View source for Jmol-Application/C3/Bond-Rotation-in-Jmol/English

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||'''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 '''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'''.


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|| '''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.
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|| 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.
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|| 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.

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|| 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.
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|| 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.

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|| 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.
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|| 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/ 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.

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|| 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. 
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