined by the program from the data it will appear automatically once the data is done collecting. The quality of the unit cell should be evaluated before beginning the collection of data that will be used to solve the structure of the crystal. One easy way to evaluate that validity of the unit cell is consider the lengths of the a, b, and c axes. Common axis lengths, depending upon the size of the compound and packing of the crystal (symmetry), are 10 to 30 Ǻ. Any axes lengths considerably longer than these are cause for questioning the validity of the unit cell especially if the compound is not a polymer of some sort that might be expected to have an especially long crystal dimension (and even that is not all that common). If a suitable unit cell has been obtained proceed to the next step. 9. Go to <acquire> on the toolbar and select <Edit-Hemi>. Go to the last column and check that the set time is equal to the dark current time used in step 7 and the seconds/frame used in step 8. Now select <Hemisphere> and start the collection of data. If the power were to shut off on the X-ray diffractometer during the data collection, the collection can be restarted by going to <acquire> on the toolbar and selecting <Resume>. Depending upon the seconds/frame used the data collection can take anywhere from 8 to 24 hours or longer. 24

25 Part 3: Data Transfer from YSU to Muskingum College (See instructor) Part 4: Preparing Data Using the SaintPlus Program 1. Open the SaintPlus program. Go to <project> on the toolbar and select <New>. Find the appropriate matrix file. It will end in.p4p and have the same file name as the convention used in step 2 of Part 2. (e.g. 03pss01a.p4p) 2. Type in the project name using up to 7 digits. (e.g. 03pss01a) When the data files are merged later an m will be added. Select <Open>. 3. Go to <SAINT> on the toolbar and select <Initialize>. Go to <SAINT> on the toolbar and select <Execute>. Check that the correct crystal class (Laue class) and lattice centering are listed. These are based in the unit cell for the crystal which was determined in step 8 of part 2. The d-spacing listed on the screen should be and the maximum wait for frame file should be Check that the cell parameters (a, b, c, α, β, γ these define the unit cell) are all the same as those determined in step 8 of part 2. There should be three lines under the Matrix (.p4p) Filename. Delete the second and third lines, but leave the first. 4. Go to the top right of the screen in the more options section and select <Integrate>. The reflection size should be set to 0.6 (x), 0.6 (y), and 0.4 (z). A check mark should be beside narrow frame, enable box size, and decay (if the sample partly decomposed over the collection period). Under the periodic o. m. updating a check should be beside enable periodic updating, constrain Laue class and crystal translation with frequency = Go to advanced integrate (bottom left button). Check the following parameters: Model Profiles: I/σ = Fraction = I/σ threshold = Resolution lower limit = Active frame ½ width = 7 Correction to intensity eds s 0.00 and Click on the Integrate+Sort+Global button and the program will begin to run. What the program is doing at this point is extracting the intensities of the diffracted X-ray data. The intensities of the various diffracted X-rays will play a key role when the program begins guessing what atoms must be present in the crystal to account for the diffraction data. A useful rule of thumb is that the more electrons an atom has the more strongly it will diffract X-rays. At the prompt hit the <enter> key to continue. 7. Close all windows up to SaintPlus. Select <SADABS> from the SaintPlus toolbar. This is an absorption correction program that helps modify the experimental data to take 25

26 into account any absorption of X-rays by the crystal and also deterioration of the crystal over the time of the date collection. Hit return to accept the maximum number of reflections allowed. Enter the number that corresponds the Laue class of your crystal see step 3 part 3. Accept [Y] for Friedel Pairs. Enter the.raw filename. e.g. 03ps01a1.raw (Note, it must end in.raw and there should be 3 files e.g. 03ps01a1.raw, 03ps01a2.raw, and 03ps01a3.raw). Enter a / after the file.raw file has been entered. Then take all the default values that are prompted until you are prompted for the number of refinement cycles. Use 100 cycles. Select [A] once the constant values are obtained. 8. Take the default values and select [A] for accept. If an error model is suggested you should use it. If no error model is suggested just continue. 9. Enter the name of the output file. 03ps01am.hkl (Note, the ending has to be m.hkl) Part 5: Solving Structures 1. You will need three files from this point for structural solution and refinement: filenamem.hkl filenamem.p4p filenamem.raw (e.g. 03ps01am.hkl) (e.g. 03ps01am.p4p) (e.g. 03ps01am.raw) 2. Open the SHELXTL program. It will be listed in the programs menu of your computer under Bruker AXS Programs. 3. Click on <project> and select <new>. Type in a project name. (e.g. 03ps01am) Select the.p4p with the same base file name as you typed in for the project. Click on <open>. 4. Select <XPREP> on the toolbar. Note, to select any default options (which are listed in brackets, []) you need only hit enter. 5. You will be prompted to select a lattice type option. Select the default value which is based on your current unit cell. At the next prompt select the default value of [H]. This will cause the program to review your data to see if the crystal class (Laue class) you have been using thus far is too high or too low in symmetry. You will be prompted to select the option the program finds most suitable. Accept this value (some letter). You will then be prompted to select [S] which will cause the program to try to identify the space group of your crystal. The space group provides a detailed accounting of exactly what symmetry is present in your crystal. The Laue class provides a more general picture of symmetry possibilities. All crystals belong to one of the 230 possible space groups. You will be prompted to select [S] again. Do so. Select the default crystal system. Select the default lattice type. Select the default space group option. You will be prompted at this point to select option D Read, modify, or merge datasets. Do NOT select this option. The data has already been merged. Instead select option C to define 26

27 the unit cell contents. Type the numbers of each atom you are expecting in your structure. Select F to set up the output files. The default filename should be acceptable. If you are prompted to enter a new file name just add a 1 to the end of the filename. When prompted about whether you want to write the intensity data file select yes by typing Y. Select Q to quit the program. If you had to change the filename by adding a 1 to the end, you need to manually change it back the project name (remove the 1 ) so SHELXTL will still recognize it. The file will be located in the work folder at the location specified in the handout describing this experiment that you were given in class. 6. Go to <edit> on the toolbar and select <edit.ins>. Change TREF to TREF Select <file> then save. 7. Select <XS> on the toolbar and the computer should begin to process the data. The program XS takes the data thus far and tries to solve it. This means the program attempts to identify the types of atoms present in the structure as well as their positions and geometric relationships. Once this is done the preliminary solution that is generated can be viewed using the programs <XP> or <XSHELL>. If everything has gone well to this point, the preliminary solution should give a picture resembling the molecule along with some spurious weak (low intensity) ghost atoms that can be eliminated. If the preliminary solution on the screen is a completely unrecognizable mass of atoms (even after symmetry expansion has been applied see step 8 part 5) then there was some problem processing the data along the way which almost always means the Laue class and/or space group were assigned incorrectly. 8. The following instructions apply to the program <XP>. Click on <XP> on the toolbar and the program window will open up. This program toggles between a command line screen where you can type in commands and a graphics screen where the molecule can be viewed, moved in space, and manipulated based on commands typed on the command line screen. Type fmol then hit enter. Scroll down the screen until you reach the end of the Q peak listings then type proj. A preliminary picture of the structure will appear. (Note, hitting the esc button on the computer will take you from the graphics screen to the command line screen.) At this point, you will need to delete unwanted atoms until the structure is correct. Before doing any of that though you should go back to the command line screen and type the command grow and hit enter. Then type proj to go back to the graphics screen. You will now see an expanded view of the molecule that includes all atoms that were not present in the original picture because they were related by symmetry to the atoms that were originally present. This usually provides a much more clear view of the molecule. (Note grow will not always produce additional atoms, but it usually does. Whether it will or not depends upon the space group of the crystal and position of the molecules within the crystal.) The command fuse is the opposite of the grow command. It gets rid of one set of symmetry equivalent atoms. When the program does not know what specific type of atom to assign it will label an atom as Q followed by some number. (e.g. Q1) 9. Atoms can be named using the command line screen. Each atom in the structure will need to be designated with an atom type (which element it is) and by a number. For 27

28 example if by using the graphics screen, you identify a Q atom such as Q5 that you know to be a carbon go the command line screen and type: (it is not case sensitive) name q5 c1 The symbol c1 designates that particular atom as a carbon atom. The number needs to be in accord with whatever numbering scheme you devise for all the atoms in your molecule. The kill command can be used to get rid of spurious atoms in the nonsymmetry expanded picture of the molecule. If for example, you decided Q15 was not a real atom just noise that atom can be deleted by typing: kill q15 All the q peaks can be killed at once if desired by typing: kill $q Once you have named all the atoms you can identify and killed any that you cannot, you need to save the file by typing on the command line: file filename (e.g. file 03ps01am) When you do this a second line will appear with a default value. Just accept this and your changes will be saved into a file with a.ins extension. (e.g. 03ps01am.ins) The structure can then be refined using the program <XL>. The refinement program takes your input in the form of atom assignments you made using XP (a model of the molecule) and matches that up with the experimental data and gives you numerical values that indicate how well they correlate. Almost always, several cycles of running through XP and XL are necessary to get a good structural model. 10. Go to <XL> on the toolbar and select <XL> not <XH>. The program will run automatically using the.ins file generated by <XP>. The program will write a.res file (with the same base filename of the.ins file) that can then be read back into <XP> to continue working on the structure. Often when the XL program runs it will generate new atoms that can be seen the second time XP is run. Continuing this pattern of running through XP and XL should produce a complete picture of the structure. This can be numerically evaluated by considering the R1 value produced by each run of XL. This value should get smaller with each run through XP followed by XL. If it does not, it indicates a problem with the structure. The general rule of thumb is that for a structure to be publishable R1 has to be lower than 7% (0.07) though the lower it is generally the better the structure is. 28