Jmol-Application/C3/Bond-Rotation-in-Jmol/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Bond Rotation in Jmol.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to, Use tools in the modelkit 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.
Slide Number 3 System Requirement	Here I am using, Ubuntu Linux OS version 20.04 Jmol version 14.32.80 Java version 11.0.16
Slide Number 4 Pre-requisites https://spoken-tutorial.org	To follow this tutorial the learner, must have knowledge of high school chemistry. must be familiar with basic operations of Jmol. For the prerequisite Jmol tutorials please visit this website.
Slide number 5 Conformations of 1,2-Dichloroethane	The most prominent conformations of 1,2- dichloroethane are anti and gauche. Anti conformer is more stable when compared to gauche. Eclipsed conformer is unstable. These conformers are interconvertible by C-C bond rotation.
Cursor on Jmol interface.	Here I have opened the Jmol Application window.
Click on the model kit menu.	Let us create a model of 1,2-dichloroethane on the Jmol panel. Click on the model kit menu on the toolbar to get the model of methane on the panel.
Cursor on the modelkit menu options. Click on one of the hydrogen atoms.	Make sure that carbon is selected in the atoms panel in the model kit menu. Click on any one of the hydrogen atoms in the methane model. This creates a model of ethane.
click on the minimize option from the model it menu.	Do the energy minimization, click on the minimize option from the model kit menu. This will display the more stable anti conformation.
In the model kit menu, select the chlorine atom with symbol C.l 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 the model kit menu, now select the chlorine atom with symbol Cl. 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 box.
Cursor on the ethane molecule.	I have selected the chlorine atom. We need to replace one hydrogen atom on each carbon with a chlorine atom.
Click on the molecule and rotate.	Rotate the ethane molecule in such a way that you can see the Newman projection.
click on the hydrogen atoms that are staggered to each other to get 1,2 dichloroethane. Cursor on chlorine atoms.	Now click on the hydrogen atoms that are opposite to each other. 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.
Click the File menu. Click on Console from the options.	To view the labeling of atoms, open the console from the File menu.
At the prompt, type, Select all Press Enter At the prompt, type, label on Press Enter	At the prompt, type, Select all and press Enter. 8 atoms are selected, Type, label on and press Enter.
Cursor on the molecule.	Close the Console window. The labels for all the atoms are now visible.
Double-click on the chlorine atom on C1. Then click on C1, next click on C2 then double-click on chlorine atom on C2.	Let's measure the dihedral angle between the two chlorine atoms in this model. 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.
Cursor on the model. 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.	This model is staggered 1,2-dichloroethane. 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.
Click on the model and rotate.	We will create models of gauche and eclipsed conformers by rotating the C-C bond.
Cursor on the model.	To create a gauche conformer, we need to rotate the C1-C2 bond by 120 degrees. There are two ways by which we can achieve this.
Slide number 6 Bond Rotation Tools	Using the bond rotating tool from the modelkit menu. Typing Jmol script commands on the Console.
Open the modelkit menu, click on the rotate bond option.	Let us first use the bond rotating tool. Open the modelkit menu, click on the rotate bond radio button to activate it.
Click on the bond connecting C1 and C2 atoms. Hover the mouse over C1 carbon atom. Cursor on Rotate branch C1 message	Click on the bond connecting C1 and C2 atoms. Hover the mouse over the C1 carbon atom. rotate branch C1 message is displayed on the panel.
Click the C1 atom and rotate it.	Click the C1 atom and rotate it. Stop rotating when you see the dihedral angle between the two chlorine atoms is -60 degrees. Users may rotate the carbon atom accordingly.
Cursor on the panel.	This conformation of 1,2-dichloroethane on the panel is gauche.
Open modelkit menu and choose Save file option. I will type as Gauche-DCE.mol, location as documents folder. Select “Files of Type” as .mol Click on Save button.	Save the model as a mol file using the Save file option in the modelkit menu. 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 the name as Gauche-DCE.mol. Click on Save button.
Rotate the model.	Let us rotate the gauche conformer to show its Newman projection.
Cursor on the model. Click on the file menu and select Console from the options.	Back to the gauche conformation. Let us use script commands and create a model of eclipsed conformation. Close the modelkit menu if it is open.
At the prompt type, select connected (C1) and not (C2);	Open the Console window from the File menu. Type the following command at the prompt to select the bond connecting C1 and C2 atoms. Press the Enter key.
At the prompt type, rotate BRANCH {C2} {C1} 60 30	Next type the following command to rotate the branch attached to C1 carbon. This command will rotate the C1 atom in the anti-clockwise direction. The number, 60 indicates the angle and 30 is the speed of rotation. I will resize the Console to show the model. Press the Enter key.
Slide Number 7 Links for Jmol Script Commands https://chemapps.stolaf.edu/jmol/docs/ rotate command: https://chemapps.stolaf.edu/jmol/docs/#rotate	For more details on script commands please use the following web links.
Slide Number 8 Link for Script commands ST video https://spoken-tutorial.org/tutorial-search/?search_foss=Jmol+Application&search_language=English.	Please watch the video on script commands. It is available on Spoken Tutorial website in the Jmol Application series
Cursor on Jmol Panel.	Back to the Jmol panel. Close the Console window. The model on the panel is of eclipsed conformation. The dihedral angle between two chlorine atoms is 0 degrees.
Open modelkit menu and choose Save file option. I will type as Eclipsed-DCE.mol, location as documents folder. Select “Files of Type” as .mol Click on Save button.	Save the model as a mol file. Use the Save file option in the model kit menu. 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 its Newman projection.
Slide Number 9 Summary	Let's summarize what we have learnt. 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
Slide Number 10 Assignment	As an assignment, Explore the rotate command to create models of conformations of n-butane.
Slide Number 11 About Spoken Tutorial Project	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 12 Spoken tutorial workshops	We conduct workshops using spoken tutorials and give certificates. For more details, please contact us.
Slide Number 13 Answers for THIS Spoken Tutorial	Please post your timed queries in this forum.
Slide Number 14 Acknowledgement	Spoken Tutorial project is funded by the Ministry of Education (MoE), Govt. of India
Acknowledgement	The script for this tutorial is contributed by Snehalatha Kaliappan. This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for watching.

Contributors and Content Editors

Madhurig, Snehalathak