Difference between revisions of "Jmol-Application/C3/Bond-Rotation-in-Jmol/English"

Title Slide

Learning Objectives

Use tools in the model-kit menu to rotate bonds.

Use script commands to rotate specific bonds in a model.

Create models of anti, gauche and eclipsed

conformers of 1,2-dicholoroethane.

System Requirement

Ubuntu Linux OS version 20.04

Jmol version 14.32.80

Java version 11.0.16

Pre-requisites

https://spoken-tutorial.org

must have knowledge of high school chemistry.

must be familiar with basic operations of Jmol.

For the prerequisite Jmol tutorials please visit this website.

Conformations of 1,2-Dichloroethane

Anti conformer is more stable when compared to gauche

Eclipsed conformer is unstable.

The conformers are interconvertible by C-C bond rotation

Click on the model kit menu on the toolbar to get the model of methane on the panel.

Click on one of the hydrogen atoms.

Click on one of the hydrogen atoms in the methane model.

This creates a model of ethane.

This will display the more stable anti conformation.

Click on the option which shows a question mark.(??)

In the input box, type the symbol of the chlorine as Cl.

Click on OK in the input dialog box.

In case you don’t find chlorine in the options, then do the following:

Click on the option which shows a question marks.

An input box opens. Type the symbol of the element in the input box.

I will type Cl for chlorine and click on OK in the input dialog box.

We need to replace one hydrogen atom on each carbon with a chlorine atom.

Cursor on chlorine atoms.

The hydrogen atoms in the model will be replaced by chlorine atoms.

Here is the model of anti conformer of 1,2 dichloroethane.

Exit the modelkit menu.

Select all

Press Enter

At the prompt, type, label on

Press Enter

Select all

and press Enter

8 atoms are selected,

Type,

label on

and press Enter

The labels for all the atoms are now visible.

Then click on C1, next click on C2 then double-click on chlorine atom on C2.

Rotate the model on the panel so that you have a clear view of the C1-C2 bond.

Double-click on the chlorine atom on C1.

Then click on C1, next click on C2 then double-click on chlorine atom on C2.

The dihedral angle of -180 degrees is displayed on the screen.

Click on the modelkit icon on the toolbar. click on save file option.

I will select the documents folder.

Select “Files of Type” as .mol

Name the file as Anti-DCE.mol

Click on Save button.

We will save this model as a mol file.

Open the model kit menu , click on Save file option.

In the dialog-box, select the file destination.

I will select the documents folder.

Select “Files of Type” as .mol

Name the file as Anti-DCE.mol

Click on Save button.

There are two ways by which we can achieve this.

Bond Rotation Tools

Typing Jmol script commands on the Console.

Open the modelkit menu, click on the rotate bond radio button to activate it.

Hover the mouse over C1 carbon atom. Cursor on Rotate branch C1 message

Hover the mouse over the C1 carbon atom.

rotate branch C1 message is displayed on the panel.

Stop rotating when you see the dihedral angle between the two chlorine atoms is -60 degrees.

Users may rotate the carbon atom accordingly.

I will type as Gauche-DCE.mol, location as documents folder.

Select “Files of Type” as .mol

Click on Save button.

Give an appropriate file name and a preferred location.

I will select the location as Documents folder.

Select Files of Type as .mol

I will type as Gauche-DCE.mol.

Click on Save button.

Click on the file menu and select Console from the options.

Let us use script commands and create a model of eclipsed conformation.

Close the modelkit menu if it is open.

select connected (C1) and not (C2);

Type the following command at the prompt to select the bond connecting C1 and C2 atoms.

Press the Enter key.

rotate BRANCH {C2} {C1} 60 30

This command will rotate the C1 atom in the anti-clockwise direction.

The numbers, 60 indicates the angle and 30 is the speed of rotation.

I will resize the Console to show the model.

Press the Enter key.

Links for Jmol Script Commands

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

rotate command:

https://chemapps.stolaf.edu/jmol/docs/#rotate

Link for Script commands ST video

https://spoken-tutorial.org/tutorial-search/?search_foss=Jmol+Application&search_language=English.

It is available on Spoken Tutorial website in the Jmol Application series

Close the Console window.

The model on the panel is of eclipsed conformation. The dihedral angle between two chlorine atoms is 0 degrees.

I will type as Eclipsed-DCE.mol, location as documents folder.

Select “Files of Type” as .mol

Click on Save button.

Give an appropriate file name and a preferred location.

I will select the location as the Documents folder.

Select “Files of Type” as .mol

I will type the name as Eclipsed-DCE.mol.

Click on Save button.

Let us rotate the eclipsed conformer to show Newman's projection.

Summary

In this tutorial, we have:

• Used tools in the model-kit menu to rotate bonds.
• Used script commands to rotate specific bonds in a model
• Created models of anti, gauche and eclipsed conformers of 1,2-dicholoroethane

Assignment

Explore the rotate command to create models of conformations of n-butane.

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Acknowledgement

* The script for this tutorial is contributed by Snehalatha Kaliappan.

• This is Madhuri Ganapathi from IIT Bombay signing off.

Thank you for joining.