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 Group '''in '''Jmol'''.
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|  Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''.
  
 
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| 00:08
 
| 00:08
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|* Draw line, that is, axis through atoms in a molecule.
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|* Draw line, that is, '''axis''' through atoms in a molecule.
  
 
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| 00:21
 
| 00:21
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|* And demonstrate point group classification.  
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|* And demonstrate '''point group''' classification.  
  
 
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|00:25
 
|00:25
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| To follow this tutorial, you should have Knowledge of undergraduate Chemistry  and familiar with operations from '''Jmol window'''.
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| To follow this tutorial, you should have knowledge of undergraduate Chemistry  and familiar with operations from '''Jmol window'''.
  
 
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|* '''Ubuntu '''Operating System version 14.04
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|* '''Ubuntu '''Operating System version '''14.04'''
  
 
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| 00:46
 
| 00:46
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|* '''Jmol''' version 12.2.32
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|* '''Jmol''' version '''12.2.32'''
  
 
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| 00:50
 
| 00:50
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|* '''Java''' version 7  and * '''Mozilla Firefox browser '''35.0
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|* '''Java''' version '''7''' and * '''Mozilla Firefox browser 35.0'''.
 
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| 01:22
 
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| I have already opened the '''Jmol '''window.
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| I have already opened the '''Jmol window'''.
  
 
|-
 
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| 01:25
 
| 01:25
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| Click on '''modelkit '''menu to get the '''ball and stick''' model of methane on the panel.
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| Click on '''modelkit '''menu to get the '''ball and stick''' model of '''methane''' on the panel.
  
 
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| 01:47
 
| 01:47
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| We need to write commands in the console to draw lines and planes through atoms.
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| We need to write commands in the '''console''' to draw lines and planes through atoms.
  
 
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| 01:53
 
| 01:53
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|  To open the Console, click on '''File''' menu.
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|  To open the '''Console''', click on '''File''' menu.
  
 
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|  This is followed by information regarding the use of the keyword.  
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|  This is followed by information regarding the use of the '''keyword'''.  
  
 
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| 02:55
 
| 02:55
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|  To draw a line that represents '''C3 rotational axis''':
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|  To draw a line that represents '''C3 rotational axis''',
  
 
|-
 
|-
 
| 02:59
 
| 02:59
−
| Type the following command at the dollar prompt in the console.
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| type the following command at the dollar prompt, in the console.
  
 
|-
 
|-
 
| 03:04
 
| 03:04
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| The '''command line''' begins with the word “'''draw'''”, followed by object ID.
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| The '''command line''' begins with the word “'''draw'''”, followed by '''object ID'''.
  
 
|-
 
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| 03:10
 
| 03:10
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| Number 250 in the command line refers to the length of the line.  
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| Number '''250''' in the command line refers to the length of the line.  
  
 
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|-
 
| 03:15
 
| 03:15
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| This is followed by the position of the line;
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| This is followed by the position of the line.
  
 
|-
 
|-
 
| 03:18
 
| 03:18
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| Within brackets atom number equal to 1 and atom number equal to 2. Press '''Enter'''.  
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| Within brackets, atom number equal to 1 and atom number equal to 2. Press '''Enter'''.  
  
 
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| 03:41
 
| 03:41
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| To draw '''C2 rotational axis''': Type the following command in the console.
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| To draw '''C2 rotational axis''', type the following command in the '''console'''.
  
 
|-
 
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| 03:47
 
| 03:47
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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 curly brackets indicate the '''Cartesian coordinates''' for the line
  
 
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| 03:59
 
| 03:59
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|  Now, on the panel, we have methane with C2 and C3 rotational axes.
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|  Now, on the panel, we have methane with C2 and C3 '''rotational axes'''.
  
 
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| 04:05
 
| 04:05
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|  To rotate along the line 1, that is C3 axis, type the following command.
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|  To rotate along the '''line 1''', that is '''C3 axis''', type the following command:
  
 
|-
 
|-
 
| 04:12
 
| 04:12
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| '''rotate $line1 60 ''' (rotate space dollar line1 space 60).
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| '''rotate $line1 60''' (rotate space dollar line1 space 60).
  
 
|-
 
|-
 
| 04:18
 
| 04:18
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| The number 60 refers to the degrees of rotation. Press '''Enter'''.
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| The number '''60''' refers to the degrees of rotation. Press '''Enter'''.
  
 
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| 04:27
 
| 04:27
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|  To spin the molecule along '''line1''', type the following command.
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|  To '''spin''' the molecule along '''line1''', type the following command:
  
 
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| 04:39
 
| 04:39
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| The number 180 refers to degrees of rotation and 60 refers to the speed of rotation. Press '''Enter'''.
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| The number '''180''' refers to degrees of '''rotation''' and '''60''' refers to the speed of rotation. Press '''Enter'''.
  
 
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| 04:48
 
| 04:48
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|  On panel, we see the '''methane''' model spin along '''line1''', that is C3 axis.  
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|  On panel, we see the '''methane''' model spin along '''line1''', that is '''C3 axis'''.  
  
 
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| 04:56
 
| 04:56
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| Draw line representing '''C3 axis of symmetry''', in a model of '''ethane'''.
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| Draw line representing '''C3 axis of symmetry''', in a model of '''ethane'''
  
 
|-
 
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| 05:02
 
| 05:02
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| And spin the model along '''C3 axis'''.  
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| and spin the model along '''C3 axis'''.  
  
 
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| Type the following command in the console.
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| type the following command in the console.
  
 
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| 05:35
 
| 05:35
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| Number 300 in the command indicates the size of the plane. Press '''Enter'''.
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| Number '''300''' in the command indicates the size of the plane. Press '''Enter'''.
  
 
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| 05:55
 
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|  In the console press up-arrow key and '''edit''' the command as follows:
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|  In the console, press up-arrow key and '''edit''' the command as follows.
  
 
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| 06:12
 
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|  Also to change the color of the plane, type the following command.
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|  Also to change the color of the plane, type the following command:
  
 
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| 06:17
 
| 06:17
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| ''';color $plane2 blue'''(semicolon color space dollar plane2 space blue). Press '''Enter'''.
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| ''';color $plane2 blue'''(semicolon color space dollar plane2 space blue). Press '''Enter'''.
  
 
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|  Using Jmol we can also show point group classification for '''methane''' as follows.
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|  Using Jmol, we can also show '''point group''' classification for '''methane''' as follows.
  
 
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| 06:36
 
| 06:36
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| Let's clear the planes drawn on methane molecule on the panel.
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| Let's clear the planes drawn on methane molecule, on the panel.
  
 
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| 06:47
 
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|  To display all the possible symmetry elements for methane: Type the following command in the console.
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|  To display all the possible symmetry elements for methane: type the following command in the console.
  
 
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|  To find out the point group classification for '''methane''', type the following command.
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|  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'''.
  
 
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| 07:14
 
| 07:14
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|  '''Td''', the point group of methane molecule, is displayed on the console.
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|  '''Td''', the point group of methane molecule, is displayed on the '''console'''.
  
 
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| 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'''.  
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| 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'''.  
  
 
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| 07:37
 
| 07:37
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| 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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| 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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| Press up-arrow key at the dollar prompt on the console till you get this command.
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| Press up-arrow key at the '''dollar prompt''', on the console, till you get this command.
  
 
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| 08:02
 
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|  Observe the panel, we see all possible symmetry elements for 'allene'.
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|  Observe the panel. We see all possible symmetry elements for 'allene'.
  
 
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| 08:09
 
| 08:09
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|  To get the point group classification for allene-
+
|  To get the '''point group''' classification for allene-
  
 
|-
 
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| 08:12
 
| 08:12
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| Again on the console press up-arrow key till you get the command '''calculate pointgroup'''. Press '''Enter'''.
+
| Again on the console, press up-arrow key till you get the command '''calculate pointgroup'''. Press '''Enter'''.
  
 
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| 08:28
 
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|  Similarly you can download molecules of your choice and calculate their point group.
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|  Similarly, you can download molecules of your choice and calculate their point group.
  
 
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| 08:38
 
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|* 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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| 09:02
 
| 09:02
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| Draw reflection plane in a model of '''dichloromethane'''.
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| Draw reflection plane in a model of '''dichloromethane'''  
  
 
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| 09:07
 
| 09:07
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| And find out the point group classification for '''ammonia''' and '''benzene'''.
+
| and find out the point group classification for '''ammonia''' and '''benzene'''.
  
 
|-
 
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|09:12
 
|09:12
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|  This video summarizes the Spoken Tutorial project.
+
|  This video summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-

Revision as of 17:54, 11 February 2016

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
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 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 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 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 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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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