Hello everyone.Welcome to this tutorial on Create and Edit molecular models in Jmol Application.
In this tutorial, we will learn to:
Substitute hydrogen atom in a molecular model with a functional group.
Add and delete bonds
Add and delete atoms and
learn how to use the Pop-up menu, also known as contextual menu.
To follow this tutorial, you should be familiar with-
Jmol Application window and
Modelkit function that is used to create molecular models.
For relevant tutorials, please visit our website.
To record this tutorial, I am using:
Ubuntu OS version 12.04
Jmol version 12.2.2
And Java version 7.
To open the Jmol Application, click on Dash home.
Type Jmol in the search box.
Jmol icon appears on the screen.
Click on the Jmol icon to open the Jmol application window.
Let's begin with the model of Propane which we had created earlier.
To open the file, click on “Open file” icon on the tool bar.
A dialog-box appears on the screen.
Click on the folder where the required file is located.
My file is located on the Desktop.
So, I will select Desktop and click on the Open button.
Type the file name in the “File or URL” text box.
Then, click on the Open button.
The Model of Propane appears on the screen.
We can substitute hydrogens in the Propane with functional groups like:
hydroxy, amino, halogens like fluro, chloro, bromo and others.
I want to add a hydroxy group to the Propane molecule to convert it to Propanol.
Open the model kit menu. A list of functional groups is available here.
Check the box against oxygen atom.
Click on the hydrogen atom attached to the first carbon atom.
Observe that the hydrogen atom is replaced by hydroxy group. Oxygen atom is seen in red color here.
Propane is now converted to 1-Propanol.
Let's now try to convert 1-Propanol to 2-chloro-1-propanol.
Select Chloro group from the model kit menu.
Click on the hydrogen atom attached to the second carbon atom.
We now have the model of 2-chloro-1-propanol. Chlorine is seen in green color here.
You can do energy minimization and save the image as dot mol file.
Here is an assignment-Create models of the following molecules:3-bromo-1-butanol and 2-amino-4-chloro-pentane.
Do energy minimization and save the image in JPEG format.
To save the image in different file formats,
use “Save current view as an image” icon in the Tool bar.
Your completed assignment should look as follows.
Now, let's go back to the Jmol Application window.
Jmol Application also offers a Pop-up menu.
You can access the pop-up menu by two different methods.
Exit the model kit menu, if it is open.
Scroll down the model kit menu and click “Exit model kit mode”.
To open the Pop-up menu, right-click the mouse button on the panel.
Pop-up menu appears on the panel.
Pop-up menu offers many functions to modify the display of atoms.
It has a variety of selection and rendering options.
Most of the functions in this menu are duplicated in the menu bar.
The items in the Pop-up menu are self-explanatory.
They don't need a detailed description.
Click on the Jmol panel to exit the Pop-up menu.
The second way to access the Pop-up menu is to click on the Jmol logo.
It is located at the bottom right corner of the Jmol panel.
Now, let's see how to edit this molecule and convert it to Ethane molecule.
For this, we will delete the hydroxy group, the chlorine group, the carbon and two hydrogen atoms.
Open the model kit menu.
Check the box against “delete atom”.
Click on the atoms you want to delete-
Oxygen, chlorine and the carbon atom.
We have to add hydrogens to this molecule, to create an ethane molecule.
Click on “add hydrogens” option from the model kit menu.
Two hydrogen atoms are added to the molecule.
We now have the model of Ethane on the screen.
Let's learn how to create alkenes and alkynes.
To introduce a double-bond in the molecule, open the model kit menu.
Check against “double” option.
Place the cursor on the bond between two carbon atoms in the Ethane molecule.
Red colored rings appear around the carbon atoms.
Click on the bond.
Observe that the single-bond is converted to a double-bond.
We have a model of Ethene on the panel.
Now, let's convert Ethene to Ethyne.
Click on the modelkit menu and check against “triple” option.
Place the cursor on the double-bond in the Ethene molecule and click on it.
The double-bond is converted to a triple-bond.
This is the model of Ethyne.
Do the energy minimization to get the most stable conformation and save.
Let's summarize.In this tutorial, we have learnt to:
Substitute the hydrogen atom in alkanes with a functional group.
Add bonds to convert alkanes to alkenes and alkynes
Add and delete atoms and
Use the Pop-up-menu.
For the Assignment-Create the models of 2-fluoro-1,3-butadiene and 2-pentyne.
Use the Pop-up menu to change the display of the model to wireframe.
Do energy minimization and save the image in PDF format.
Your completed assignment should look as follows.
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This is Snehalatha from IIT Bombay, signing off. Thank you for joining.