CHE 450G: Practical Inorganic Chemistry

U of KY Dept of Chemistry

Instructions for CrystalDesigner

What is CrystalDesigner, anyway?

CrystalDesigner is a computer program that will draw representations of solid state structures. It is published by CrystalStructure Design AS in Norway. It can display solid state lattices with ease, including ball and stick as well as polyhedral representations (or hybrids thereof).

NOTE: For best performance, you will want to run this program from a PowerPC. There are four of these available in the Chemistry-Physics computer lab! You can also find the program on the file server in the basement of Grehan Hall Lab (Journalism).

If you'd like a copy to use on your own computer you can download a free evaluation copy of CrystalDesigner from the manufacturer's web site. While you can not print or copy with the free version, you can generate and save structures. Therefore, you only need to use the licensed version to print. If you want to purchase the program, student licenses are $99.

You can also use CrystalDesigner on computers in the Inorganic research labs. Ask Drs. Ladipo or Selegue for information. In addition, you can print your files on a color laser printer (for free) on those computers.

Instructions

1. On the microlab Superserver in Chemistry-Physics or Grehan (Journalism) you will find a folder labelled Instructor's Software. Double click to open it. Open the folder titled CrystalDesigner 6.0.1 by double clicking on it.

2. Inside you will find the program in addition to a tutorial in MS Word format. You can also find a manual/tutorial on-line at http://www.crystaldesigner.no/UserGuide/Contents.html.

   For now, simply open (double click) the folder called Data Files.

3. If you click on the first data file, Al₂MgO₄, a bunch of windows will open, including 3 different views of the crystal structure.

4. Blow up one of the unit cell windows by clicking the second small box from the right in the window titlebar (System 8.x).

5. There will be two floating windows in front of your structure. One has nothing in it, so click on its close box (the square in the left side of its titlebar) to get rid of it. The other one looks like this:

   

   Top row: The arrow is a selection tool, the two-headed arrow lets you resize the drawing in the window and the icon on the far right allows you to freely rotate the unit cell in any direction by clicking the mouse and dragging.

   Rows 2 and 3: These let you rotate the unit cell or axes in the indicated directions by clicking and dragging. Click on one of these and try it!

   Projection: "Jumps" to a new view defined by Miller indices (something we haven't covered, but ask me if you want to know about them).

6. Play! Learn how to use it and then later on you can make a new file and type in the X-ray data for compounds that you make during the course such as YBa₂Cu₃O_7-x. These make great figures for your lab reports and presentations. Instructions are given below.

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   Tips and tricks

   Showing more than one unit cell:

   To see a larger or smaller chunk of solid you can pick a new size such as 3 x 3 x 3 unit cells from the Size menu. Alternatively, you can choose a size of your desire, including fractions of a unit cell.

   Showing bonds

   To show bonds choose Insert/Modify Bonds from the Bonds menu.

   Choose the atoms you wish to have displayed as bonded (for example Na and Cl) then click Add and then OK. You may need to go back and set bonding/distance criteria for these if too many or too few bonds are drawn.

   Showing specific planes of the crystal

   Select New Plane View from the Windows menu.

   You will be presented with a dialog asking which planes you wish to see. Again, these use Miller indices, but the planes will be displayed in preview mode for you.

   To see more of a plane use the Size menu and select Distance from the origin.

   To see a thicker slice of the structure use the Size menu and select Other Plane Size. This will bring up a dialog where you can select thicker slices. Note: these distances are in picometers (1 picometer = 1 Angstrom), so unless you ask for a slice thicker than 150 pm you probably won't see any difference!

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   Creating a new structure

   • Select New Structure from the File menu.

   

   • Select the Crystal System by using the pulldown menu (currently set to "None"). A number of new places to enter data will appear:

   

   • You can now select a Space Group by using the pulldown menu (you can not do this if the crystal system is "None").

   • Enter values for the unit cell parameters. The units are pm. 100 pm = 1 Angstroms.

   • Enter the Atom Positions. For each unique atom, put in the element, a label (such as Cu1, Cu2 etc.), the fractional coordinates and a radius. If you don't know the radius, hit the "Lookup" button and it will offer you some choices. Solid state oxides are ionic, so use ionic radii for your structures.

     To add new atoms select Add Atom Position from the Edit Menu.

   

   • From here, things are no different from the example files. Good luck.

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   Notes and Cautions

   • You can create polyhedral representations (such as those you've seen in the literature showing Cu-O square square pyramids etc.) by selecting Insert Polyhedra Around...Copper from the Polyhedra menu when you're in Unit Cell View.

   • The Color Shading option under the Render menu may take a long time to draw on a slow machine. Definitely try it if you are on a PPC machine.

   • Be careful about drawing large chunks (4 x 4 x 4 of the zeolite for example) unless you want to wait a while!

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