Difference between revisions of "Jmol-Application/C4/Symmetry-and-Point-Groups/English-timed"
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| − | | We will use '''Jmol''' to display these symmetry | + | | We will use '''Jmol''' to display these '''symmetry element'''s in a molecule. |
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| − | | Console window opens on the screen. | + | | The Console window opens on the screen. |
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| 02:04 | | 02:04 | ||
| − | | We will use '''draw '''keyword in the command line to draw lines and planes. | + | | We will use '''draw '''keyword in the '''command line''' to draw lines and planes. |
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| 02:19 | | 02:19 | ||
| − | | A web-page opens with a list of keywords used for writing script | + | | A web-page opens with a list of keywords used for writing '''script command'''s in Jmol. |
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| 02:26 | | 02:26 | ||
| − | | Scroll down and click on word '''draw '''in the list. | + | | Scroll down and click on the word '''draw '''in the list. |
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| 03:04 | | 03:04 | ||
| − | | The '''command line''' begins with the word | + | | The '''command line''' begins with the word “draw”, followed by '''object ID'''. |
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| − | | In this command, the numbers in curly brackets indicate the '''Cartesian coordinates''' for the line | + | | In this command, the numbers in the curly brackets indicate the '''Cartesian coordinates''' for the line |
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| 03:59 | | 03:59 | ||
| − | | Now, on the panel, we have methane with C2 and C3 '''rotational axes'''. | + | | Now, on the panel, we have methane with '''C2''' and '''C3''' '''rotational axes'''. |
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| − | | | + | | "spin $line1 180 60" '''(spin space dollar line1 space 180 space 60)'''. |
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| 04:48 | | 04:48 | ||
| − | | On panel, we see the '''methane''' model spin along '''line1''', that is '''C3 axis'''. | + | | On the panel, we see the '''methane''' model spin along '''line1''', that is '''C3 axis'''. |
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| 05:02 | | 05:02 | ||
| − | | and spin the model along '''C3 axis'''. | + | | and '''spin''' the model along '''C3 axis'''. |
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| To do so, first delete the lines on the '''methane''' model by typing the following command. | | To do so, first delete the lines on the '''methane''' model by typing the following command. | ||
| − | + | "draw off" '''(draw space off)'''. Press '''Enter'''. | |
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| 05:41 | | 05:41 | ||
| − | | Observe the reflection plane going through atoms 1, 2 and 3 in the methane molecule. | + | | Observe the '''reflection plane''' going through atoms 1, 2 and 3 in the methane molecule. |
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| 06:01 | | 06:01 | ||
| − | | Edit '''plane1''' to '''plane2''' and '''atomno2''' to 4 and '''atomno3''' to 5. | + | | Edit '''plane1''' to '''plane2''' and '''atomno2''' to '''4''' and '''atomno3''' to '''5'''. |
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| 06:12 | | 06:12 | ||
| − | | Also to change the color of the plane, type the following command: | + | | Also, to change the color of the plane, type the following command: |
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| 06:17 | | 06:17 | ||
| − | | | + | | ";color $plane2 blue" '''(semicolon color space dollar plane2 space blue)'''. Press '''Enter'''. |
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| 06:47 | | 06:47 | ||
| − | | To display all the possible symmetry | + | | To display all the possible '''symmetry element'''s for methane: type the following command in the console. |
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| 06:54 | | 06:54 | ||
| − | | | + | | "draw pointgroup" '''(draw space pointgroup)'''. Press '''Enter'''. |
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| To find out the '''point group''' classification for '''methane''', type the following command: | | To find out the '''point group''' classification for '''methane''', type the following command: | ||
| − | + | "calculate pointgroup" (calculate space pointgroup). Press '''Enter'''. | |
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| 07:37 | | 07:37 | ||
| − | | If you are connected to internet- click on the '''File''' menu, scroll down to '''Get Mol ''' and type: | + | | 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'''. |
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| 07:48 | | 07:48 | ||
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| 07:52 | | 07:52 | ||
| − | | Press up-arrow key at the '''dollar prompt''', on the console, till you get this command | + | | Press up-arrow key at the '''dollar prompt''', on the console, till you get this command: |
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| 08:02 | | 08:02 | ||
| − | | Observe the panel. We see all possible symmetry elements for 'allene'. | + | | Observe the panel. We see all possible symmetry elements for '''allene'''. |
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| 08:09 | | 08:09 | ||
| − | | To get the '''point group''' classification for allene- | + | | To get the '''point group''' classification for allene - |
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| 08:12 | | 08:12 | ||
| − | | Again on the console, press up-arrow key till you get the command | + | | Again, on the console, press up-arrow key till you get the command "calculate pointgroup". Press '''Enter'''. |
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| 08:21 | | 08:21 | ||
| − | | The point group classification for '''allene''', that is '''D2d, '''is displayed on the | + | | The point group classification for '''allene''', that is '''D2d, '''is displayed on the Console. |
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| 08:38 | | 08:38 | ||
| − | |* To draw lines, that is, C2 and C3 rotational axes through atoms in '''methane''' molecule. | + | |* To draw lines, that is, '''C2''' and '''C3''' '''rotational axes''' through atoms in '''methane''' molecule. |
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| 08:45 | | 08:45 | ||
| − | |* Spin and rotate the molecule along the axis. | + | |* '''Spin''' and '''rotate''' the molecule along the axis. |
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| 08:49 | | 08:49 | ||
| − | |* Draw reflection plane through atoms in '''methane''' molecule. | + | |* Draw '''reflection plane''' through atoms in '''methane''' molecule. |
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Revision as of 17:32, 2 June 2016
| | |
| 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 |
| 01:06 | * 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. |
| 03:27 | 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- |
| 04:56 | 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. |
| 05:59 | 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- |
| 09:02 | 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. |
