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

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 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_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