Jmol-Application/C2/Surfaces-and-Orbitals/English-timed
From Script | Spoken-Tutorial
Revision as of 17:34, 9 March 2017 by PoojaMoolya (Talk | contribs)
| |
|
|---|---|
| 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: |
| 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: |
| 11:42 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
