Difference between revisions of "Jmol-Application/C4/Symmetry-and-Point-Groups/English-timed"

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{| Border =1
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{| border =1
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|<center>Time</center>
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|'''Time'''
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| <center>Narration</center>
+
|'''Narration'''
  
 
|-
 
|-
−
| 00:01
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|00:01
−
| Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''.
+
|Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''.
  
 
|-
 
|-
−
| 00:06
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|00:06
−
| In this tutorial, we will learn to:  
+
|In this tutorial, we will learn to:  
  
 
|-
 
|-
−
| 00:08
+
|00:08
−
|* Draw line, that is, '''axis''' through atoms in a molecule.
+
|Draw line, that is, '''axis''' through atoms in a molecule.
  
 
|-
 
|-
−
| 00:12
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|00:12
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|* '''Spin''' and rotate the molecule along the axis.
+
|'''Spin''' and rotate the molecule along the axis.
  
 
|-
 
|-
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| 00:17
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|00:17
−
|* Draw plane through atoms in a molecule.
+
|Draw plane through atoms in a molecule.
  
 
|-
 
|-
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| 00:21
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|00:21
−
|* And demonstrate '''point group''' classification.  
+
|And demonstrate '''point group''' classification.  
  
 
|-
 
|-
 
|00:25
 
|00:25
−
| To follow this tutorial, you should have knowledge of undergraduate Chemistry  and familiar with operations from '''Jmol window'''.
+
|To follow this tutorial, you should have knowledge of undergraduate Chemistry  and familiar with operations from '''Jmol window'''.
  
 
|-
 
|-
−
| 00:35
+
|00:35
−
| If not, for relevant tutorials, please visit our website.  
+
|If not, for relevant tutorials, please visit our website.  
  
 
|-
 
|-
−
| 00:39
+
|00:39
−
| To record this tutorial, I am using:
+
|To record this tutorial, I am using:
  
 
|-
 
|-
−
| 00:42
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|00:42
−
|* '''Ubuntu Operating System''' version 14.04
+
|'''Ubuntu Operating System''' version 14.04
  
 
|-
 
|-
−
| 00:46
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|00:46
−
|* '''Jmol''' version 12.2.32
+
|'''Jmol''' version 12.2.32
  
 
|-
 
|-
−
| 00:50
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|00:50
−
|* '''Java''' version 7  and * Mozilla Firefox browser 35.0.
+
|'''Java''' version 7  and * Mozilla Firefox browser 35.0.
−
|-
+
−
| 00:57
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−
|  Often, symmetry in molecules is described in terms of symmetry elements like:
+
  
 
|-
 
|-
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| 01:03
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|00:57
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|* Axis of symmetry  
+
|Often, symmetry in molecules is described in terms of symmetry elements like:
  
 
|-
 
|-
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| 01:05
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|01:03
−
|* Plane of symmetry
+
|Axis of symmetry  
  
 
|-
 
|-
−
| 01:06
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|01:05
−
|* Center of symmetry etc.
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|Plane of symmetry Center of symmetry etc.
  
 
|-
 
|-
−
| 01:09
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|01:09
−
| We will use '''Jmol''' to display these '''symmetry element'''s in a molecule.
+
|We will use '''Jmol''' to display these '''symmetry element'''s in a molecule.
  
 
|-
 
|-
−
| 01:14
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|01:14
−
| Let us begin this tutorial by drawing '''C3 rotational axis''' through atoms in a model of '''methane'''.  
+
|Let us begin this tutorial by drawing '''C3 rotational axis''' through atoms in a model of '''methane'''.  
  
 
|-
 
|-
−
| 01:22
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|01:22
−
| I have already opened the '''Jmol window'''.
+
|I have already opened the '''Jmol window'''.
  
 
|-
 
|-
−
| 01:25
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|01:25
−
| Click on '''modelkit '''menu to get the '''ball and stick''' model of '''methane''' on the panel.
+
|Click on '''modelkit '''menu to get the '''ball and stick''' model of '''methane''' on the panel.
  
 
|-
 
|-
−
| 01:31
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|01:31
−
| Label the atoms in the '''methane''' molecule by using '''Display''' menu in the tool bar.
+
|Label the atoms in the '''methane''' molecule by using '''Display''' menu in the tool bar.
  
 
|-
 
|-
−
| 01:37
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|01:37
−
| Click on '''Display,''' scroll down to '''Label '''and click on''' Number''' option.
+
|Click on '''Display,''' scroll down to '''Label '''and click on''' Number''' option.
  
 
|-
 
|-
−
| 01:43
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|01:43
−
| All the atoms in the '''methane '''molecule are now numbered.
+
|All the atoms in the '''methane '''molecule are now numbered.
  
 
|-
 
|-
−
| 01:47
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|01:47
−
| We need to write commands in the '''console''' to draw lines and planes through atoms.
+
|We need to write commands in the '''console''' to draw lines and planes through atoms.
  
 
|-
 
|-
−
| 01:53
+
|01:53
−
| To open the '''Console''', click on '''File''' menu.
+
|To open the '''Console''', click on '''File''' menu.
  
 
|-
 
|-
−
| 01:57
+
|01:57
−
| Scroll down to''' Console''' and click on it.
+
|Scroll down to''' Console''' and click on it.
  
 
|-
 
|-
−
| 02:01
+
|02:01
−
| The Console window opens on the screen.
+
|The Console window opens on the screen.
  
 
|-
 
|-
−
| 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.
  
 
|-
 
|-
−
| 02:10
+
|02:10
−
| Detailed information on '''Jmol script commands''' is available at this website.  
+
|Detailed information on '''Jmol script commands''' is available at this website.  
  
 
|-
 
|-
−
| 02:15
+
|02:15
−
| Open the website in any web browser.
+
|Open the website in any web browser.
  
 
|-
 
|-
−
| 02:19
+
|02:19
−
| A web-page opens with a list of keywords used for writing '''script command'''s in Jmol.
+
|A web-page opens with a list of keywords used for writing '''script command'''s in Jmol.
  
 
|-
 
|-
−
| 02:26
+
|02:26
−
| Scroll down and click on the word '''draw '''in the list.
+
|Scroll down and click on the word '''draw '''in the list.
  
 
|-
 
|-
−
| 02:31
+
|02:31
−
| A '''page''' opens with details about the '''draw '''keyword.  
+
|A '''page''' opens with details about the '''draw '''keyword.  
  
 
|-
 
|-
−
| 02:36
+
|02:36
−
| A general syntax for the '''draw''' command is given at the top of the '''page'''.
+
|A general syntax for the '''draw''' command is given at the top of the '''page'''.
  
 
|-
 
|-
−
| 02:42
+
|02:42
−
| This is followed by information regarding the use of the '''keyword'''.  
+
|This is followed by information regarding the use of the '''keyword'''.  
  
 
|-
 
|-
 
|02:47
 
|02:47
−
| Let us now go back to the '''Jmol panel'''.
+
|Let us now go back to the '''Jmol panel'''.
  
 
|-
 
|-
−
| 02:51
+
|02:51
−
| I am using '''Kmag '''screen magnifier to magnify the console window.
+
|I am using '''Kmag '''screen magnifier to magnify the console window.
  
 
|-
 
|-
−
| 02:55
+
|02:55
−
| To draw a line that represents '''C3 rotational axis''',  
+
|To draw a line that represents '''C3 rotational axis''',  
  
 
|-
 
|-
−
| 02:59
+
|02:59
−
| type the following command at the dollar prompt, in the console.
+
|type the following command at the dollar prompt, in the console.
  
 
|-
 
|-
−
| 03:04
+
|03:04
−
| The '''command line''' begins with the word “draw”, followed by '''object ID'''.
+
|The '''command line''' begins with the word “draw”, followed by '''object ID'''.
  
 
|-
 
|-
−
| 03:10
+
|03:10
−
| Number '''250''' in the command line refers to the length of the line.  
+
|Number '''250''' in the command line refers to the length of the line.  
  
 
|-
 
|-
−
| 03:15
+
|03:15
−
| This is followed by the position of the line.
+
|This is followed by the position of the line.
  
 
|-
 
|-
−
| 03:18
+
|03:18
−
| Within brackets, atom number equal to 1 and atom number equal to 2. Press '''Enter'''.  
+
|Within brackets, atom number equal to 1 and atom number equal to 2. Press '''Enter'''.  
  
 
|-
 
|-
−
| 03:26
+
|03:26
−
| Observe the panel.
+
|Observe the panel.A line passing through atoms 1 and 2 is drawn on the model of '''methane.'''
  
 
|-
 
|-
−
| 03:27
+
|03:33
−
| 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.
−
 
+
−
|-
+
−
| 03:33
+
−
| This line can now act as an axis for rotation.
+
  
 
|-
 
|-
 
|03:37
 
|03:37
−
| We can draw more than one line on a given model.
+
|We can draw more than one line on a given model.
  
 
|-
 
|-
−
| 03:41
+
|03:41
−
| To draw '''C2 rotational axis''', type the following command in the '''console'''.
+
|To draw '''C2 rotational axis''', type the following command in the '''console'''.
  
 
|-
 
|-
−
| 03:47
+
|03:47
−
| In this command, the numbers in the 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
  
 
|-
 
|-
−
| 03:54
+
|03:54
−
| followed by a command to specify the color of the line. Press '''Enter'''.  
+
|followed by a command to specify the color of the line. Press '''Enter'''.  
  
 
|-
 
|-
−
| 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'''.
  
 
|-
 
|-
−
| 04:05
+
|04:05
−
| To rotate along the '''line 1''', that is '''C3 axis''', type the following command:  
+
|To rotate along the '''line 1''', that is '''C3 axis''', type the following command:  
  
 
|-
 
|-
−
| 04:12
+
|04:12
−
| '''rotate $line1 60''' (rotate space dollar line1 space 60).
+
|'''rotate $line1 60''' (rotate space dollar line1 space 60).
  
 
|-
 
|-
−
| 04:18
+
|04:18
−
| The number '''60''' refers to the degrees of rotation. Press '''Enter'''.
+
|The number '''60''' refers to the degrees of rotation. Press '''Enter'''.
  
 
|-
 
|-
−
| 04:24
+
|04:24
−
| Observe the rotation along '''line1.'''  
+
|Observe the rotation along '''line1.'''  
  
 
|-
 
|-
−
| 04:27
+
|04:27
−
| To '''spin''' the molecule along '''line1''', type the following command:
+
|To '''spin''' the molecule along '''line1''', type the following command:
  
 
|-
 
|-
−
| 04:32
+
|04:32
−
| "spin $line1 180 60" '''(spin space dollar line1 space 180 space 60)'''.
+
|"spin $line1 180 60" '''(spin space dollar line1 space 180 space 60)'''.
  
 
|-
 
|-
−
| 04:39
+
|04:39
−
| The number '''180''' refers to degrees of '''rotation''' and '''60''' refers to the speed of rotation. Press '''Enter'''.
+
|The number '''180''' refers to degrees of '''rotation''' and '''60''' refers to the speed of rotation. Press '''Enter'''.
  
 
|-
 
|-
−
| 04:48
+
|04:48
−
| On the 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'''.  
  
 
|-
 
|-
−
| 04:55
+
|04:55
−
| As an assignment-
+
|As an assignment-Draw line representing '''C3 axis of symmetry''', in a model of '''ethane'''
  
 
|-
 
|-
−
| 04:56
+
|05:02
−
| Draw line representing '''C3 axis of symmetry''', in a model of '''ethane'''
+
|and '''spin''' the model along '''C3 axis'''.
  
 
|-
 
|-
−
| 05:02
+
|05:06
−
| and '''spin''' the model along '''C3 axis'''.  
+
|Back to the Jmol panel.
  
 
|-
 
|-
−
| 05:06
+
|05:08
−
| Back to the Jmol panel.
+
|We can also draw planes going through a set of atoms in a molecule.
  
 
|-
 
|-
−
| 05:08
+
|05:12
−
| We can also draw planes going through a set of atoms in a molecule.
+
|To do so, first delete the lines on the '''methane''' model by typing the following command.  
−
 
+
−
|-
+
−
| 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'''.
 
"draw off" '''(draw space off)'''. Press '''Enter'''.
  
 
|-
 
|-
−
| 05:24
+
|05:24
−
| To draw reflection plane going through atoms 1, 2 and 3 of the methane molecule:
+
|To draw reflection plane going through atoms 1, 2 and 3 of the methane molecule:
  
 
|-
 
|-
−
| 05:31
+
|05:31
−
| type the following command in the console.
+
|type the following command in the console.
  
 
|-
 
|-
−
| 05:35
+
|05:35
−
| Number '''300''' in the command indicates the size of the plane. Press '''Enter'''.
+
|Number '''300''' in the command indicates the size of the plane. Press '''Enter'''.
  
 
|-
 
|-
−
| 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.
  
 
|-
 
|-
−
| 05:49
+
|05:49
−
| To draw a second reflection plane through atoms 1, 4 and 5:
+
|To draw a second reflection plane through atoms 1, 4 and 5:
  
 
|-
 
|-
−
| 05:55
+
|05:55
−
| In the console, press up-arrow key and '''edit''' the command as follows.
+
|In the console, press up-arrow key and '''edit''' the command as follows.
  
 
|-
 
|-
−
| 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'''.
  
 
|-
 
|-
−
| 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:
  
 
|-
 
|-
−
| 06:17
+
|06:17
−
| ";color $plane2 blue" '''(semicolon color space dollar plane2 space blue)'''. Press '''Enter'''.
+
|"color $plane2 blue" '''(semicolon color space dollar plane2 space blue)'''. Press '''Enter'''.
  
 
|-
 
|-
−
| 06:24
+
|06:24
−
| On the panel, we see the two reflection planes in the '''methane''' molecule.
+
|On the panel, we see the two reflection planes in the '''methane''' molecule.
  
 
|-
 
|-
−
| 06:29
+
|06:29
−
| Using Jmol, we can also show '''point group''' classification for '''methane''' as follows.
+
|Using Jmol, we can also show '''point group''' classification for '''methane''' as follows.
  
 
|-
 
|-
−
| 06:36
+
|06:36
−
| Let's clear the planes drawn on methane molecule, on the panel.
+
|Let's clear the planes drawn on methane molecule, on the panel.
  
 
|-
 
|-
−
| 06:41
+
|06:41
−
| In the console, type:  '''draw off ''' (draw space off). Press '''Enter'''.
+
|In the console, type:  '''draw off ''' (draw space off). Press '''Enter'''.
  
 
|-
 
|-
−
| 06:47
+
|06:47
−
| To display all the possible '''symmetry element'''s for methane: type the following command in the console.
+
|To display all the possible '''symmetry element'''s for methane: type the following command in the console.
  
 
|-
 
|-
−
| 06:54
+
|06:54
−
| "draw pointgroup"  '''(draw space pointgroup)'''. Press '''Enter'''.
+
|"draw pointgroup"  '''(draw space pointgroup)'''. Press '''Enter'''.
  
 
|-
 
|-
−
| 06:59
+
|06:59
−
| We see the symmetry elements of '''methane''' displayed on the panel.
+
|We see the symmetry elements of '''methane''' displayed on the panel.
  
 
|-
 
|-
−
| 07:04
+
|07:04
−
| 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'''.
 
"calculate pointgroup"  (calculate space pointgroup). Press '''Enter'''.
  
 
|-
 
|-
−
| 07:14
+
|07:14
−
| '''Td''', the point group of methane molecule, is displayed on the '''console'''.
+
|'''Td''', the point group of methane molecule, is displayed on the '''console'''.
  
 
|-
 
|-
−
| 07:20
+
|07:20
−
| Another classic example for point group demonstration is '''allene'''.  
+
|Another classic example for point group demonstration is '''allene'''.  
  
 
|-
 
|-
−
| 07:25
+
|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'''.  
+
|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
+
|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'''.
+
|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
+
|07:48
−
| Press up-arrow key at the '''dollar prompt''', on the console, till you get this command:
+
|To display all possible symmetry elements for '''allene:'''
  
 
|-
 
|-
−
| 07:59
+
|07:52
−
| '''draw pointgroup '''. Press '''Enter'''.
+
|Press up-arrow key at the '''dollar prompt''', on the console, till you get this command:
  
 
|-
 
|-
−
| 08:02
+
|07:59
−
| Observe the panel. We see all possible symmetry elements for '''allene'''.
+
|'''draw pointgroup '''. Press '''Enter'''.
  
 
|-
 
|-
−
| 08:09
+
|08:02
−
| To get the '''point group''' classification for allene -
+
|Observe the panel. We see all possible symmetry elements for '''allene'''.
  
 
|-
 
|-
−
| 08:12
+
|08:09
−
| Again, on the console, press up-arrow key till you get the command "calculate pointgroup". Press '''Enter'''.
+
|To get the '''point group''' classification for allene -
  
 
|-
 
|-
−
| 08:21
+
|08:12
−
| The point group classification for '''allene''', that is '''D2d, '''is displayed on the Console.
+
|Again, on the console, press up-arrow key till you get the command "calculate pointgroup". Press '''Enter'''.
  
 
|-
 
|-
−
| 08:28
+
|08:21
−
| Similarly, you can download molecules of your choice and calculate their point group.
+
|The point group classification for '''allene''', that is '''D2d, '''is displayed on the Console.
  
 
|-
 
|-
−
| 08:34
+
|08:28
−
| Let's summarize. In this tutorial, we learnt: 
+
|Similarly, you can download molecules of your choice and calculate their point group.
  
 
|-
 
|-
−
| 08:38
+
|08:34
−
|* To draw lines, that is, '''C2''' and '''C3''' '''rotational axes''' through atoms in '''methane''' molecule.
+
|Let's summarize. In this tutorial, we learnt: 
  
 
|-
 
|-
−
| 08:45
+
|08:38
−
|* '''Spin''' and '''rotate''' the molecule along the axis.
+
|To draw lines, that is, '''C2''' and '''C3''' '''rotational axes''' through atoms in '''methane''' molecule.
  
 
|-
 
|-
−
| 08:49
+
|08:45
−
|* Draw '''reflection plane''' through atoms in '''methane''' molecule.
+
|'''Spin''' and '''rotate''' the molecule along the axis.
  
 
|-
 
|-
−
| 08:54
+
|08:49
−
|* And demonstrate point group classification using examples of '''methane '''and''' allene.'''
+
|Draw '''reflection plane''' through atoms in '''methane''' molecule.
  
 
|-
 
|-
−
| 09:01
+
|08:54
−
| As an assignment-
+
|And demonstrate point group classification using examples of '''methane '''and''' allene.'''
  
 
|-
 
|-
−
| 09:02
+
|09:01
−
| Draw reflection plane in a model of '''dichloromethane'''  
+
|As an assignment-Draw reflection plane in a model of '''dichloromethane'''  
  
 
|-
 
|-
−
| 09:07
+
|09:07
−
| and find out the point group classification for '''ammonia''' and '''benzene'''.
+
|and find out the point group classification for '''ammonia''' and '''benzene'''.
  
 
|-
 
|-
 
|09:12
 
|09:12
−
| This video summarizes the '''Spoken Tutorial''' project.
+
|This video summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 09:15
+
|09:15
−
| If you do not have good bandwidth, you can download and watch it.  
+
|If you do not have good bandwidth, you can download and watch it.  
  
 
|-
 
|-
−
| 09:20
+
|09:20
−
| We conduct workshops using spoken tutorials and give certificates. Please contact us.
+
|We conduct workshops using spoken tutorials and give certificates. Please contact us.
  
 
|-
 
|-
−
| 09:27
+
|09:27
−
| The spoken-tutorial project is funded by NMEICT, MHRD, govt of India.
+
|The spoken-tutorial project is funded by NMEICT, MHRD, govt of India.
  
 
|-
 
|-
−
| 09:33
+
|09:33
−
| This is Snehalatha from '''IIT Bombay''', signing off.  
+
|This is Snehalatha from '''IIT Bombay''', signing off.  
 
Thank you for joining.  
 
Thank you for joining.  
−
 
 
|}
 
|}

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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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