Jmol-Application/C2/Surfaces-and-Orbitals/English
Title of script: Surfaces and Orbitals
Author: Snehalatha Kaliappan
Keywords: Molecular visualization, 3D models of chemical structures, Alicyclic and Aromatic molecules, surface topology, Atomic and Molecular orbitals, Video tutorial, Jmol tutorial.
Outline:-
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| Slide Number 1
Title Slide |
Welcome to this tutorial on Surfaces and Orbitals in Jmol Application. |
| Slide Number 2
Learning Objectives |
In this tutorial, we will learn to,
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| Slide Number 3
Pre-requisites |
To follow this tutorial, you should know how to create and edit molecular models in Jmol Application.
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| Slide Number 4
System Requirement |
To record this tutorial, I am using
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| Cursor on Jmol panel | I have opened a new Jmol application window.
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| Cursor on Jmol panel | Let us first create a model of cyclohexane.
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| Click on the modelkit icon in the tool bar | Click on modelkit menu.
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| Cursor on Jmol panel | To create cyclohexane, we have to make a hydrocarbon chain of six carbon atoms. |
| Cursor on methane. | We will substitute the hydrogen in the model with a methyl group. |
| Cursor on the hydrogen of the methane.
Click on the hydrogen. |
To do so, we will place the cursor on the hydrogen and click on it.
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| Cursor on the Ethane molecule >> Click on hydrogen. | Repeat this step another 2 times and replace one hydrogen at a time with a methyl group.
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| Click on Rotate molecule tool and rotate the model. | Now, rotate the structure on screen using the Rotate molecule tool.
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| Cursor on the butane structure | This is the structure of butane on the panel.
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| Click on hydrogen at the end of the chain. | Click on hydrogen on any of the carbon atoms present at the end of the chain. |
| Cursor on pentane structure. | Here is a model of pentane on the panel. |
| Cursor on hydrogen atom. | Click on one of the hydrogens, that is close to the end of the carbon chain. |
| Cursor on Cyclohexane. | A model of cyclohexane is created on the panel. |
| Use minimize option in the modelkit menu to optimize the structure. | |
| The model of Cyclohexane is now, in its most stable “chair” conformation. | |
| Open modelkit menu and scroll down to Drag to bond option. | Alternately, we can also use Drag to bond option in modelkit menu to create cyclic structures.
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| I will use a model of pentane to demonstrate this feature. | |
| Open new Jmol window with pentane structure.
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This is a model of pentane on the panel.
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| Click on carbon at one end of the chain. | Place the cursor on the carbon present at one end of the chain.
Hold down the mouse button. |
| Bring the cursor to other end of the chain and click on the carbon. | Without releasing the mouse button, bring the cursor to the carbon present at the other end of the chain.
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| Cursor on the panel | We have a model of cyclopentane on the panel. |
| Now Let us go back to the Jmol panel with the model of cyclohexane.
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| Cursor on Cyclohexane. | Let us now convert cyclohexane to a benzene ring.
We have to introduce double bonds at alternate positions in the cyclohexane ring. |
| Click on “modelkit” icon. | Open the modelkit menu. |
| Click on the bond between two carbon atoms. | Place the cursor on the bond between any two carbon atoms and click on it. |
| Cursor on cyclohexene. | We now have cyclohexene on the panel. |
| Cursor on the panel. | Next, we need to introduce two more double bonds in the structure, to convert it to benzene. |
| Click on the bond between next two carbon atoms >> Repeat the above step. | Click on the bond between the next two alternate carbon atoms.
We have a model of benzene on the panel. |
| Cursor on Benzene. | Do the energy minimization to get a stable conformation. |
| Cursor on panel | Surface topology of the molecules can be displayed by using Jmol Application.
Ensure that the modelkit menu is closed if it is open. |
| Right click to open Pop-up-menu | Now, right-click on the panel, to open the Pop-up menu. |
| Scroll down to “Surfaces” | Scroll down and select “Surfaces”.
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| Select “Molecular Surface”. | For demonstration purpose, I will select Molecular surface. |
| Cursor on Benzene. | The model of Benzene is displayed with a molecular surface. |
| Right click to open Pop-up-menu.
scroll down to 'Surfaces' |
Let us change it to another surface, say, Dot Surface. |
| Click on Solvent accessible surface. | So, open the Pop-up menu again, and choose Dot Surface. |
| We can also make the surfaces opaque or translucent. | |
| Right click to open Pop-up-menu >> Select 'Surfaces' Scroll down >> Click on 'Make Opaque' | To do so, open the Pop-up menu again, choose Surfaces and select Make Opaque option.
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| Right click to open Pop-up-menu. Scroll down to “Surfaces”. | To turn off the surface option, open the Pop-up menu and choose Surfaces. |
| Click on “Off”. | Now, scroll down to Off and click on it.
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| Cursor on Jmol panel. | Jmol can display atomic and molecular orbitals of molecules.
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| Cursor on Jmol panel. | Atomic orbitals can be displayed on screen by writing commands on the console. |
| Click on file option in the menu bar.
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Open a new Jmol window by clicking on File and New. |
| Scroll down the options in the 'File' menu.
Click on 'Console' option. |
Now open the console window by clicking on File and then on Console. |
| Cursor on the console. | The console window opens on the screen.
I am using Kmag Screen magnifier to magnify the console window. |
| On the console, at the $ prompt, type:
isosurface phase atomicorbital |
The command line for atomic orbitals starts with isosurface phase atomicorbital.
At the $ prompt type isosurface phase atomicorbital. This is followed by quantum numbers n.l.m that are specific for each atomic orbital. |
| Type: 2 0 0 | To display 's' orbital. type 2 0 0
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| Press Enter key | Press Enter key to execute the command.
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| Cursor on the console. | Here are few more examples of atomic orbitals and the corresponding script commands. |
| Cursor on the console.
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The command line is same for all atomic orbitals.
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| Delete 2 0 0 and type 2 1 1 | Edit n, l and m numbers to 2 1 1. |
| Press Enter key. | Press Enter key and see the 'px' orbital on the Jmol panel. |
| Press up arrow key on the keyboard. | Press up arrow key again and edit n, l and m to 3 2 and -1. |
| Press enter key. | Press Enter key and see the 'dxy' orbital on the Jmol panel.
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| Cursor on the panel. | We can also save these images in different file formats like jpg, png or pdf. |
| Slide Number 5
Script commands for Atomic Orbitals.
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Here is a list of commands for all atomic orbitals (s, p, d, and f). |
| Slide Number 6
Types of Atomic Orbitals |
Shown on this slide are models of atomic orbitals.
They were created with the help of script commands written on the console. |
| Here I ave opened a new Jmol panel and console to show how to display molecular orbitals.
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| Open a new Jmol window and click on modelkit mode. | We have a model of methane on the panel. |
| Cursor on methane. | Methane has molecular orbitals of the type sp3. |
| Slide number 7
Molecular Orbitals |
TheLinear Combination of Atomic Orbitals (LCAO) method is used to create molecular orbitals.
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| Type lcaocartoon create sp3a
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At the dollar prompt type lcaocartoon create sp3
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| Cursor on the jmol panel. | Observe the model of methane with sp3 hybridized molecular orbitals. |
| To display sp2 hybridized molecular orbitals, we will take ethene as an example. | |
| Open a new Jmol panel with Ethene molecule. | This is a molecule of ethene on the panel. |
| Cursor on the panel | Ethene molecule has three sp2 hybridized molecular orbitals. They are named as sp2a, sp2b and sp2c. |
| Type lcaocartoon create sp2a | Type lcaocartoon create sp2a and press Enter.
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| Press the up arrow key. | Press up arrow key and change sp2a to sp2b and press Enter. |
| Press the up arrow key. | Again, press up arrow key and change sp2b to sp2c and press Enter. |
| Press the up arrow key. | Finally for the pi bond, edit the name of the orbital as pz. |
| Rotate the model. | On the panel, we have ethene molecule with all the molecular orbitals. |
| Slide number 8
Types of molecular orbitals |
This slide shows examples of few other molecules with molecular orbitals. |
| Slide number 9 | Explore the website for Jmol Script documentation for more information. |
| Slide Number 10
Summary |
Let's summarize.
In this tutorial we have learnt to
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| Slide Number 11
Summary |
* Display Atomic orbitals (s, p, d, f)
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| Slide Number 12
Assignment |
Here is an assignment
Refer the following link for list of commands. |
| Slide Number 13
Acknowledgement |
Watch the video available at this URL.
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial It summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it |
| Slide Number 14 | The Spoken Tutorial Project Team:
Conducts workshops using spoken tutorials Gives certificates to those who pass an on-line test For more details, please write to contact@spoken-tutorial.org |
| Slide number 15 | Spoken Tutorial Project is a part of the Talk to a Teacher project
It is supported by the National Mission on Education through ICT, MHRD, Government of India More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro ] |
| This is Snehalatha from IIT Bombay signing off. Thank you for joining. |
