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

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'''Title of script''': Surfaces and Orbitals
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== '''Title of script''': Surfaces and Orbitals
  
 
'''Author: '''Snehalatha Kaliappan
 
'''Author: '''Snehalatha Kaliappan
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Latest revision as of 16:55, 1 September 2020

== 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.

Visual Cue
Narration
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,
  • Create models of Alicyclic and Aromatic molecules.
  • Display different surfaces of molecules.
  • Display Atomic and Molecular orbitals.
Slide Number 3

Pre-requisites

To follow this tutorial, you should know how to create and edit molecular models in Jmol Application.

If not, watch the relevant tutorials available at our website.

Slide Number 4

System Requirement

To record this tutorial, I am using
  • Ubuntu OS version. 12.04
  • Jmol version 12.2.2 and
  • Java (JRE) version 7
Cursor on Jmol panel I have opened a new Jmol application window.
Cursor on Jmol panel Let us first create a model of cyclohexane.
Click on the modelkit icon in the tool bar Click on modelkit menu.

A model of methane appears on the panel.

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.

This is a model of ethane on screen.

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.

Click on the hydrogens in such a way that the structure forms a circle.

Click on Rotate molecule tool and rotate the model. Now, rotate the structure on screen using the Rotate molecule tool.
Cursor on the butane structure This is the structure of butane on the panel.


Click on the modelkit menu.

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.
Click on minimize option in the modelkit menu Use minimize option in the modelkit menu to optimize the structure.
Cursor on the panel. 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.
Cursor on the panel. I will use a model of pentane to demonstrate this feature.
Open new Jmol window with pentane structure.

Open modelkit menu and check against Drag to bond option.

This is a model of pentane on the panel.


To convert this into cyclopentane, select Drag to bond option from the modelkit menu.

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.

Now release the mouse button.

Cursor on the panel We have a model of cyclopentane on the panel.
Cursor on the panel Now Let us go back to the Jmol panel with the model of cyclohexane.
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.

To view different surfaces, open the pop-up menu.

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".


A sub-menu opens with many options.

  • Dot Surface
  • van der Waal's
  • and some others.
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.
Cursor on the panel. 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.


Observe that the benzene model has become opaque.

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”. scroll down to Off and click on it.

Now, we have a model of benzene without any surfaces.

<<Pause>>

Cursor on Jmol panel. Jmol can display atomic and molecular orbitals of molecules.
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.


Select 'New' and click on it.

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 ($) dollar prompt type isosurface phase atomicorbital.

This is followed by quantum numbers n. l and m that are specific for each atomic orbital.

Type: 2 0 0 To display 's' orbital. type 2 0 0


Numbers 2, 0, 0 represent n, l and m quantum numbers respectively.

Press Enter key Press Enter key to execute the command.


We have s orbital displayed on the panel.

Cursor on the console. Here are few more examples of atomic orbitals and the corresponding script commands.
Cursor on the console.

Press up arrow key on the keyboard.

The command line is same for all atomic orbitals.


To display the previous command on the console, press up arrow key on the keyboard.

Delete 2 0 0 and type 2 1 1 Edit n, l and m quantum 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.
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.

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.

Cursor on the panel. Here I have opened a new Jmol panel and console to show how to display molecular orbitals.


Hybridized molecular orbitals such as sp3, sp2 and sp can be displayed using Jmol.

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

Linear Combination of Atomic Orbitals (LCAO) method is used to create molecular orbitals.

So, the command line starts with 'lcaocartoon', followed by create and the name of the orbital.

Type lcaocartoon create sp3a


>> Press Enter

At the dollar prompt type lcaocartoon create sp3


Press Enter.

Cursor on the Jmol panel. Observe the model of methane with sp3 hybridized molecular orbitals.
Cursor on Jmol panel. To display sp2 hybridized molecular orbitals, we will take ethene as an example.
Use “Open a file” option in the tool bar to open model of ethene. This is a molecule of ethene on the panel.
Cursor on the panel Ethene molecule has three sp2 hybridized molecular orbitals. They are named sp2a, sp2b and sp2c.
Type lcaocartoon create sp2a At the dollar prompt, type lcaocartoon create sp2a and press Enter.

Observe the sp2 orbital on the ethene model on the panel.

Press the up arrow key. Press up arrow key and change sp2a to sp2b, press Enter.
Press the up arrow key. Again, press up arrow key and change sp2b to sp2c, 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

  • Create a model of cyclohexane and cyclopentane
  • Create a model of benzene
  • Display surface topology of molecules.
Slide Number 11

Summary

We also learnt to
  • Display Atomic orbitals (s, p, d, f)
  • Display Molecular orbitals (sp3, sp2 and sp) by writing script commands on the console.
Slide Number 12

Assignment

Here is an assignment
  • Create a model of 2-Butene and display molecular orbitals.
  • Explore lcaocartoon command to change the color and size of molecular orbitals.

Refer the following link for list of commands.

http://chemapps.stolaf.edu/jmol/docs/‎

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. 
==

Contributors and Content Editors

Madhurig, Nancyvarkey, Snehalathak

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