Welcome to this tutorial on Surfaces and Orbitals in Jmol Application.
In this tutorial, we will learn to:
Create models of alicyclic and aromatic molecules.
Display different surfaces of molecules.
Display atomic and molecular orbitals.
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.
To record this tutorial, I am using:
Ubuntu OS version 12.04
Jmol version 12.2.2 and
Java (JRE) version 7.
I have opened a new Jmol application window.
Let us first create a model of cyclohexane.
Click on modelkit menu.
A model of methane appears on the panel.
To create cyclohexane, we have to make a hydrocarbon chain of six carbon atoms.
We will substitute the hydrogen in the model with a methyl group.
To do so, we will place the cursor on the hydrogen and click on it.
This is a model of ethane on screen.
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.
Now, rotate the structure on screen using the Rotate molecule tool.
This is the structure of butane on the panel.
Click on the modelkit menu.
Click on hydrogen on any of the carbon atoms present at the end of the chain.
Here is a model of pentane on the panel.
Click on one of the hydrogens, that is close to the end of the carbon chain.
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.
Alternately, we can also use Drag to bond option in the modelkit menu to create cyclic structures.
I will use a model of pentane to demonstrate this feature.
This is a model of pentane, on the panel.
To convert this into cyclopentane, select Drag to bond option from the modelkit menu.
Place the cursor on the carbon present at one end of the chain.
Hold down the mouse button.
Without releasing the mouse button, bring the cursor to the carbon present at the other end of the chain.
Now, release the mouse button.
We have a model of cyclopentane on the panel.
Now, let us go back to the Jmol panel with the model of cyclohexane.
Let us now convert cyclohexane to a benzene ring.
We have to introduce double-bonds at alternate positions in the cyclohexane ring.
Open the modelkit menu.
Place the cursor on the bond between any two carbon atoms and click on it.
We now have cyclohexene 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 the next two alternate carbon atoms.
We have a model of benzene on the panel.
Do the energy minimization to get a stable conformation.
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.
Now, right-click on the panel to open the Pop-up menu.
Scroll down and select "Surfaces".
A sub-menu opens with many options-
Dot Surface,
van der Waal's,and some others.
For demonstration purpose, I will select Molecular surface.
The model of Benzene is displayed with a molecular surface.
Let us change it to another surface, say, Dot Surface.
So, open the pop-up menu again and choose Dot Surface.
We can also make the surfaces opaque or translucent.
To do so, open the Pop-up menu.
Scroll down to Surfaces and select Make Opaque option.
Observe that the benzene model has become opaque.
To turn off the surface option- open the pop-up menu, choose Surfaces,
scroll down to Off and click on it.
Now, we have a model of benzene without any surfaces.
Jmol can display atomic and molecular orbitals of molecules.
Atomic orbitals can be displayed on the screen by writing commands on the console.
Open a new Jmol window by clicking on File and New.
Now, open the console window by clicking on File and then on Console.
The console window opens on the screen.
I am using KMag Screen magnifier to magnify the console window.
The command line for atomic orbitals starts with isosurface phase atomicorbital.
At the ($) dollar prompt, type: "isosurface phase atomic orbital".
This is followed by quantum numbers n, l and m that are specific for each atomic orbital.
To display 's' orbital, type: 2 0 0
The Numbers 2, 0, 0 represent n, l and m quantum numbers respectively.
Press Enter key to execute the command.
We have s-orbital displayed on the panel.
Here are few more examples of atomic orbitals and the corresponding script commands.
The command line is same for all atomic orbitals.
To display the previous command on the console, press up-arrow key on the keyboard.
Edit n, l and m quantum numbers to 2 1 1.
Press Enter key and see the 'px' orbital on the Jmol panel.
Press up-arrow key again and edit n, l and m to 3 2 and -1.
Press Enter key and see the 'dxy' orbital on the Jmol panel.
We can also save these images in different file formats like jpg, png or pdf.
Here is a list of commands for all atomic orbitals (s, p, d, and f).
Shown on this slide are models of atomic orbitals.
They were created with the help of script commands written on the console.
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.
We have a model of methane on the panel.
Methane has molecular orbitals of the type sp3.
Linear Combination of Atomic Orbitals i.e. LCAO method is used to create molecular orbitals.
So, the command line starts with 'lcaocartoon', followed by create and the name of the orbital.
At the dollar prompt, type: "lcaocartoon create sp3"
press Enter.
Observe the model of methane with sp3 hybridized molecular orbitals.
To display sp2 hybridized molecular orbitals, we will take ethene as an example.
This is a molecule of ethene on the panel.
Ethene molecule has three sp2 hybridized molecular orbitals. They are named sp2a, sp2b and sp2c.
At the dollar prompt, type: "lcaocartoon create sp2a", press Enter.
Observe the sp2 orbital in the ethene molecule on the panel.
Press up-arrow key and change sp2a to sp2b, press Enter.
Again, press up-arrow key and change sp2b to sp2c, press Enter.
Finally for the pi bond, edit the name of the orbital as pz.
On the panel, we have ethene molecule with all the molecular orbitals.
This slide shows examples of few other molecules with molecular orbitals.
Explore the website for Jmol Script documentation for more information.
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.
We also learned to:Display Atomic orbitals (s, p, d, f)
Display Molecular orbitals (sp3, sp2 and sp) by writing script commands on the console.
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.
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