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

Time	Narration
00:01	Welcome to this tutorial on Symmetry and Point Groups in Jmol.
00:06	In this tutorial, we will learn to:
00:08	Draw line, that is, axis through atoms in a molecule.
00:12	Spin and rotate the molecule along the axis.
00:17	Draw plane through atoms in a molecule.
00:21	And demonstrate point group classification.
00:25	To follow this tutorial, you should have knowledge of undergraduate Chemistry and familiar with operations from Jmol window.
00:35	If not, for relevant tutorials, please visit our website.
00:39	To record this tutorial, I am using:
00:42	Ubuntu Operating System version 14.04
00:46	Jmol version 12.2.32
00:50	Java version 7 and * Mozilla Firefox browser 35.0.
00:57	Often, symmetry in molecules is described in terms of symmetry elements like:
01:03	Axis of symmetry
01:05	Plane of symmetry Center of symmetry etc.
01:09	We will use Jmol to display these symmetry elements in a molecule.
01:14	Let us begin this tutorial by drawing C3 rotational axis through atoms in a model of methane.
01:22	I have already opened the Jmol window.
01:25	Click on modelkit menu to get the ball and stick model of methane on the panel.
01:31	Label the atoms in the methane molecule by using Display menu in the tool bar.
01:37	Click on Display, scroll down to Label and click on Number option.
01:43	All the atoms in the methane molecule are now numbered.
01:47	We need to write commands in the console to draw lines and planes through atoms.
01:53	To open the Console, click on File menu.
01:57	Scroll down to Console and click on it.
02:01	The Console window opens on the screen.
02:04	We will use draw keyword in the command line to draw lines and planes.
02:10	Detailed information on Jmol script commands is available at this website.
02:15	Open the website in any web browser.
02:19	A web-page opens with a list of keywords used for writing script commands in Jmol.
02:26	Scroll down and click on the word draw in the list.
02:31	A page opens with details about the draw keyword.
02:36	A general syntax for the draw command is given at the top of the page.
02:42	This is followed by information regarding the use of the keyword.
02:47	Let us now go back to the Jmol panel.
02:51	I am using Kmag screen magnifier to magnify the console window.
02:55	To draw a line that represents C3 rotational axis,
02:59	type the following command at the dollar prompt, in the console.
03:04	The command line begins with the word “draw”, followed by object ID.
03:10	Number 250 in the command line refers to the length of the line.
03:15	This is followed by the position of the line.
03:18	Within brackets, atom number equal to 1 and atom number equal to 2. Press Enter.
03:26	Observe the panel.A line passing through atoms 1 and 2 is drawn on the model of methane.
03:33	This line can now act as an axis for rotation.
03:37	We can draw more than one line on a given model.
03:41	To draw C2 rotational axis, type the following command in the console.
03:47	In this command, the numbers in the curly brackets indicate the Cartesian coordinates for the line
03:54	followed by a command to specify the color of the line. Press Enter.
03:59	Now, on the panel, we have methane with C2 and C3 rotational axes.
04:05	To rotate along the line 1, that is C3 axis, type the following command:
04:12	rotate $line1 60 (rotate space dollar line1 space 60).
04:18	The number 60 refers to the degrees of rotation. Press Enter.
04:24	Observe the rotation along line1.
04:27	To spin the molecule along line1, type the following command:
04:32	"spin $line1 180 60" (spin space dollar line1 space 180 space 60).
04:39	The number 180 refers to degrees of rotation and 60 refers to the speed of rotation. Press Enter.
04:48	On the panel, we see the methane model spin along line1, that is C3 axis.
04:55	As an assignment-Draw line representing C3 axis of symmetry, in a model of ethane
05:02	and spin the model along C3 axis.
05:06	Back to the Jmol panel.
05:08	We can also draw planes going through a set of atoms in a molecule.
05:12	To do so, first delete the lines on the methane model by typing the following command. "draw off" (draw space off). Press Enter.
05:24	To draw reflection plane going through atoms 1, 2 and 3 of the methane molecule:
05:31	type the following command in the console.
05:35	Number 300 in the command indicates the size of the plane. Press Enter.
05:41	Observe the reflection plane going through atoms 1, 2 and 3 in the methane molecule.
05:49	To draw a second reflection plane through atoms 1, 4 and 5:
05:55	In the console, press up-arrow key and edit the command as follows.
06:01	Edit plane1 to plane2 and atomno2 to 4 and atomno3 to 5.
06:12	Also, to change the color of the plane, type the following command:
06:17	";color $plane2 blue" (semicolon color space dollar plane2 space blue). Press Enter.
06:24	On the panel, we see the two reflection planes in the methane molecule.
06:29	Using Jmol, we can also show point group classification for methane as follows.
06:36	Let's clear the planes drawn on methane molecule, on the panel.
06:41	In the console, type: draw off (draw space off). Press Enter.
06:47	To display all the possible symmetry elements for methane: type the following command in the console.
06:54	"draw pointgroup" (draw space pointgroup). Press Enter.
06:59	We see the symmetry elements of methane displayed on the panel.
07:04	To find out the point group classification for methane, type the following command: "calculate pointgroup" (calculate space pointgroup). Press Enter.
07:14	Td, the point group of methane molecule, is displayed on the console.
07:20	Another classic example for point group demonstration is allene.
07:25	We can draw the structure of allene, on the panel, using the modelkit menu. Or, we can also download the structure of allene from chemical structure database.
07:37	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.
07:48	To display all possible symmetry elements for allene:
07:52	Press up-arrow key at the dollar prompt, on the console, till you get this command:
07:59	draw pointgroup . Press Enter.
08:02	Observe the panel. We see all possible symmetry elements for allene.
08:09	To get the point group classification for allene -
08:12	Again, on the console, press up-arrow key till you get the command "calculate pointgroup". Press Enter.
08:21	The point group classification for allene, that is D2d, is displayed on the Console.
08:28	Similarly, you can download molecules of your choice and calculate their point group.
08:34	Let's summarize. In this tutorial, we learnt:
08:38	To draw lines, that is, C2 and C3 rotational axes through atoms in methane molecule.
08:45	Spin and rotate the molecule along the axis.
08:49	Draw reflection plane through atoms in methane molecule.
08:54	And demonstrate point group classification using examples of methane and allene.
09:01	As an assignment-Draw reflection plane in a model of dichloromethane
09:07	and find out the point group classification for ammonia and benzene.
09:12	This video summarizes the Spoken Tutorial project.
09:15	If you do not have good bandwidth, you can download and watch it.
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09:27	The spoken-tutorial project is funded by NMEICT, MHRD, govt of India.
09:33	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14