Jmol-Application/C3/Crystal-Structure-and-Unit-Cell/English

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Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Crystal Structure and unit cell in Jmol.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to,
  • Download CIF that is Crystallographic Information file from Crystallography Open Database.
  • Open CIF in Jmol.
  • Display unit cell and unit cell parameters on Jmol panel.
Slide Number 3

Learning Objectives

* And display crystal structures of different crystal systems.
  • For example Cubic, Hexagonal and Rhombohedral.
Slide Number 4

Pre-requisites

To follow this tutorial you should have

Knowledge of high school chemistry.

And familiar with operations from Jmol window.

If not, for relevant tutorials, please visit our website.

Slide Number 5

System Requirement

To record this tutorial, I am using,

Ubuntu Operating System version 14.04

Jmol version 12.2.32

Java version 7 and

Mozilla Firefox browser 35.0

Slide Number 6

Crystal Systems

Crystal structures are grouped under seven crystal systems.

This table shows the list of crystal systems and their corresponding lattice parameters.

Examples for crystals of various compounds and minerals are listed here.

Slide Number 6 We will display crystal structures of Sodium chloride, Graphite and Calcite on Jmol panel.
Slide Number 7

Crystallographic Information File (CIF)

To display the crystal structure on Jmol panel:

We need to download the Crystallographic Information File of a particular crystal.

CIF is a standard text file format for representing crystallographic information.

CIF format has the file extension .cif.

Slide Number 8

Crystallography Open Database (COD)

Crystallography Open Database is an open-access database.

The downloadable CIF are available at COD website.

The website can be accessed through the given link.

www.crystallography.net

Cursor on slide number 8 Let us open COD database website and download some CIF files.
Open www.crystallography.net in web browser. Here I have opened the COD website.
Cursor on the web page. On the left side of the page, information is divided under various headings.
Point the cursor to the headings Under the heading Accessing COD Data,

There are sub-headings like Browse, Search etc.

Click on “Search”


Scroll down the page.

Click on Search option.

A new page opens.

On the Search page we find many options to search for CIF files.

Click on “Hints and Tips

Scroll down the page.

Click on Hints and Tips link.

A page opens with information on how to use search options effectively.

Cursor on the page Go back to the Search page.
Cursor on the page. We can search for the crystal structure using
  • COD ID
  • OpenBabel Fastsearch or
  • Type the name of the chemical or mineral in the text box.
Cursor on the text box. For example to search for the CIF file of Sodium Chloride:
Type “Halite” in the text box. Type “Halite” which is the mineral name for sodium chloride, in the text box.
Type Na and Cl in the elements box Scroll down to elements box.

Type the symbol for Sodium that is Na and Cl for chloride.

Cursor on the Number of distinct elements box. Scroll down to, Number of distinct elements box.

Here we have an option to type minimum and maximum elements.

Type 2 in the minimum box. Type 2 in the minimum box, if you want crystal structure with only two elements.

That is Sodium and Chloride .

Click on send button. Click on Send button.
Cursor on the web page. A web page opens with crystal structure data files for Sodium chloride.
Right click on COD ID. Right click on the COD ID and click on “open the link in a new tab”.

This page has detailed information regarding the particular crystal structure.

Press back arrow. Go back to the database web page.
Click on “archive of CIF files” located on the right-hand side of the page.

A dialog box opens on the screen,

Select Open with option.

Click on OK button.

Click on the link “archive of CIF files” located on the right-hand side of the page.

A dialogue box opens on the screen,

Select Open with option.

Click on OK button.

Cursor on the page. A folder with many CIF files for sodium chloride crystal opens on the screen.
Click on CIF number 9003308

Click on “Extract” button (on the tool bar)

Select the files you want to download by clicking on them.

Click on “Extract” button on the tool bar.

Click on Extract button. Save the files at a convenient location on your system.

Click on Extract. Close the window.

Cursor on the search page. Go back to the search page.

Now download CIF files for graphite and calcite using same procedure as before.

Cursor on the search page. We will now open the CIF file of sodium chloride in Jmol.
Open a new Jmol window.

Cursor on Jmol panel.

Here I have opened the Jmol window.
Navigate to “CIF-files” folder on the desktop. Select “nacl.cif”. Click on “Open a file” icon in the tool bar.

Navigate to the location of the CIF file of sodium chloride.

which we have downloaded from the COD database.

Click on Open.

Cursor on the panel. Unit cell of sodium chloride crystal opens on the screen.
Slide Number 9

Unit cell

Unit cell is the smallest repeating unit in a crystal.

Stacking of these unit cells in 3 dimensions will form the basis of the crystal structure.

Cursor on Jmol panel. Back to the Jmol Panel.
Cursor on the panel. Relevant data for unit cell is displayed on the left-hand side of the panel.

It begins with the space group classification.

Highlight the vectors a, b and c.

Angles alpha, beta and gamma.

Sodium Chloride belongs to the cubic lattice system. Hence the vectors a, b and c are equal.

The angles alpha, beta and gamma are 90 degrees.

Right click the mouse button. Right click to open the pop-up menu.
Scroll down to Symmetry option.

Scroll down the sub-menu.

Highlight the reload options.

Scroll down to Symmetry option.

In the sub-menu we have options to display symmetry elements.

We can also display blocks of unit cells using the options in the sub-menu.

Click on Reload {1 1 1} For example click on Reload {1 1 1} option.
Cursor on the panel. On the panel we have a unit cell block, showing face center cubic lattice.
Open the pop-up menu, scroll down to style then scheme and click on CPK Spacefill. To change the display;

Open the pop-up menu, scroll down to style then scheme.

And click on CPK Spacefill.

Cursor on the panel. Here on the panel we have the crystal structure in CPK display.
Right click the mouse button and click on Reload {4 4 4 6 6 6 1} Open the pop-up menu again scroll down to symmetry and click on Reload {4 4 4 6 6 6 1}option.

This option loads the 27 cell block on Jmol panel.

Open the pop-up menu and click on Reload {1 1 1} option. Open the pop-up menu go to symmetry go back to Reload {1 1 1} option.
Open the pop-up menu scroll down to symmetry in the sub-menu.

Click on mirrorplane x z y option .

To display the symmetry elements, open the pop-up menu again.

Scroll down to symmetry in the sub-menu and click on mirrorplane (x z y) option .

Cursor on the sub-menu

Click on the first option that shows space group.

On the panel we have a cubic lattice with mirrorplane (x z y) displayed.
Cursor on the panel. Let us now load the CIF file for graphite ,which belongs to hexagonal crystal system.
Click on “Open a file” option on the tool bar. As shown earlier use Open a file option to load the CIF file for graphite on the panel.
Cursor on the panel. Unit cell for graphite opens on the panel.
Cursor on the unit cell parameters. Observe the unit cell parameters,

The vectors a equal to b but not equal to c.

Cursor on the unit cell parameters. Angles, alpha and beta equal to 90 degrees.

And gamma equal to 120 degrees.

Open the pop-up menu go to Symmetry option and click on Reload {444 666 1} Open the pop-up menu scroll down to Symmetry and click on Reload {444 666 1} option.
Cursor on the panel. Hexagonal lattice arrangement of atoms is shown on the screen.
Open the pop-up menu go to style, go to scheme click on wireframe option. To change the display , open the pop-up menu go to style, go to scheme click on wireframe option.
Cursor on the panel. Similarly I have opened a CIF file of mineral calcite on the panel.
Cursor on the panel. Calcite belongs to the rhombohedral crystal system.
Cursor on the panel. You can open the CIF of any crystal system and explore the structure and symmetry options.
Slide Number 10

Summary

Let's summarize,

In this tutorial we have learnt to

  • Download CIF from Crystallography Open Database.
  • Open CIF in Jmol.
  • Display unit cell and unit cell parameters.
Slide Number 11

Summary

* And display crystal structures of sodium chloride, graphite and calcite.
Slide Number 12

Assignment

For assignment

Download CIF for quartz crystal from COD database.

Display unit cell on Jmol panel and explore the symmetry options.

Slide Number 13

Acknowledgement

This video summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

Slide Number 14 We Conducts workshops using spoken tutorials and

Give certificates.

Please contact us.

Slide number 15 The spoken tutorial project is funded by NMEICT-MHRD govt of India.
Slide number 15 This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Snehalathak