Difference between revisions of "Jmol-Application/C2/Surfaces-and-Orbitals/English-timed"

From Script | Spoken-Tutorial
Jump to: navigation, search
(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 | …')
 
 
(8 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
 
+
{|border=1
−
{| border=1
+
|'''Time'''
−
! <center>Time</center>
+
|'''Narration'''
−
! <center>Narration</center>
+
  
 
|-
 
|-
−
| 00:01
+
|00:01
−
| Welcome to this tutorial on '''Surfaces and Orbitals '''in '''Jmol Application.'''
+
|Welcome to this tutorial on '''Surfaces and Orbitals '''in '''Jmol Application.'''
  
 
|-
 
|-
−
| 00:07
+
|00:07
−
| In this tutorial, we will learn to,
+
|In this tutorial, we will learn to:
  
 
|-
 
|-
−
| 00:10
+
|00:10
−
| Create models of '''Alicyclic''' and '''Aromatic''' molecules.
+
|Create models of '''alicyclic''' and '''aromatic''' molecules.
  
 
|-
 
|-
−
| 00:14
+
|00:14
−
| Display different surfaces of molecules.
+
|Display different surfaces of molecules.
  
 
|-
 
|-
−
| 00:18
+
|00:18
−
| Display Atomic and Molecular orbitals.
+
|Display '''atomic''' and '''molecular orbitals'''.
  
 
|-
 
|-
−
| 00:22
+
|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.'''
  
 
|-
 
|-
−
| 00:29
+
|00:29
−
| If not, watch the relevant tutorials available at our website.
+
|If not, watch the relevant tutorials available at our website.
  
 
|-
 
|-
−
| 00:35
+
|00:35
−
| To record this tutorial, I am using
+
|To record this tutorial, I am using:
  
 
|-
 
|-
−
| 00:38
+
|00:38
−
| '''Ubuntu '''OS version. 12.04
+
|'''Ubuntu '''OS version '''12.04'''
  
 
|-
 
|-
−
| 00:42
+
|00:42
−
| '''Jmol '''version 12.2.2 and  
+
|'''Jmol '''version '''12.2.2''' and  
  
 
|-
 
|-
−
| 00:45
+
|00:45
−
| '''Java (JRE)''' version 7
+
|'''Java (JRE)''' version '''7'''.
  
 
|-
 
|-
Line 53: Line 52:
  
 
|-
 
|-
−
| 00:52
+
|00:52
−
| Let us first create a model of''' cyclohexane.'''
+
|Let us first create a model of''' cyclohexane.'''
  
 
|-
 
|-
−
| 00:56
+
|00:56
−
| Click on '''modelkit menu'''.  
+
|Click on '''modelkit''' menu.  
  
 
|-
 
|-
−
| 00:59
+
|00:59
−
| A model of '''methane '''appears on the '''panel.'''
+
|A model of '''methane '''appears on the '''panel.'''
  
 
|-
 
|-
−
| 01:03
+
|01:03
 
|To create '''cyclohexane, '''we have to make a '''hydrocarbon''' chain of six '''carbon''' atoms.
 
|To create '''cyclohexane, '''we have to make a '''hydrocarbon''' chain of six '''carbon''' atoms.
  
 
|-
 
|-
 
|01:09
 
|01:09
−
| We will substitute the '''hydrogen''' in the model with a '''methyl '''group.  
+
|We will substitute the '''hydrogen''' in the model with a '''methyl '''group.  
  
 
|-
 
|-
−
| 01:13
+
|01:13
−
| To do so, we will place the cursor on the '''hydrogen '''and click on it.  
+
|To do so, we will place the cursor on the '''hydrogen '''and click on it.  
  
 
|-
 
|-
−
| 01:18
+
|01:18
−
| This is a model of '''ethane''' on screen.
+
|This is a model of '''ethane''' on '''screen'''.
  
 
|-
 
|-
−
| 01:21
+
|01:21
−
| Repeat this step another 2 times and replace one '''hydrogen''' at a time with a '''methyl''' group.
+
|Repeat this step another 2 times and replace one '''hydrogen''' at a time with a '''methyl''' group.
  
 
|-
 
|-
−
| 01:28
+
|01:28
−
| Click on the '''hydrogens''' in such a way that the structure forms a circle.  
+
|Click on the '''hydrogens''' in such a way that the structure forms a circle.  
  
 
|-
 
|-
−
| 01:33
+
|01:33
−
| Now, rotate the structure on screen using the '''Rotate molecule '''tool.
+
|Now, rotate the structure on screen using the '''Rotate molecule '''tool.
  
 
|-
 
|-
−
| 01:38
+
|01:38
 
|This is the structure of '''butane''' on the panel.
 
|This is the structure of '''butane''' on the panel.
  
 
|-
 
|-
−
| 01:41
+
|01:41
−
| Click on the '''modelkit menu.'''
+
|Click on the '''modelkit''' menu.
  
 
|-
 
|-
−
| 01:45
+
|01:45
−
| Click on '''hydrogen''' on any of the '''carbon''' atoms present at the end of the chain.
+
|Click on '''hydrogen''' on any of the '''carbon''' atoms present at the end of the chain.
  
 
|-
 
|-
−
| 01:52
+
|01:52
−
| Here is a model of '''pentane '''on the '''panel.'''
+
|Here is a model of '''pentane '''on the '''panel.'''
  
 
|-
 
|-
−
| 01:55
+
|01:55
−
| Click on one of the '''hydrogens,''' that is close to the end of the '''carbon '''chain.
+
|Click on one of the hydrogens, that is close to the end of the '''carbon '''chain.
  
 
|-
 
|-
−
| 02:00
+
|02:00
−
| A model of '''cyclohexane''' is created on the '''panel.'''
+
|A model of '''cyclohexane''' is created on the panel.
  
 
|-
 
|-
 
|02:04
 
|02:04
−
|Use minimize option in the '''modelkit menu''' to optimize the structure.
+
|Use '''minimize''' option in the '''modelkit''' menu to optimize the structure.
  
 
|-
 
|-
−
| 02:09
+
|02:09
−
| The model of '''Cyclohexane''' is now, in its most stable “'''chair'''” '''conformation'''.
+
|The model of '''Cyclohexane''' is now in its most stable “'''chair'''” '''conformation'''.
  
 
|-
 
|-
 
|02:15
 
|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 the '''modelkit''' menu to create '''cyclic structure'''s.
  
 
|-
 
|-
−
| 02:24
+
|02:24
−
| I will use a model of '''pentane''' to demonstrate this feature.
+
|I will use a model of '''pentane''' to demonstrate this feature.
  
 
|-
 
|-
−
| 02:29
+
|02:29
−
| This is a model of '''pentane''' on the '''panel'''.
+
|This is a model of '''pentane''', on the '''panel'''.
  
 
|-
 
|-
−
| 02:32
+
|02:32
−
| To convert this into '''cyclopentane''', select '''Drag to bond''' option from the '''modelkit''' menu.
+
|To convert this into '''cyclopentane''', select '''Drag to bond''' option from the '''modelkit''' menu.
  
 
|-
 
|-
−
| 02:40
+
|02:40
 
|Place the cursor on the '''carbon''' present at one end of the chain.
 
|Place the cursor on the '''carbon''' present at one end of the chain.
  
 
|-
 
|-
−
| 02:45
+
|02:45
−
| Hold down the mouse button.
+
|Hold down the '''mouse button'''.
  
 
|-
 
|-
−
| 02:47
+
|02:47
−
| Without releasing the mouse button, bring the cursor to the '''carbon '''present at the other end of the chain.  
+
|Without releasing the '''mouse button''', bring the cursor to the '''carbon '''present at the other end of the chain.  
  
 
|-
 
|-
−
| 02:54
+
|02:54
−
| Now release the mouse button.
+
|Now, release the '''mouse button'''.
  
 
|-
 
|-
−
| 02:57
+
|02:57
−
| We have a model of '''cyclopentane''' on the '''panel'''.
+
|We have a model of '''cyclopentane''' on the panel.
  
 
|-
 
|-
−
| 03:01
+
|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'''.  
  
 
|-
 
|-
−
| 03:06
+
|03:06
−
| Let us now convert '''cyclohexane''' to a '''benzene''' ring.
+
|Let us now convert '''cyclohexane''' to a '''benzene ring'''.
  
 
|-
 
|-
−
| 03:10
+
|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.
  
 
|-
 
|-
−
| 03:16
+
|03:16
−
|Open the '''modelkit menu.'''
+
|Open the '''modelkit''' menu.
  
 
|-
 
|-
−
| 03:19
+
|03:19
−
|Place the cursor on the bond between any two '''carbon '''atoms and click on it.
+
|Place the cursor on the '''bond''' between any two '''carbon '''atoms and click on it.
  
 
|-
 
|-
−
| 03:25
+
|03:25
−
| We now have '''cyclohexene''' on the '''panel'''.
+
|We now have '''cyclohexene''' on the '''panel'''.
  
 
|-
 
|-
−
| 03:29
+
|03:29
−
| Next, we need to introduce two more double bonds in the structure, to convert it to '''benzene'''.
+
|Next, we need to introduce two more double-bonds in the structure to convert it to '''benzene'''.
  
 
|-
 
|-
−
| 03:36
+
|03:36
−
| Click on the bond between the next two alternate '''carbon''' atoms.
+
|Click on the '''bond''' between the next two alternate '''carbon''' atoms.
  
 
|-
 
|-
−
| 03:41
+
|03:41
−
| We have a model of '''benzene''' on the '''panel'''.
+
|We have a model of '''benzene''' on the panel.
  
 
|-
 
|-
 
|03:44
 
|03:44
−
| Do the energy minimization to get a '''stable''' '''conformation'''.
+
|Do the '''energy minimization''' to get a stable '''conformation'''.
  
 
|-
 
|-
 
|03:49
 
|03:49
−
| '''Surface topology''' of the molecules can be displayed by using''' Jmol Application.'''
+
|'''Surface topology''' of the molecules can be displayed by using''' Jmol Application.'''
  
 
|-
 
|-
−
| 03:56
+
|03:56
−
| To view different surfaces, open the pop-up menu.
+
|To view different surfaces, open the '''pop-up menu'''.
  
 
|-
 
|-
−
| 04:01
+
|04:01
−
| Ensure that the '''modelkit menu''' is closed, if it is open.
+
|Ensure that the '''modelkit menu''' is closed, if it is open.
  
 
|-
 
|-
−
| 04:06
+
|04:06
−
| Now, right-click on the '''panel''', to open the Pop-up menu.  
+
|Now, right-click on the '''panel''' to open the Pop-up menu.  
  
 
|-
 
|-
−
| 04:10
+
|04:10
−
| Scroll down and select '''"Surfaces"'''.  
+
|Scroll down and select '''"Surfaces"'''.  
−
 
+
  
 
|-
 
|-
−
| 04:14
+
|04:14
−
| A sub-menu opens with many options.
+
|A sub-menu opens with many options-
  
 
|-
 
|-
−
| 04:18
+
|04:18
−
| '''Dot Surface'''
+
|'''Dot Surface''',
  
 
|-
 
|-
−
| 04:20
+
|04:20
−
| '''van der Waal's'''
+
|'''van der Waal's''',and some others.
  
 
|-
 
|-
−
| 04:21
+
|04:23
−
| and some others.
+
|For demonstration purpose, I will select '''Molecular surface'''.
  
 
|-
 
|-
−
| 04:23
+
|04:28
−
|  For demonstration purpose, I will select '''Molecular surface'''.
+
|The model of '''Benzene''' is displayed with a '''molecular surface.'''
  
 
|-
 
|-
−
| 04:28
+
|04:33
−
| The model of '''Benzene'''  is displayed with a '''molecular surface.'''
+
|Let us change it to another surface, say, '''Dot Surface.'''
  
 
|-
 
|-
−
| 04:33
+
|04:38
−
| Let us change it to another surface, say, '''Dot Surface.'''
+
|So, open the pop-up menu again and choose '''Dot Surface'''.
  
 
|-
 
|-
−
| 04:38
+
|04:44
−
| So, open the Pop-up menu again, and choose '''Dot Surface'''.
+
|We can also make the surfaces opaque or translucent.
  
 
|-
 
|-
−
| 04:44
+
|04:48
−
| We can also make the surfaces opaque or translucent.
+
|To do so, open the Pop-up menu.
  
 
|-
 
|-
−
| 04:48
+
|04:52
−
| To do so, open the Pop-up menu,
+
|Scroll down to '''Surfaces''' and select '''Make Opaque''' option.
  
 
|-
 
|-
−
| 04:52
+
|04:59
−
|Scroll down to '''Surfaces''' and select '''Make Opaque''' options
+
|Observe that the '''benzene '''model has become opaque.
−
 
+
  
 
|-
 
|-
−
| 04:59
+
|05:03
−
| Observe that the '''benzene '''model has become opaque.
+
|To turn off the surface option- open the pop-up menu, choose '''Surfaces''',
  
 
|-
 
|-
−
| 05:03
+
|05:10
−
| To turn off the surface option, open the Pop-up menu, choose '''Surfaces'''.  
+
|scroll down to '''Off''' and click on it.
  
 
|-
 
|-
−
| 05:10
+
|05:15
−
| scroll down to '''Off''' and click on it.
+
|Now, we have a model of '''benzene''' without any surfaces.
  
 
|-
 
|-
−
| 05:15
+
|05:20
−
| Now, we have a model of '''benzene''' without any surfaces.
+
|'''Jmol''' can display '''atomic''' and '''molecular orbitals''' of molecules.
  
 
|-
 
|-
−
| 05:20
+
|05:25
−
| '''Jmol''' can display '''atomic''' and '''molecular orbitals''' of molecules.
+
|'''Atomic orbitals''' can be displayed on the screen by writing commands on the '''console'''.
  
 
|-
 
|-
−
| 05:25
+
|05:32
−
| '''Atomic orbitals''' can be displayed on screen by writing commands on the '''console'''.
+
|Open a new '''Jmol '''window by clicking on '''File '''and '''New'''.
  
 
|-
 
|-
−
| 05:32
+
|05:37
−
| Open a new '''Jmol '''window by clicking on '''File '''and '''New'''.
+
|Now, open the '''console''' window by clicking on '''File '''and then on''' Console.'''
  
 
|-
 
|-
−
| 05:37
+
|05:43
−
| Now open the '''console''' window by clicking on '''File '''and then on''' Console.'''
+
−
 
+
−
|-
+
−
| 05:43
+
 
|The''' console '''window opens on the screen.
 
|The''' console '''window opens on the screen.
  
 
|-
 
|-
−
| 05:47
+
|05:47
−
| I am using''' Kmag Screen magnifier''' to magnify the '''console''' window.
+
|I am using''' KMag Screen magnifier''' to magnify the '''console''' window.
  
 
|-
 
|-
−
| 05:53
+
|05:53
−
| The command line for atomic orbitals starts with '''isosurface phase atomicorbital. '''
+
|The '''command line''' for atomic orbitals starts with '''isosurface phase atomicorbital. '''
  
 
|-
 
|-
−
| 06:00
+
|06:00
−
| At the''' ($) dollar prompt''' type '''isosurface phase atomicorbital'''.
+
|At the''' ($) dollar prompt''', type: "isosurface phase atomic orbital".
  
 
|-
 
|-
−
| 06:06
+
|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
+
|06:14
−
| To display ''''s' orbital. '''type 2 0 0
+
|To display 's' orbital, type: '''2 0 0'''
−
 
+
  
 
|-
 
|-
−
| 06:20
+
|06:20
 
|The Numbers 2, 0, 0 represent''' n, l '''and '''m quantum numbers '''respectively.
 
|The Numbers 2, 0, 0 represent''' n, l '''and '''m quantum numbers '''respectively.
  
 
|-
 
|-
−
| 06:27
+
|06:27
−
| Press '''Enter''' key to execute the command.
+
|Press '''Enter''' key to execute the command.
−
 
+
  
 
|-
 
|-
−
| 06:31
+
|06:31
−
| We have '''s orbital''' displayed on the panel.
+
|We have '''s-orbital''' displayed on the panel.
  
 
|-
 
|-
−
| 06:35
+
|06:35
−
| Here are few more examples of '''atomic orbitals '''and the corresponding '''script commands.'''
+
|Here are few more examples of '''atomic orbitals '''and the corresponding '''script commands.'''
  
 
|-
 
|-
 
|06:41
 
|06:41
−
|The command line is same for all '''atomic orbitals.'''
+
|The '''command line''' is same for all '''atomic orbitals.'''
−
 
+
  
 
|-
 
|-
−
| 06:45
+
|06:45
−
| To display the previous command on the '''console''', press up arrow key on the keyboard.
+
|To display the previous command on the '''console''', press up-arrow key on the keyboard.
  
 
|-
 
|-
−
| 06:51
+
|06:51
−
|Edit '''n, l '''and '''m '''quantum numbers to  2 1 1.
+
|Edit '''n, l '''and '''m '''quantum numbers to  '''2 1 1'''.
  
 
|-
 
|-
 
|06:58
 
|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.'''
  
 
|-
 
|-
−
| 07:05
+
|07:05
−
| Press up arrow key again and edit '''n, l '''and '''m '''to 3  2 and -1.
+
|Press up-arrow key again and edit '''n, l '''and '''m '''to 3  2 and -1.
  
 
|-
 
|-
−
| 07:13
+
|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.'''
  
 
|-
 
|-
−
| 07:19
+
|07:19
−
| We can also save these images in different file formats like '''jpg, png''' or '''pdf'''.  
+
|We can also '''save''' these images in different file formats like '''jpg, png''' or '''pdf'''.  
  
 
|-
 
|-
−
| 07:27
+
|07:27
−
| Here is a list of commands for all '''atomic orbitals (s, p, d, '''and '''f).'''
+
|Here is a list of commands for all '''atomic orbitals (s, p, d, '''and '''f).'''
  
 
|-
 
|-
−
| 07:35
+
|07:35
−
| Shown on this slide are models of '''atomic orbitals.'''
+
|Shown on this '''slide''' are models of '''atomic orbitals.'''
  
 
|-
 
|-
−
| 07:40
+
|07:40
−
| They were created with the help of '''script commands '''written on the '''console'''.
+
|They were created with the help of '''script commands '''written on the '''console'''.
  
 
|-
 
|-
 
|07:45
 
|07:45
−
| Here I have opened a new '''Jmol panel''' and '''console''' to show how to display '''molecular orbitals.'''
+
|Here, I have opened a new '''Jmol panel''' and '''console''' to show how to display '''molecular orbitals.'''
−
 
+
  
 
|-
 
|-
−
| 07:53
+
|07:53
−
| '''Hybridized molecular orbitals '''such as '''sp<sup>3</sup>, sp<sup>2 '''</sup>and '''sp '''can be displayed using '''Jmol.'''
+
|'''Hybridized molecular orbitals '''such as '''sp<sup>3</sup>, sp<sup>2 '''</sup>and '''sp '''can be displayed using '''Jmol.'''
  
 
|-
 
|-
−
| 08:02
+
|08:02
−
| We have a model of '''methane''' on the panel.
+
|We have a model of '''methane''' on the panel.
  
 
|-
 
|-
−
| 08:06
+
|08:06
−
| '''Methane''' has '''molecular orbitals''' of the type '''sp<sup>3</sup>.'''
+
|'''Methane''' has '''molecular orbitals''' of the type '''sp<sup>3</sup>.'''
  
 
|-
 
|-
 
|08:11
 
|08:11
−
| '''Linear Combination of Atomic Orbitals i.e. LCAO''' method is used to create '''molecular orbitals. '''
+
|'''Linear Combination of Atomic Orbitals i.e. LCAO''' method is used to create '''molecular orbitals. '''
  
 
|-
 
|-
−
| 08:21
+
|08:21
−
| So, the command line starts with ''''lcaocartoon', '''followed by '''create '''and the name of the '''orbital.'''
+
|So, the command line starts with ''''lcaocartoon', '''followed by '''create '''and the name of the '''orbital.'''
  
 
|-
 
|-
 
|08:30
 
|08:30
−
 
+
|At the dollar prompt, type: "lcaocartoon create sp3"
−
 
+
−
 
+
−
| At the '''dollar prompt''' type''' lcaocartoon create sp3'''
+
  
 
|-
 
|-
−
| 08:36
+
|08:36
−
| Press '''Enter. '''
+
|press '''Enter. '''
  
 
|-
 
|-
−
| 08:38
+
|08:38
−
| Observe the model of '''methane '''with '''sp3 hybridized molecular orbitals.'''
+
|Observe the model of '''methane '''with '''sp3 hybridized molecular orbitals.'''
  
 
|-
 
|-
−
| 08:45
+
|08:45
 
|To display '''sp2 hybridized molecular orbitals,''' we will take '''ethene '''as an example.  
 
|To display '''sp2 hybridized molecular orbitals,''' we will take '''ethene '''as an example.  
  
 
|-
 
|-
−
| 08:52
+
|08:52
−
| This is a molecule of '''ethene''' on the '''panel.'''
+
|This is a molecule of '''ethene''' on the panel.
  
 
|-
 
|-
 
|08:56
 
|08:56
−
| '''Ethene''' molecule has three '''sp2 hybridized molecular orbitals.''' They are named '''sp2a, sp2b '''and '''sp2c.'''
+
|'''Ethene''' molecule has three '''sp2 hybridized molecular orbitals.''' They are named '''sp2a, sp2b '''and '''sp2c.'''
  
 
|-
 
|-
−
| 09:08
+
|09:08
−
| At the '''dollar prompt''', type''' lcaocartoon create sp2a ''', press '''Enter.'''
+
|At the dollar prompt, type:  "lcaocartoon create sp2a", press '''Enter.'''
  
 
|-
 
|-
−
| 09:17
+
|09:17
−
| Observe the '''sp2 '''orbital on the '''ethene''' model on the panel.
+
|Observe the '''sp2 '''orbital in the '''ethene''' molecule on the panel.
  
 
|-
 
|-
−
| 09:22
+
|09:22
−
| Press up arrow key and change '''sp2a''' to '''sp2b, '''press '''Enter.'''
+
|Press up-arrow key and change '''sp2a''' to '''sp2b, '''press '''Enter.'''
  
 
|-
 
|-
−
| 09:31
+
|09:31
−
| Again, press up arrow key and change '''sp2b''' to '''sp2c,'''  press '''Enter.'''  
+
|Again, press up-arrow key and change '''sp2b''' to '''sp2c,'''  press '''Enter.'''  
  
 
|-
 
|-
−
| 09:41
+
|09:41
 
|Finally for the''' pi bond, '''edit the name of the orbital as '''pz.'''
 
|Finally for the''' pi bond, '''edit the name of the orbital as '''pz.'''
  
 
|-
 
|-
 
|09:48
 
|09:48
−
| On the '''panel,''' we have '''ethene''' molecule with all the '''molecular orbitals.'''
+
|On the panel, we have '''ethene''' molecule with all the '''molecular orbitals.'''
  
 
|-
 
|-
−
| 09:55
+
|09:55
−
| This slide shows examples of few other molecules with '''molecular orbitals.'''
+
|This slide shows examples of few other molecules with '''molecular orbitals.'''
  
 
|-
 
|-
−
| 10:01
+
|10:01
−
| Explore the website for '''Jmol Script '''documentation for more information.  
+
|Explore the website for '''Jmol Script '''documentation for more information.  
  
 
|-
 
|-
−
| 10:08
+
|10:08
−
| Let's summarize.
+
|Let's summarize.
  
 
|-
 
|-
−
| 10:10
+
|10:10
−
| In this tutorial we have learnt to
+
|In this tutorial, we have learnt to:
  
 
|-
 
|-
−
| 10:12
+
|10:12
−
| Create a model of '''cyclohexane''' and '''cyclopentane'''
+
|Create a model of '''cyclohexane''' and '''cyclopentane'''
  
 
|-
 
|-
−
| 10:17
+
|10:17
−
| Create a model of '''benzene'''
+
|Create a model of '''benzene'''
  
 
|-
 
|-
−
| 10:19
+
|10:19
−
| Display '''surface topology''' of molecules.
+
|Display '''surface topology''' of molecules.
  
 
|-
 
|-
−
| 10:23
+
|10:23
−
| We also learnt to
+
|We also learned to:Display '''Atomic orbitals (s, p, d, f)'''
  
 
|-
 
|-
−
| 10:24
+
|10:29
−
| Display '''Atomic orbitals (s, p, d, f)'''
+
|Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''.
−
|-
+
−
| 10:29
+
−
| Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''.
+
  
 
|-
 
|-
−
| 10:38
+
|10:38
−
| Here is an assignment
+
|Here is an assignment-
  
 
|-
 
|-
−
| 10:40
+
|10:40
−
| Create a model of '''2-Butene''' and display '''molecular orbitals.'''
+
|Create a model of '''2-Butene''' and display '''molecular orbitals.'''
  
 
|-
 
|-
−
| 10:45
+
|10:45
−
| Explore''' lcaocartoon '''command to change the color and size of '''molecular orbitals.'''
+
|Explore''' lcaocartoon '''command to change the color and size of '''molecular orbitals.'''
  
 
|-
 
|-
−
| 10:52
+
|10:52
−
| Refer the following link for list of commands.
+
|Refer the following link for list of commands.
  
 
|-
 
|-
−
| 10:57
+
|10:57
−
| Watch the video available at this URL.
+
|Watch the video available at this URL:
−
 
+
http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
−
[http://spoken-tutorial.org/What http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial]
+
  
 
|-
 
|-
−
| 11:01
+
|11:01
−
| It summarizes the Spoken Tutorial project
+
|It summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 11:04
+
|11:04
−
| 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.
  
 
|-
 
|-
−
| 11:09
+
|11:09
−
| The Spoken Tutorial Project Team:  
+
|The Spoken Tutorial Project team:  
  
 
|-
 
|-
−
| 11:11
+
|11:11
−
| Conducts workshops using spoken tutorials
+
|Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 11:15
+
|11:15
−
| Gives certificates to those who pass an on-line test  
+
|Gives certificates to those who pass an on-line test.
  
 
|-
 
|-
−
| 11:19
+
|11:19
−
| For more details, please write to contact@spoken-tutorial.org  
+
|For more details, please write to: '''contact@spoken-tutorial.org'''
  
 
|-
 
|-
 
|11:26
 
|11:26
−
| Spoken Tutorial Project is a part of the Talk to a Teacher project  
+
|'''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.
  
 
|-
 
|-
−
| 11:30
+
|11:30
−
| It is supported by the National Mission on Education through ICT, MHRD, Government of India
+
|It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
−
| 11:37
+
|11:37
−
| More information on this Mission is available at this link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro] ]
+
|More information on this mission is available at this link:
 +
http://spoken-tutorial.org/NMEICT-Intro
  
 
|-
 
|-
−
| 11:42
+
|11:42
−
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
|This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
−
 
+
 
|}
 
|}

Latest revision as of 17:42, 28 March 2017

Time Narration
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 the 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,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 option.
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 the 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 atomic orbital".
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 in the ethene molecule 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 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.
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_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

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

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Surfaces-and-Orbitals/English-timed&oldid=34547"