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

Madhurig at 12:26, 16 December 2025

2025-12-16T12:26:17Z

Snehalathak at 10:49, 3 February 2023

2023-02-03T10:49:45Z

Snehalathak at 10:49, 3 February 2023

2023-02-03T10:49:25Z

Snehalathak at 10:48, 3 February 2023

2023-02-03T10:48:55Z

Madhurig at 08:14, 3 February 2023

2023-02-03T08:14:36Z

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Madhurig at 07:47, 3 February 2023

2023-02-03T07:47:02Z

Snehalathak: Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on '''Bond Rotation in Jmol.''' |- || '''Slide Numbe..."

2023-01-27T12:49:36Z

Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on '''Bond Rotation in Jmol.''' |- || '''Slide Numbe..."

New page

{|border=1
||'''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.

|-
|| '''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

The 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 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 dialog 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.
|| Rotate the molecule so that you can view the C-C bond.

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.
|| First, let us 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 on C1 atom and rotate it.
|| Click on 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 the Documents folder.

Select '''Files of Type''' as .mol

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

Click on '''Save''' button.
|-
|| Rotate the model.
|| Let us rotate the '''gauche''' conformer to show '''Newman's''' 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 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 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.

|-
|| '''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 weblinks.

|-
|| '''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 '''Newman's''' projection.

|-
|| '''Slide Number 9'''

'''Summary'''
|| Let's summarize what we have learnt.

* 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'''
|| 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 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 joining.
|-
|}

@@ Line 391: / Line 391: @@
 '''Link for Script commands ST video'''
-'''https://spoken-tutorial.org/tutorial-search/?search_foss=Jmol+Application&search_language=English'''.
+'''https://spoken-tutorial.org/tutorial-search/search_foss=Jmol+Application&search_language=English'''.
 || Please watch the video on '''script commands'''.

← Older revision		Revision as of 10:49, 3 February 2023
Line 22:		Line 22:
	* Create models of '''anti''', '''gauche '''and '''eclipsed'''		* Create models of '''anti''', '''gauche '''and '''eclipsed'''

−	'''conformers''' of '''1,2-dicholoroethane'''.	+	'''conformers''' of '''1,2-dicholoroethane'''.

← Older revision		Revision as of 10:49, 3 February 2023
Line 22:		Line 22:
	* Create models of '''anti''', '''gauche '''and '''eclipsed'''		* Create models of '''anti''', '''gauche '''and '''eclipsed'''

−	'''conformers''' of '''1,2-dicholoroethane'''.	+	'''conformers''' of '''1,2-dicholoroethane'''.

← Older revision		Revision as of 10:48, 3 February 2023
Line 14:		Line 14:
	\|\| In this tutorial, we will learn to,		\|\| In this tutorial, we will learn to,

−	* Use tools in the '''~~model-kit~~ ''' menu to rotate bonds.	+	* Use tools in the '''modelkit ''' menu to rotate bonds.

@@ Line 66: / Line 66: @@
-'''Eclipsed''' conformer is unstable
+'''Eclipsed''' conformer is unstable.
@@ Line 246: / Line 246: @@
 |-
 || Click on the model and rotate.
-|| Rotate the molecule so that you can view the C-C bond.
+|| We will create models of '''gauche''' and '''eclipsed''' conformers by rotating the C-C bond.
-−
 We will create models of '''gauche''' and '''eclipsed''' conformers by rotating the C-C bond.
 |-
 || Cursor on the model.
@@ Line 265: / Line 263: @@
 |-
 || Open the modelkit menu, click on the '''rotate bond''' option.
-|| First, let us use the bond rotating tool.
+|| Let us first use the bond rotating tool.
@@ Line 276: / Line 274: @@
-Hover the mouse over the C1 carbon atom. '''Rotate branch C1 '''message is displayed on the panel.
+Hover the mouse over the C1 carbon atom.
 |-
@@ Line 306: / Line 306: @@
-I will select the location as the Documents folder.
+I will select the location as Documents folder.
@@ Line 312: / Line 312: @@
-I will type as '''Gauche-DCE.mol''', location as documents folder.
+I will type as '''Gauche-DCE.mol'''.
@@ Line 333: / Line 333: @@
 |-
-||
+|| At the prompt type,
-−
 At the prompt type,
 '''select connected (C1) and not (C2);'''
@@ Line 344: / Line 342: @@
-Press Enter key.
+Press the Enter key.
 |-
 || At the prompt type,
@@ Line 382: / Line 380: @@
-|| For more details on script commands please use the following weblinks.
+|| For more details on script commands please use the following web links.
 |-
@@ Line 403: / Line 401: @@
-The model on the panel is of '''eclipsed''' conformation. The dihedral angle between two chlorine atoms is 0 degrees.
+The model on the panel is of '''eclipsed''' conformation.
 |-
@@ Line 444: / Line 443: @@
 || 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'''
+* Created models of '''anti, gauche '''and''' eclipsed''' conformers of 1,2-dicholoroethane
-* conformers of 1,2-dicholoroethane
 |-
@@ Line 454: / Line 452: @@
 '''Assignment'''
-|| Explore the rotate command to create models of conformations of n butane.
+|| As an assignment,
 |-
@@ Line 482: / Line 482: @@
 ||
 * Please post your timed queries in this forum.
 |-
@@ Line 489: / Line 488: @@
 '''Acknowledgement '''
-|| Spoken Tutorial project is funded by Ministry of Education (MoE), Govt. of India
+|| Spoken Tutorial project is funded by the Ministry of Education (MoE), Govt. of India
 |-
 || '''Acknowledgement '''