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www.JCE.DivCHED.org • Vol. 82 No. 10 October 2005 • Journal of Chemical Education 1555

Previous articles have eloquently addressed the numer-ous benefits of integrating single crystal X-ray diffraction intothe curricula of the disciplines of science such as chemistry,biology, biochemistry, physics, and geology (1–3). Despitethis demonstrated pedagogical value, single crystal X-ray dif-fraction has not been widely incorporated into the under-graduate science curriculum. One of the biggest impedimentshas been a lack of access to the requisite instrumentation.The purchase costs of diffractometers are comparable to 400MHz NMR systems and they are less expensive to operateand maintain. However, the budgets of most primarily un-dergraduate institutions, PUIs, are currently struggling tofund the instruments that are more widely considered essen-tial (e.g., by ACS accrediting committees) and they lack theadditional financial resources required to purchase and main-tain a less widely held instrument such as a single crystal X-ray diffractometer. A solution to this problem was identifiedat Youngstown State University and implemented throughthe formation of a Web Accessible Single Crystal X-ray facil-ity, the Youngstown State University–Primarily Undergradu-ate Institution Undergraduate Diffraction Consortium(YSU–PUI UDC). The formation of this consortium wasmade possible by several grants from the National ScienceFoundation and the Ohio Board of Regents along with in-ternal funding. It is dedicated to undergraduate instructionin both formal courses and research. The facility is fully ac-cessible over the Web so that participating PUI faculty andtheir students are able to control the diffractometer remotelyas well as access data bases located at YSU. Diffractometertime and the single crystal X-ray diffraction software are pro-vided to consortium members free of charge. The distanceoperation aspects of the facility are especially valuable to fac-ulty and students in geographically remote regions, to thosefrom institutions having a smaller total or more sporadicdemand for crystallography, to those from less well fundedinstitutions, and to those whose disabilities make travel prob-lematic.

Utilizing this facility, a single crystal X-ray diffractionexperiment was carried out in the laboratory portion of theadvanced inorganic chemistry course at Muskingum College,a private four-year liberal arts institution, over the course oftwo three-hour laboratory periods. The motivation behindthe experiment was to give a group of undergraduate stu-dents with virtually no knowledge of X-ray diffraction andlittle understanding of the nature of crystalline solids a bet-ter understanding of both. Clearly, one cannot make studentsinto X-ray crystallographers based on one experiment. How-ever, the students have the opportunity to develop an en-

hanced understanding of how the process works and howpowerful of a tool it can be for compound characterization.To give the students some background related to the experi-ment, about two hours was spent in the lecture componentof the course discussing relevant background topics such asthe fundamentals of solid state symmetry, Bragg’s Law, and abasic schematic of an X-ray diffractometer. The experimentdescribed herein also fits into organic synthesis and charac-terization, biochemistry, instrumental methods, and physi-cal chemistry laboratory classes.

The Experiment

BackgroundThe structure of the crystalline compound, (η6-p-

fluoroaniline)chromium(tricarbonyl), was determined in thisexperiment (Figure 1). Although, this compound had beenpreviously prepared (4) and structurally characterized (5) viasingle crystal X-ray diffraction, the crystallographic data werenot available to the students. This crystal offered a couple ofadvantages that were thought to work well with this type ofexperiment. The compound is a molecular species with a fairlyuncomplicated structure and gives high quality crystals. Fur-ther, its structure can be solved in a straightforward manner,which was thought to be best for students using crystallog-raphy for the first time. From an inorganic chemistry stand-point, the compound also proved to be a valuable exampleof several fundamental transition-metal inorganic chemistryconcepts such the eighteen electron rule, hapticity, and typesof metal-ligand bonding (4, 6). In their lab reports, the stu-dents had to consider the implications of the molecular struc-tures they calculated to discuss these aspects of the bondingin this complex. Using arene carbonyl complexes in this wayhas been discussed previously in some detail (4).

The Incorporation of Single Crystal X-ray Diffraction Winto the Undergraduate Chemistry CurriculumUsing Internet-Facilitated Remote Diffractometer ControlP. S. Szalay*Department of Chemistry, Muskingum College, New Concord, OH 43762; *pszalay@muskingum.edu

M. Zeller and A. D. HunterDepartment of Chemistry, Youngstown State University, Youngstown, OH 44555

Figure 1. A thermal ellipsoid plot of the structure of (η6-p-fluoro-aniline)chromium(tricarbonyl).

In the Laboratory

1556 Journal of Chemical Education • Vol. 82 No. 10 October 2005 • www.JCE.DivCHED.org

Procedure

The experiment consists of several different stages. Theprimary features of these stages will be summarized in thissection (List 1). Expanded details of the various stages areincluded in the Supplemental Material.W

The first stage involved identifying and mounting a suit-able crystal. In the second stage, the crystal to be analyzedwas centered in the path of the X-ray beam of the diffrac-tometer at the YSU host site by a YSU student or faculty mem-ber. Beginning at this point all further experimental steps andmanipulations were carried out at the Muskingum Collegeremote site. The third stage consisted of evaluating the suit-ably of the crystal for analysis by single crystal X-ray diffrac-tion. This was accomplished through collection of a rotationalframe (Figure 2) and determination of a preliminary unit cellby collecting a subset of the full diffraction data. In the fourthstage, the program RLATT was used to check for concernsabout twinning and to verify that the unit cell obtained wasreasonable for the data collected thus far.

In the fifth stage, the collection of the first several framesof data was monitored to observe what was happening in thedata collection process (e.g., how the detector was movingthrough reciprocal space). At this point, one can either leavethe diffractometer to collect a full research quality data setsuitable for publication (6–18 hours), collect a fast data setsuitable for most chemical purposes (1–3 hours), or termi-nate the data collection and use a full publication quality dataset that had been collected at YSU earlier. The time con-straints of the lab meeting only once a week for three hoursled to the decision to carry out this experiment at MuskingumCollege by collecting a few frames of data, terminating thedata collection, and then using a previously collected full dataset. Copies of several such full data sets are available fromYSU. The full data set for (η6-p-fluoroaniline)chromium(tricarbonyl) was transferred to Muskingum College via theInternet prior to the start of the experiment. Copies were thenplaced on all of the workstations in a convenient computerlab. If a third laboratory period were available or the studentswere able to come into lab outside of regular class hours, re-search quality data collection could have been continued over-night and the data processed the following week.Alternatively, a fast data set with less X-ray exposure timeper frame of data (full reciprocal space coverage but lowersignal-to-noise ratio in the data) could be collected over 1–3hours while the students solved one or more practice struc-tures (2). In all of these cases, the complete diffraction dataset is sent from the diffractometer via the Internet or on aCD to the remote site.

At this point, the remote aspect of the experiment wascompleted and the sixth and final stage of the experimentbegan. The students completed the rest of the experimentworking individually at workstations equipped only with theraw diffraction data and the suite of Bruker AXS structuresolution 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, thecorrect space group had been determined, and then the struc-ture was solved and refined to a publishable level. To aid thestudents 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 includedinstructive comments on what was being accomplished asthese programs ran. This outline is included with the Supple-mental Material.W

The students were instructed to continue to refine theirstructures until they reached certain standard crystallographicconditions. Thus, all nonhydrogen atoms had to be refinedanisotropically, all hydrogen atoms had to be either locatedin the electron density map or added in calculated positionsand refined isotropically, and convergence of the data had tobe obtained (i.e., no significant changes in atomic positionsor displacement parameters upon refinement). The reportsfor the experiment had to include a discussion of the elec-tronic structure and bonding of the compound as well as ageometric analysis of the structure. Generation of the tablesand thermal ellipsoid plots needed for the publication of astructure and a thermal ellipsoid plot were also required.

Hazards

This experiment involved minimal hazards. All of theexperimental work carried out by the instructor and the stu-dents involving the use of X-rays was done from a remotesite.

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

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www.JCE.DivCHED.org • Vol. 82 No. 10 October 2005 • Journal of Chemical Education 1557

Results and Discussion

The reports prepared by the students demonstrated thatthe objectives of the experiment were met. Again, it is im-portant to emphasize that this experiment is not intended totransform students into X-ray crystallographers. The moti-vation behind the experiment was to give a group of under-graduate students with virtually no knowledge of X-raydiffraction and little understanding of the nature of crystal-line solids a better understanding of both. All of the students,with the aid of the handouts and occasional instructor inputwere able to complete all report requirements as describedabove.

Stereomicroscopes may not be available in all chemistrylaboratories, but are commonly available in biology and ge-ology laboratories. The brass pins were purchased from theCharles Supper Company. Glass fibers can be made by plac-ing a capillary tube in a flame, waiting until it melts, andthen pulling the ends in opposite directions. The long fiberscan then be cut to fit the brass pins using a razor blade.Quick-drying epoxy can be used to secure the glass fibers inthe brass pins.

The remote control of the diffractometer was accom-plished using the program PC Anywhere (7). This programwas also used to transfer diffraction data from the YSU hostsite to the Muskingum College remote site. This software isinexpensive and commercially available through numeroussources. All aspects of the diffractometer operation and pro-cessing of the experimental diffraction data to ultimately solveand refine the crystal structure of the compound were car-ried out using the Bruker AXS Single Crystal XRD suite ofprograms (SHELXTL and XSHELL) (8). As mentioned pre-viously, some specific information regarding the operationof these programs is presented within the SupplementalMaterial.W A detailed description of several of these programswas previously published and can be referenced for additionalinformation (9). More detailed guides are also available (10).The Bruker AXS programs were obtained at no charge toMuskingum College through participation in the YSU–PUIUDC. Membership in this consortium is still open to PUI’sby contacting A. D. Hunter at YSU. Similar PUI diffractionconsortia have been formed elsewhere (e.g., Central StatesX-ray Diffraction Consortium directed by M. R. Bond atSoutheast Missouri State University or by K. Kantardjieff atCalifornia State University Fullerton) and may be open tonew members.

Acknowledgments

MZ was supported by NSF grant 0111511. The diffrac-tometer was funded by NSF grant 0087210, by the OhioBoard of Regents grant CAP-491, and by YSU. Some of thecrystallographic education materials were funded by NSF9980921.

WSupplemental Material

Details of each of the experimental stages and alternativeoptions, copies of the student handouts, and a presentationdeveloped by A. D. Hunter that covers some of the basics ofcrystallography are available in this issue of JCE Online.

Literature Cited

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 Crys-tallographic Annual Meeting, May 25, 1999. (c) Hunter,A. D.; DiMuzio, S. J. American Chemical Society Divi-sion of Chemical Education, University of Michigan at AnnArbor, 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 Crystallogra-phy Association Annual Meeting, Reading University,Reading, England, Apr 8, 2001; CP-17. (f ) Hunter, A. D.;DiMuzio, S. J. 222nd American Chemical Society NationalMeeting, 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 NationalMeeting, Orlando, FL, Apr 2002. (h) Hunter, A. D.;DiMuzio, S. J.; McSparrin, L.; Snyder, W. The Fall 2002American Chemical Society Conference, Boston, MA, Aug2002.

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 TricarbonylChemistry. In Inorganic Experiments; Woollins, J. D., Ed.;VCH: New York, 2003; pp 364–367.

5. Zeller, M.; Hunter, Allen D.; Regula, Jody L.; Szalay, PaulS. 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 X-ray Solutions, 1998. http://www.bruker-axs.de/ (accessed Jul2005).

9. Crundwell, G.; Phan, J.; Kantardieff, K. A. J. Chem. Educ.1999, 76, 1242.

10. Hunter, A. D. Allen Hunter’s Youngstown State UniversityX-Ray Structure Analysis Lab Manual: A Beginner’s Introduc-tion, Fall 1998 Version F98D1 1997, 1998, 275 pages. Themanual has been released electronically as pdf files to ap-proximately 200 individuals at over 150 universities aroundthe world. Described in J. Chem. Educ. 1999, 76, 163 andin the ACA and IUCr Newsletters. For the CompleteManual, see: http://www.as.ysu.edu/~adhunter/YSUSC/Manual/Manual.W99D1.pdf (accessed Jul 2005). For theCovers 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 XIVon Growing Single Crystals, see: http://www.as.ysu.edu/~adhunter/YSUSC/Manual/ChapterXIV.pdf (accessed Jul2005).

1

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 (η6-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

2

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 (η6-p-

fluoroaniline)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

3

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.

4

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

5

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.10

6

The students were instructed to continue to refine their structures until they reached

certain standard crystallographic conditions. 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). 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.

7

Handout Given to the Students

Experiment X: Single crystal X-ray diffraction Objective: Work in conjuction with your instructor and individually to determine the crystal structure of (η6-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 nonhydrogen 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.

8

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 K� 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: �3

Z:

Density (calculated): Mg/m3

Absorption coefficient: mm-1

F(000): the number of electrons in the unit cell

Crystal size: 0.663 × 0.265 × 0.120 mm

Crystal shape, color: block, yellow

Reflections collected:

Goodness-of-fit on F2:

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

9

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 (0.75 – 0.15 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

10

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 issingle 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 6.237. Go to <crystal> on the toolbar and select <Unit Cell> and check the settings. 6.2, 251.6, 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 �. 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.

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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 0.75000 and the maximum wait for frame file should be 0.000. Check that the cell parameters (a, b, c, �, �, � – 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 = 100. 5. Go to “advanced integrate” (bottom left button). Check the following parameters: Model Profiles: I/� = 5.0000 Fraction = 0.0500 I/� threshold = 4.0000 Resolution lower limit = 9999.0000 Active frame ½ width = 7 Correction to intensity eds’s 0.00 and 1.00 6. 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

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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 (e.g. 03ps01am.hkl) filenamem.p4p (e.g. 03ps01am.p4p) filenamem.raw (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. (eg. 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 the unit cell contents. Type the numbers of each atom you are expecting in your

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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 2000”. 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

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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.

1

Introduction toX-Ray Diffraction

Chemistry 1516

Introduction to Diffraction & X-Ray Crystallography

2

The States of MatterOrder & Disorder

Ordering Types– Positional Order– Orientational Order

Ordering Range– Short Range– Long Range

2

Introduction to Diffraction & X-Ray Crystallography

3

The States of MatterDisordered Phases

Phase Types– Plasma Phase– Gas Phase– Liquid Phase

Degree of Order– None to Limited

Introduction to Diffraction & X-Ray Crystallography

4

The States of MatterThe Solid Phase

Solid Types– Amorphous Materials

• Glass– Crystalline Materials

• Powders• Single Crystals

Degree of Order– None to Almost Complete

3

Introduction to Diffraction & X-Ray Crystallography

5

The States of MatterNeither Fish Nor Fowl

Liquid Crystalline Materials– Molecular Shapes– Consumer Displays

Degree of Order– Partial Positional and/or Orientational

Introduction to Diffraction & X-Ray Crystallography

6

DiffractionLight & EM Radiation

Electromagnetic Radiation

4

Introduction to Diffraction & X-Ray Crystallography

7

DiffractionWaves & EM Radiation

Characteristics of Light - λ, φ, A

Introduction to Diffraction & X-Ray Crystallography

8

DiffractionX-Rays & EM Radiation

λ ≈ 1Å = 1×10-10m ≈ Atomic Dimensions

5

Introduction to Diffraction & X-Ray Crystallography

9

Diffraction of WavesSingle Slit

Direction ofTravel

Bre

akw

a te r

Br e

akw

ate r

Introduction to Diffraction & X-Ray Crystallography

10

Diffraction of WavesTwo Slits

Direction ofTravel of the

Incident Waves

Bre

akw

ater

Bre

a kw

ater

0 0 0

1 0 0

2 0 0

-1 0 0

-2 0 0

Constructive Inteference (Positive Peak)

Destructive Interference (Zero Height)

Constructive Inteference (Negative Peak)

6

Introduction to Diffraction & X-Ray Crystallography

11

Diffraction of WavesConstructive & Destructive Interference

Introduction to Diffraction & X-Ray Crystallography

12

DiffractionDiffraction Gratings & Reciprocal Space

⇒

ICE Slides

7

Introduction to Diffraction & X-Ray Crystallography

13

DiffractionUnit Cells & Contents ⇒ Diffraction

Pattern

⇒

Introduction to Diffraction & X-Ray Crystallography

14

DiffractometerSchematic

X-Ray Source

Monochromator andCollimator

Crystal

Goniometer

Beam StopDetector

2 θ

8

Introduction to Diffraction & X-Ray Crystallography

15

Diffractometers at YSUDiffraction Lab

Introduction to Diffraction & X-Ray Crystallography

16

Diffractometers at YSUP4s

9

Introduction to Diffraction & X-Ray Crystallography

17

Diffractometers at YSUP4s

Introduction to Diffraction & X-Ray Crystallography

18

Diffractometers at YSUAPEX

10

Introduction to Diffraction & X-Ray Crystallography

19

Diffractometers at YSUAPEX

Introduction to Diffraction & X-Ray Crystallography

20

X-Ray Structure Solution

Diffraction Peaks– Peak Numbering (hkl)– Peak Intensity– No Peak Phase!

11

Introduction to Diffraction & X-Ray Crystallography

21

Rotation Camera

Introduction to Diffraction & X-Ray Crystallography

22

Rotation Photographs

12

Introduction to Diffraction & X-Ray Crystallography

23

Rotation PhotographsInformation

Is the Sample Crystalline?What are the Unit Cell Parameters?

x

y

z

a

b

c

α

γ

β

Unit Cell Angles - α, β, γUnit Cell Lengths - a, b, c

Introduction to Diffraction & X-Ray Crystallography

24

Unit CellParameters

x

y

z

a

b

c

α

γ

β

Unit Cell Angles - α, β, γUnit Cell Lengths - a, b, c

13

Introduction to Diffraction & X-Ray Crystallography

25

Unit CellsCrystal Lattice & Unit Cells

Introduction to Diffraction & X-Ray Crystallography

26

Crystal Structure SolutionCrystal Lattice & Unit Cells

Unit Cell Parameters ⇔

Locations of Diffraction Spots

14

Introduction to Diffraction & X-Ray Crystallography

27

Crystal Structure SolutionCrystal Content & Atoms

Introduction to Diffraction & X-Ray Crystallography

28

Crystal Structure SolutionCrystal Content & Atoms

Atomic Positions ⇔

Diffraction Spot Intensities & Phases