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

PoojaMoolya at 04:34, 29 March 2017

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PoojaMoolya at 13:12, 28 March 2017

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PoojaMoolya at 12:13, 9 March 2017

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Sandhya.np14 at 11:53, 24 June 2016

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Sandhya.np14 at 11:23, 24 June 2016

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Sandhya.np14 at 05:11, 16 June 2016

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Sandhya.np14 at 12:02, 2 June 2016

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Sandhya.np14 at 12:24, 11 February 2016

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Sandhya.np14 at 12:18, 14 September 2015

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PoojaMoolya: Created page with "{| Border =1 |Time | Narration |- | 00:01 | Welcome to this tutorial on '''Symmetry and Point Group '''in Jmol'''.''' |- | 00:06 | In thi..."

2015-03-30T07:09:25Z

Created page with "{| Border =1 |<center>Time</center> | <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Symmetry and Point Group '''in Jmol'''.''' |- | 00:06 | In thi..."

New page

{| Border =1
|<center>Time</center>
| <center>Narration</center>

|-
| 00:01
| Welcome to this tutorial on '''Symmetry and Point Group '''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
| With in 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
| Lets 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.

|}

@@ Line 5: / Line 5: @@
 |-
 |00:01
-| Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''.
+|Welcome to this tutorial on '''Symmetry and Point Groups '''in '''Jmol'''.
 |-
@@ Line 286: / Line 286: @@
 |-
 |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'''.
 |-

@@ Line 346: / Line 346: @@
 |-
 | 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

@@ Line 324: / Line 324: @@
 |-
-| 05:59
+| 06:59
 |  We see the symmetry elements of '''methane''' displayed on the panel.

@@ Line 17: / Line 17: @@
 |-
 | 00:12
-|* Spin and rotate the molecule along the axis.
+|* '''Spin''' and rotate the molecule along the axis.
 |-
@@ Line 41: / Line 41: @@
 |-
 | 00:42
-|* '''Ubuntu '''Operating System version '''14.04'''
+|* '''Ubuntu Operating System''' version 14.04
 |-
 | 00:46
-|* '''Jmol''' version '''12.2.32'''
+|* '''Jmol''' version 12.2.32
 |-
 | 00:50
-|* '''Java''' version '''7'''  and * '''Mozilla Firefox browser 35.0'''.
+|* '''Java''' version 7  and * Mozilla Firefox browser 35.0.
 |-
 | 00:57

@@ Line 68: / Line 68: @@
 |-
 | 01:09
-| We will use '''Jmol''' to display these symmetry elements in a molecule.
+| We will use '''Jmol''' to display these '''symmetry element'''s in a molecule.
 |-
@@ Line 108: / Line 108: @@
 |-
 | 02:01
-|  Console window opens on the screen.
+|  The Console window opens on the screen.
 |-
 | 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.
 |-
@@ Line 124: / Line 124: @@
 |-
 | 02:19
-| A web-page opens with a list of keywords used for writing script commands in Jmol.
+| A web-page opens with a list of keywords used for writing '''script command'''s in Jmol.
 |-
 | 02:26
-|  Scroll down and click on word '''draw '''in the list.
+|  Scroll down and click on the word '''draw '''in the list.
 |-
@@ Line 160: / Line 160: @@
 |-
 | 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'''.
 |-
@@ Line 196: / Line 196: @@
 |-
 | 03:47
-| 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
 |-
@@ Line 204: / Line 204: @@
 |-
 | 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'''.
 |-
@@ Line 228: / Line 228: @@
 |-
 | 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)'''.
 |-
@@ Line 236: / Line 236: @@
 |-
 | 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'''.
 |-
@@ Line 248: / Line 248: @@
 |-
 | 05:02
-| and spin the model along '''C3 axis'''.
+| and '''spin''' the model along '''C3 axis'''.
 |-
@@ Line 261: / Line 261: @@
 | 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'''.
 |-
@@ Line 277: / Line 277: @@
 |-
 | 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.
 |-
@@ Line 289: / Line 289: @@
 |-
 | 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
-|  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
-| ''';color $plane2 blue'''(semicolon color space dollar plane2 space blue). Press '''Enter'''.
+| ";color $plane2 blue" '''(semicolon color space dollar plane2 space blue)'''. Press '''Enter'''.
 |-
@@ Line 317: / Line 317: @@
 |-
 | 06:47
-|  To display all the possible symmetry elements 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
-| '''draw pointgroup ''' '''(draw space pointgroup)'''. Press '''Enter'''.
+| "draw pointgroup"  '''(draw space pointgroup)'''. Press '''Enter'''.
 |-
@@ Line 330: / Line 330: @@
 | 07:04
 |  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'''.
 |-
@@ Line 346: / Line 346: @@
 |-
 | 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
@@ Line 353: / Line 353: @@
 |-
 | 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:
 |-
@@ Line 361: / Line 361: @@
 |-
 | 08:02
-|  Observe the panel. We see all possible symmetry elements for 'allene'.
+|  Observe the panel. We see all possible symmetry elements for '''allene'''.
 |-
 | 08:09
-|  To get the '''point group''' classification for allene-
+|  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'''.
+| 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.'''
+|  The point group classification for '''allene''', that is '''D2d, '''is displayed on the Console.
 |-
@@ Line 385: / Line 385: @@
 |-
 | 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.
 |-
 | 08:45
-|* Spin and rotate the molecule along the axis.
+|* '''Spin''' and '''rotate''' the molecule along the axis.
 |-
 | 08:49
-|* Draw reflection plane through atoms in '''methane''' molecule.
+|* Draw '''reflection plane''' through atoms in '''methane''' molecule.
 |-