Difference between revisions of "Jmol-Application/C4/Symmetry-and-Point-Groups/English-timed"
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| − | | Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''. | + | |Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''. |
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| − | |" | + | |"color $plane2 blue" '''(semicolon color space dollar plane2 space blue)'''. Press '''Enter'''. |
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Latest revision as of 10:04, 29 March 2017
| 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. |
| 09:20 | We conduct workshops using spoken tutorials and give certificates. Please contact us. |
| 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. |
