Jmol-Application/C4/Symmetry-and-Point-Groups/English

Visual Cue	Narration
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, Knowledge of undergraduate 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 Symmetry Elements	Often, symmetry in molecules is described in terms of symmetry elements like: Axis of symmetry Plane of symmetry Center of symmetry etc We will use Jmol to display these symmetry elements in a molecule.
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. We need to write commands in the console to draw lines and planes through atoms.
Click on File menu, scroll down to Console and click.	To open the Console click on File menu. Scroll down to Console and click on it.
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. www.chemapps.stolaf.edu/jmol/docs/
Open the web page using firefox web browser. chemapps.stolaf.edu/jmol/docs/ Cursor on the webpage.	Open the website in any web browser. A web page opens with a list of keywords used for writing script commands in Jmol.
Click on the word “draw”	Scroll down and Click on word draw in the list. A page opens with details about the draw keyword. A general syntax for the draw command is given at the top of the page.
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. I am using Kmag screen magnifier to magnify the console window.
At the dollar prompt type, draw line1 250 (atomno=1) (atomno=2) Press enter	To draw a line that represents C3 rotational axis: Type the following command at the dollar prompt in the console. draw line1 250 (atomno=1) (atomno=2) The command line begins with the word “draw”, followed by object ID. Number 250 in the command line refers to the length of the line. This is followed by the position of the line; With in brackets atom number equal to 1 and atom number equal to 2. Press enter.
Cursor on the panel.	Observe the panel. A line passing through atoms 1 and 2 is drawn on the model of methane. This line can now act as an axis for rotation.
At the dollar prompt, type draw line2 {2 0 0} {0 0 0} {-2 0 0};color $line2 blue Press enter	We can draw more than one line on a given model. To draw C2 rotational axis: Type the following command in the console. draw line2 {2 0 0} {0 0 0} {-2 0 0};color $line2 white. In this command, numbers in curly brackets indicate the Cartesian coordinates for the line. Followed by a command to specify the color of the line. press enter.
Cursor on the panel.	Now on the panel we have methane with C2 and C3 rotational axes.
At the dollar prompt, type rotate $line1 50 Press enter	To rotate along the line 1 that is C3 axis , type the following command rotate $line1 60 (rotate space dollar line1 space 60) The number 60 refers to the degrees of rotation. press enter.
Cursor on the panel.	Observe the rotation along line1.
At the $ prompt type, Spin $line1 180 50 Press enter	To spin the molecule along line1 type the following command. spin $line1 180 50 (spin space dollar line1 space 180 space 60) The number 180 refers to degrees of rotation and 60 refers to the speed of rotation) Press enter.
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. 2. And spin the model along C3 axis.
Cursor on the panel.	Back to the Jmol panel. We can also draw planes going through a set of atoms in a molecule.
Cursor on the Console.	To do so, first delete the lines on the methane model by typing the following command. draw off (draw space off) Press enter
Cursor on the panel. At the $ prompt type, 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: Type the following command in the console. draw plane1 300 plane (atomno=1) (atomno=2) (atomno=3) Number 300 in the command indicates the size of the plane. 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: Edit plane1 to plane2, and atomno2 to 4 and atomno3 to 5.
At the $ prompt type, ;color dollar plane2 blue Press enter	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. Lets clear the planes drawn on methane molecule on the panel.
Cursor on the Console.	In the console type, draw off (draw space off) Press enter
At the dollar prompt on the console, type, draw pointgroup press enter	To display all the possible symmetry elements for methane: Type the following command in the console. draw pointgroup (draw space pointgroup) press enter.
Cursor on the panel.	We see the symmetry elements of methane displayed on the panel.
At the $ prompt, type, calculate point group press enter	To find out the point group classification for methane, type the following command. calculate pointgroup (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. We can draw the structure of allene on the panel using the modelkit menu. Or
Cursor on the panel.	We can also download the structure of allene from chemical structure database. If you are connected to internet , click on the File menu scroll down to Get Mol and, Type “allene” in the text box . Click on OK.
Cursor on the console. Press up arrow key till you get, draw point group press enter.	To display all possible symmetry elements for allene: Press up arrow key at the dollar prompt on the console till you get this command. draw pointgroup press enter
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. Again on the console press up arrow key till you get the command calculate pointgroup press enter
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 1. Draw lines that is C2 and C3 rotational axes through atoms in methane molecule. 2. Spin and rotate the molecule along the axis. 3. Draw reflection plane through atoms in methane molecule.
Slide Number 10 Summary	4. And demonstrate point group classification using examples of methane and allene.
Slide Number 11 Assignment	As an assignment, 1. Draw reflection plane in a model of dichloromethane. 2. And find out the point group classification for ammonia and benzene.
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.

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Snehalathak