Jmol-Application/C4/Symmetry-and-Point-Groups/English
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Slide Number 1
Title Slide |
Welcome to this tutorial on Symmetry and Point Group in Jmol. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to
1. Draw line, that is axis through atoms in a molecule. 2. Spin and rotate the molecule along the axis. 3. Draw plane through atoms in a molecule. |
Slide Number 3
Learning Objectives |
4. And demonstrate point group classification. |
Slide Number 4
Pre-requisites |
To follow this tutorial you should have,
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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
Symmetry Elements |
Often, symmetry in molecules is described in terms of symmetry elements like:
Plane of symmetry Center of symmetry etc
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Cursor on Jmol panel. | Let us begin this tutorial by drawing C3 rotational axis through atoms in a model of methane.
I have already opened the Jmol window. Click on modelkit menu to get the ball and stick model of methane on the panel. |
Cursor on the panel. | Label the atoms in the methane molecule by using display menu in the tool bar. |
Click on Display menu, scroll down to Label. From the sub-menu click on Number option. | Click on Display, scroll down to Label and Click on Number option. |
Cursor on the panel. | All the atoms in the methane molecule are now numbered.
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Click on File menu, scroll down to Console and click. | To open the Console click on File menu.
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Cursor on the panel. | Console window opens on the screen. |
Cursor on the Console. | We will use draw keyword in the command line to draw lines and planes. |
Slide Number 7
Jmol Script Commands |
Detailed information on Jmol script commands is available at this website.
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Open the web page using firefox web browser. chemapps.stolaf.edu/jmol/docs/
Cursor on the webpage. |
Open the website in any web browser.
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Click on the word “draw” | Scroll down and Click on word draw in the list.
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Scroll down the page. | This is followed by information regarding the use of the keyword. |
Cursor on Jmol panel. | Let us now go back to the Jmol panel.
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At the dollar prompt type,
draw line1 250 (atomno=1) (atomno=2)
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To draw a line that represents C3 rotational axis:
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Cursor on the panel. | Observe the panel.
A line passing through atoms 1 and 2 is drawn on the model of methane.
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At the dollar prompt, type
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We can draw more than one line on a given model.
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Cursor on the panel. | Now on the panel we have methane with C2 and C3 rotational axes. |
At the dollar prompt, type
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To rotate along the line 1 that is C3 axis , type the following command
(rotate space dollar line1 space 60)
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Cursor on the panel. | Observe the rotation along line1. |
At the $ prompt type,
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To spin the molecule along line1 type the following command.
(spin space dollar line1 space 180 space 60)
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Cursor on the panel. | On panel we see the methane model spin along line1, that is C3 axis. |
Slide Number 8
Assignment |
As an assignment
1. Draw line representing C3 axis of symmetry in a model of ethane.
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Cursor on the panel. | Back to the Jmol panel.
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Cursor on the Console. | To do so, first delete the lines on the methane model by typing the following command.
(draw space off) Press enter |
Cursor on the panel.
draw plane1 300 plane (atomno=1) (atomno=2) Press enter |
To draw reflection plane going through atoms 1, 2 and 3 of the methane molecule:
press enter. |
Cursor on the panel | Observe the reflection plane going through atoms 1, 2 and 3 in the methane molecule. |
Cursor on the panel. | To draw a second reflection plane through atoms, 1, 4 and 5: |
Press up arrow key and edit the command.
Delete 1 in plane1 and type 2. Delete 3 in atomno3 and type 5. |
In the console press up arrow key and edit the command as follows:
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At the $ prompt type,
;color dollar plane2 blue
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Also to change the color of the plane type the following command.
;color $plane2 blue (semicolon color space dollar plane2 space blue) press enter. |
Cursor on the panel. | On the panel we see the two reflection planes in the methane molecule. |
Cursor on the panel. | Using Jmol we can also show point group classification for methane as follows.
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Cursor on the Console. | In the console type,
(draw space off) Press enter |
At the dollar prompt on the console, type,
draw pointgroup
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To display all the possible symmetry elements for methane:
Type the following command in the console.
(draw space pointgroup) press enter. |
Cursor on the panel. | We see the symmetry elements of methane displayed on the panel. |
At the $ prompt, type,
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To find out the point group classification for methane, type the following command.
(calculate space pointgroup) press enter |
Cursor on the console. | Td the point group of methane molecule, is displayed on the console. |
Cursor on the panel. | Another classic example for point group demonstration is allene.
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Cursor on the panel. | We can also download the structure of allene from chemical structure database.
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Cursor on the console.
Press up arrow key till you get, draw point group press enter. |
To display all possible symmetry elements for allene:
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Cursor on the panel. | Observe the panel, we see all possible symmetry elements for allene. |
Press up arrow key again, till you get
calculate point group press enter |
To get the point group classification for allene.
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Cursor on the console. | The point group classification for allene, that is D2d is displayed on the Console. |
Cursor on the panel. | Similarly you can download molecules of your choice and calculate their point group. |
Slide Number 9
Summary |
Let's summarize, in this tutorial we learnt to
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Slide Number 10
Summary |
4. And demonstrate point group classification using examples of methane and allene. |
Slide Number 11
Assignment |
As an assignment,
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Slide Number 12
Acknowledgement |
This video summarizes the Spoken Tutorial project.
If you do not have good bandwidth, you can download and watch it |
Slide Number 13 | We Conduct workshops using spoken tutorials and
give certificates. please contact us. |
Slide number 14 | The spoken-tutorial project is funded by NMEICT, MHRD govt of India. |
This is Snehalatha from IIT Bombay signing off.
Thank you for joining. |