Jmol-Application/C2/Surfaces-and-Orbitals/English-timed - Revision history

PoojaMoolya at 12:12, 28 March 2017

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PoojaMoolya at 12:06, 28 March 2017

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PoojaMoolya at 12:04, 9 March 2017

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Sandhya.np14 at 12:30, 5 June 2016

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Sandhya.np14 at 07:35, 25 April 2016

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Sandhya.np14 at 07:44, 22 April 2016

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Sandhya.np14 at 11:13, 15 April 2016

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Sandhya.np14 at 05:40, 14 September 2015

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PoojaMoolya at 06:44, 20 October 2014

2014-10-20T06:44:28Z

PoojaMoolya: Created page with ' {| border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on '''Surfaces and Orbitals '''in '''Jmol Application.''' |- | 00:07 | …'

2014-08-20T05:01:33Z

Created page with ' {| border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Surfaces and Orbitals '''in '''Jmol Application.''' |- | 00:07 | …'

New page

{| border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 00:01
| Welcome to this tutorial on '''Surfaces and Orbitals '''in '''Jmol Application.'''

|-
| 00:07
| In this tutorial, we will learn to,

|-
| 00:10
| Create models of '''Alicyclic''' and '''Aromatic''' molecules.

|-
| 00:14
| Display different surfaces of molecules.

|-
| 00:18
| Display Atomic and Molecular orbitals.

|-
| 00:22
| To follow this tutorial, you should know how to create and edit molecular models in '''Jmol Application.'''

|-
| 00:29
| If not, watch the relevant tutorials available at our website.

|-
| 00:35
| To record this tutorial, I am using

|-
| 00:38
| '''Ubuntu '''OS version. 12.04

|-
| 00:42
| '''Jmol '''version 12.2.2 and

|-
| 00:45
| '''Java (JRE)''' version 7

|-
|00:48
|I have opened a new '''Jmol application''' window.

|-
| 00:52
| Let us first create a model of''' cyclohexane.'''

|-
| 00:56
| Click on '''modelkit menu'''.

|-
| 00:59
| A model of '''methane '''appears on the '''panel.'''

|-
| 01:03
|To create '''cyclohexane, '''we have to make a '''hydrocarbon''' chain of six '''carbon''' atoms.

|-
|01:09
| We will substitute the '''hydrogen''' in the model with a '''methyl '''group.

|-
| 01:13
| To do so, we will place the cursor on the '''hydrogen '''and click on it.

|-
| 01:18
| This is a model of '''ethane''' on screen.

|-
| 01:21
| Repeat this step another 2 times and replace one '''hydrogen''' at a time with a '''methyl''' group.

|-
| 01:28
| Click on the '''hydrogens''' in such a way that the structure forms a circle.

|-
| 01:33
| Now, rotate the structure on screen using the '''Rotate molecule '''tool.

|-
| 01:38
|This is the structure of '''butane''' on the panel.

|-
| 01:41
| Click on the '''modelkit menu.'''

|-
| 01:45
| Click on '''hydrogen''' on any of the '''carbon''' atoms present at the end of the chain.

|-
| 01:52
| Here is a model of '''pentane '''on the '''panel.'''

|-
| 01:55
| Click on one of the '''hydrogens,''' that is close to the end of the '''carbon '''chain.

|-
| 02:00
| A model of '''cyclohexane''' is created on the '''panel.'''

|-
|02:04
|Use minimize option in the '''modelkit menu''' to optimize the structure.

|-
| 02:09
| The model of '''Cyclohexane''' is now, in its most stable “'''chair'''” '''conformation'''.

|-
|02:15
| Alternately, we can also use '''Drag to bond''' option in '''modelkit''' menu to create''' '''cyclic structures.

|-
| 02:24
| I will use a model of '''pentane''' to demonstrate this feature.

|-
| 02:29
| This is a model of '''pentane''' on the '''panel'''.

|-
| 02:32
| To convert this into '''cyclopentane''', select '''Drag to bond''' option from the '''modelkit''' menu.

|-
| 02:40
|Place the cursor on the '''carbon''' present at one end of the chain.

|-
| 02:45
| Hold down the mouse button.

|-
| 02:47
| Without releasing the mouse button, bring the cursor to the '''carbon '''present at the other end of the chain.

|-
| 02:54
| Now release the mouse button.

|-
| 02:57
| We have a model of '''cyclopentane''' on the '''panel'''.

|-
| 03:01
| Now Let us go back to the '''Jmol panel '''with the model of '''cyclohexane'''.

|-
| 03:06
| Let us now convert '''cyclohexane''' to a '''benzene''' ring.

|-
| 03:10
| We have to introduce double bonds at alternate positions in the '''cyclohexane '''ring.

|-
| 03:16
|Open the '''modelkit menu.'''

|-
| 03:19
|Place the cursor on the bond between any two '''carbon '''atoms and click on it.

|-
| 03:25
| We now have '''cyclohexene''' on the '''panel'''.

|-
| 03:29
| Next, we need to introduce two more double bonds in the structure, to convert it to '''benzene'''.

|-
| 03:36
| Click on the bond between the next two alternate '''carbon''' atoms.

|-
| 03:41
| We have a model of '''benzene''' on the '''panel'''.

|-
|03:44
| Do the energy minimization to get a '''stable''' '''conformation'''.

|-
|03:49
| '''Surface topology''' of the molecules can be displayed by using''' Jmol Application.'''

|-
| 03:56
| To view different surfaces, open the pop-up menu.

|-
| 04:01
| Ensure that the '''modelkit menu''' is closed, if it is open.

|-
| 04:06
| Now, right-click on the '''panel''', to open the Pop-up menu.

|-
| 04:10
| Scroll down and select '''"Surfaces"'''.

|-
| 04:14
| A sub-menu opens with many options.

|-
| 04:18
| '''Dot Surface'''

|-
| 04:20
| '''van der Waal's'''

|-
| 04:21
| and some others.

|-
| 04:23
| For demonstration purpose, I will select '''Molecular surface'''.

|-
| 04:28
| The model of '''Benzene''' is displayed with a '''molecular surface.'''

|-
| 04:33
| Let us change it to another surface, say, '''Dot Surface.'''

|-
| 04:38
| So, open the Pop-up menu again, and choose '''Dot Surface'''.

|-
| 04:44
| We can also make the surfaces opaque or translucent.

|-
| 04:48
| To do so, open the Pop-up menu,

|-
| 04:52
|Scroll down to '''Surfaces''' and select '''Make Opaque''' options

|-
| 04:59
| Observe that the '''benzene '''model has become opaque.

|-
| 05:03
| To turn off the surface option, open the Pop-up menu, choose '''Surfaces'''.

|-
| 05:10
| scroll down to '''Off''' and click on it.

|-
| 05:15
| Now, we have a model of '''benzene''' without any surfaces.

|-
| 05:20
| '''Jmol''' can display '''atomic''' and '''molecular orbitals''' of molecules.

|-
| 05:25
| '''Atomic orbitals''' can be displayed on screen by writing commands on the '''console'''.

|-
| 05:32
| Open a new '''Jmol '''window by clicking on '''File '''and '''New'''.

|-
| 05:37
| Now open the '''console''' window by clicking on '''File '''and then on''' Console.'''

|-
| 05:43
|The''' console '''window opens on the screen.

|-
| 05:47
| I am using''' Kmag Screen magnifier''' to magnify the '''console''' window.

|-
| 05:53
| The command line for atomic orbitals starts with '''isosurface phase atomicorbital. '''

|-
| 06:00
| At the''' ($) dollar prompt''' type '''isosurface phase atomicorbital'''.

|-
| 06:06
| This is followed by '''quantum numbers n. l''' and '''m''' that are specific for each '''atomic orbital.'''

|-
| 06:14
| To display ''''s' orbital. '''type 2 0 0

|-
| 06:20
|The Numbers 2, 0, 0 represent''' n, l '''and '''m quantum numbers '''respectively.

|-
| 06:27
| Press '''Enter''' key to execute the command.

|-
| 06:31
| We have '''s orbital''' displayed on the panel.

|-
| 06:35
| Here are few more examples of '''atomic orbitals '''and the corresponding '''script commands.'''

|-
|06:41
|The command line is same for all '''atomic orbitals.'''

|-
| 06:45
| To display the previous command on the '''console''', press up arrow key on the keyboard.

|-
| 06:51
|Edit '''n, l '''and '''m '''quantum numbers to 2 1 1.

|-
|06:58
| Press '''Enter '''key and see the ''''px' orbital '''on the '''Jmol panel.'''

|-
| 07:05
| Press up arrow key again and edit '''n, l '''and '''m '''to 3 2 and -1.

|-
| 07:13
| Press '''Enter '''key and see the ''''dxy' orbital '''on the '''Jmol panel.'''

|-
| 07:19
| We can also save these images in different file formats like '''jpg, png''' or '''pdf'''.

|-
| 07:27
| Here is a list of commands for all '''atomic orbitals (s, p, d, '''and '''f).'''

|-
| 07:35
| Shown on this slide are models of '''atomic orbitals.'''

|-
| 07:40
| They were created with the help of '''script commands '''written on the '''console'''.

|-
|07:45
| Here I have opened a new '''Jmol panel''' and '''console''' to show how to display '''molecular orbitals.'''

|-
| 07:53
| '''Hybridized molecular orbitals '''such as '''sp3, sp2 '''and '''sp '''can be displayed using '''Jmol.'''

|-
| 08:02
| We have a model of '''methane''' on the panel.

|-
| 08:06
| '''Methane''' has '''molecular orbitals''' of the type '''sp3.'''

|-
|08:11
| '''Linear Combination of Atomic Orbitals i.e. LCAO''' method is used to create '''molecular orbitals. '''

|-
| 08:21
| So, the command line starts with ''''lcaocartoon', '''followed by '''create '''and the name of the '''orbital.'''

|-
|08:30

| At the '''dollar prompt''' type''' lcaocartoon create sp3'''

|-
| 08:36
| Press '''Enter. '''

|-
| 08:38
| Observe the model of '''methane '''with '''sp3 hybridized molecular orbitals.'''

|-
| 08:45
|To display '''sp2 hybridized molecular orbitals,''' we will take '''ethene '''as an example.

|-
| 08:52
| This is a molecule of '''ethene''' on the '''panel.'''

|-
|08:56
| '''Ethene''' molecule has three '''sp2 hybridized molecular orbitals.''' They are named '''sp2a, sp2b '''and '''sp2c.'''

|-
| 09:08
| At the '''dollar prompt''', type''' lcaocartoon create sp2a ''', press '''Enter.'''

|-
| 09:17
| Observe the '''sp2 '''orbital on the '''ethene''' model on the panel.

|-
| 09:22
| Press up arrow key and change '''sp2a''' to '''sp2b, '''press '''Enter.'''

|-
| 09:31
| Again, press up arrow key and change '''sp2b''' to '''sp2c,''' press '''Enter.'''

|-
| 09:41
|Finally for the''' pi bond, '''edit the name of the orbital as '''pz.'''

|-
|09:48
| On the '''panel,''' we have '''ethene''' molecule with all the '''molecular orbitals.'''

|-
| 09:55
| This slide shows examples of few other molecules with '''molecular orbitals.'''

|-
| 10:01
| Explore the website for '''Jmol Script '''documentation for more information.

|-
| 10:08
| Let's summarize.

|-
| 10:10
| In this tutorial we have learnt to

|-
| 10:12
| Create a model of '''cyclohexane''' and '''cyclopentane'''

|-
| 10:17
| Create a model of '''benzene'''

|-
| 10:19
| Display '''surface topology''' of molecules.

|-
| 10:23
| We also learnt to

|-
| 10:24
| Display '''Atomic orbitals (s, p, d, f)'''
|-
| 10:29
| Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''.

|-
| 10:38
| Here is an assignment

|-
| 10:40
| Create a model of '''2-Butene''' and display '''molecular orbitals.'''

|-
| 10:45
| Explore''' lcaocartoon '''command to change the color and size of '''molecular orbitals.'''

|-
| 10:52
| Refer the following link for list of commands.

|-
| 10:57
| Watch the video available at this URL.

[http://spoken-tutorial.org/What http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial]

|-
| 11:01
| It summarizes the Spoken Tutorial project

|-
| 11:04
| If you do not have good bandwidth, you can download and watch it

|-
| 11:09
| The Spoken Tutorial Project Team:

|-
| 11:11
| Conducts workshops using spoken tutorials

|-
| 11:15
| Gives certificates to those who pass an on-line test

|-
| 11:19
| For more details, please write to contact@spoken-tutorial.org

|-
|11:26
| Spoken Tutorial Project is a part of the Talk to a Teacher project

|-
| 11:30
| It is supported by the National Mission on Education through ICT, MHRD, Government of India

|-
| 11:37
| More information on this Mission is available at this link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro] ]

|-
| 11:42
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 1: / Line 1: @@
-{| border=1
+{|border=1
- | center
+|'''Time'''
- | Narration
+|'''Narration'''
 |-

@@ Line 126: / Line 126: @@
 |-
 |02:15
-| Alternately, we can also use '''Drag to bond''' option in '''modelkit''' menu to create cyclic structures.
+| Alternately, we can also use '''Drag to bond''' option in '''modelkit''' menu to create '''cyclic structure'''s.
 |-

@@ Line 14: / Line 14: @@
 |-
 | 00:10
-|* Create models of '''alicyclic''' and '''aromatic''' molecules.
+|Create models of '''alicyclic''' and '''aromatic''' molecules.
 |-
 | 00:14
-|* Display different surfaces of molecules.
+|Display different surfaces of molecules.
 |-
 | 00:18
-|* Display '''atomic''' and '''molecular orbitals'''.
+|Display '''atomic''' and '''molecular orbitals'''.
 |-
 | 00:22
-|  To follow this tutorial, you should know how to create and '''edit''' molecular models in '''Jmol Application.'''
+| To follow this tutorial, you should know how to create and '''edit''' molecular models in '''Jmol Application.'''
 |-
@@ Line 38: / Line 38: @@
 |-
 | 00:38
-|* '''Ubuntu '''OS version '''12.04'''
+|'''Ubuntu '''OS version '''12.04'''
 |-
 | 00:42
-|* '''Jmol '''version '''12.2.2''' and
+|'''Jmol '''version '''12.2.2''' and
 |-
 | 00:45
-|* '''Java (JRE)''' version '''7'''.
+|'''Java (JRE)''' version '''7'''.
 |-
@@ Line 230: / Line 230: @@
 |-
 | 04:20
-|  '''van der Waal's''',
+|  '''van der Waal's''',and some others.
-−
-|-
-| 04:21
-|  and some others.
 |-
@@ Line 466: / Line 462: @@
 |-
 | 10:12
-|* Create a model of '''cyclohexane''' and '''cyclopentane'''
+|Create a model of '''cyclohexane''' and '''cyclopentane'''
 |-
 | 10:17
-|* Create a model of '''benzene'''
+| Create a model of '''benzene'''
 |-
 | 10:19
-|* Display '''surface topology''' of molecules.
+| Display '''surface topology''' of molecules.
-−
-|-
-|  10:23
-|  We also learned to:
 |-
-| 10:24
+| 10:23
-|* Display '''Atomic orbitals (s, p, d, f)'''
+| We also learned to:Display '''Atomic orbitals (s, p, d, f)'''
 |-
 | 10:29
-|* Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''.
+| Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''.
 |-
@@ Line 523: / Line 515: @@
 |-
 | 11:11
-|* Conducts workshops using spoken tutorials.
+| Conducts workshops using spoken tutorials.
 |-
 | 11:15
-|* Gives certificates to those who pass an on-line test.
+| Gives certificates to those who pass an on-line test.
 |-
@@ Line 534: / Line 526: @@
 |-
-|11:26
+| 11:26
 | '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.

@@ Line 310: / Line 310: @@
 |-
 | 06:00
-| At the''' ($) dollar prompt''', type: '''isosurface phase atomicorbital'''.
+| At the''' ($) dollar prompt''', type: '''isosurface phase atomic orbital'''.
 |-
 | 06:06
-| This is followed by '''quantum numbers n. l''' and '''m''' that are specific for each '''atomic orbital.'''
+| This is followed by '''quantum numbers n, l''' and '''m''' that are specific for each '''atomic orbital.'''
 |-
 | 06:14
-|  To display ''''s' orbital, '''type: '''2 0 0'''
+|  To display 's' orbital, type: '''2 0 0'''
 |-
@@ Line 350: / Line 350: @@
 |-
 |06:58
-| Press '''Enter '''key and see the ''''px' orbital '''on the '''Jmol panel.'''
+| Press '''Enter '''key and see the 'px' orbital on the '''Jmol panel.'''
 |-
@@ Line 358: / Line 358: @@
 |-
 | 07:13
-| Press '''Enter '''key and see the ''''dxy' orbital '''on the '''Jmol panel.'''
+| Press '''Enter '''key and see the 'dxy' orbital on the '''Jmol panel.'''
 |-
@@ Line 370: / Line 370: @@
 |-
 | 07:35
-| Shown on this slide are models of '''atomic orbitals.'''
+| Shown on this '''slide''' are models of '''atomic orbitals.'''
 |-

@@ Line 162: / Line 162: @@
 |-
 | 03:01
-| Now Let us go back to the '''Jmol panel '''with the model of '''cyclohexane'''.
+| Now, let us go back to the '''Jmol panel '''with the model of '''cyclohexane'''.
 |-
@@ Line 170: / Line 170: @@
 |-
 | 03:10
-| We have to introduce double-bonds at alternate positions in the '''cyclohexane '''ring.
+| We have to introduce '''double-bond'''s at alternate positions in the '''cyclohexane '''ring.
 |-

@@ Line 219: / Line 219: @@
 | 04:10
 | Scroll down and select '''"Surfaces"'''.
 |-
@@ Line 264: / Line 263: @@
 | 04:52
 |Scroll down to '''Surfaces''' and select '''Make Opaque''' options
 |-
@@ Line 304: / Line 302: @@
 |-
 | 05:47
-| I am using''' Kmag Screen magnifier''' to magnify the '''console''' window.
+| I am using''' KMag Screen magnifier''' to magnify the '''console''' window.
 |-
@@ Line 321: / Line 319: @@
 | 06:14
 |  To display ''''s' orbital. '''type 2 0 0
 |-
@@ Line 330: / Line 327: @@
 | 06:27
 | Press '''Enter''' key to execute the command.
 |-
@@ Line 343: / Line 339: @@
 |06:41
 |The command line is same for all '''atomic orbitals.'''
 |-
@@ Line 384: / Line 379: @@
 |07:45
 | Here I have opened a new '''Jmol panel''' and '''console''' to show how to display '''molecular orbitals.'''
 |-
@@ Line 408: / Line 402: @@
 |-
 |08:30
 | At the '''dollar prompt''' type''' lcaocartoon create sp3'''
@@ Line 459: / Line 450: @@
 |-
 | 09:55
- | This slide shows examples of few other molecules with '''molecular orbitals.'''
+| This slide shows examples of few other molecules with '''molecular orbitals.'''
 |-
@@ Line 492: / Line 483: @@
 | 10:24
 | Display '''Atomic orbitals (s, p, d, f)'''
 |-
 | 10:29