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

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(Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on '''Bond Rotation in Jmol.''' |- || '''Slide Numbe...")
 
 
(4 intermediate revisions by 2 users not shown)
Line 7: Line 7:
  
 
'''Title Slide'''
 
'''Title Slide'''
−
|| Welcome to this tutorial on '''Bond Rotation in Jmol.'''
+
|| Welcome to this tutorial on '''Bond Rotation in Jmol'''.
 
|-
 
|-
 
|| '''Slide Number 2'''
 
|| '''Slide Number 2'''
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.  
  
  
−
Use script commands to rotate specific bonds in a model.
+
* Use script commands to rotate specific bonds in a model.
  
  
−
Create models of '''anti, gauche '''and '''eclipsed'''
+
* Create models of '''anti''', '''gauche '''and '''eclipsed'''
  
−
'''conformers of '''1,2-dicholoroethane.
+
'''conformers''' of '''1,2-dicholoroethane'''.
  
  
Line 29: Line 29:
  
 
'''System Requirement'''
 
'''System Requirement'''
−
|| Here I am using
+
|| Here I am using,
  
−
'''Ubuntu Linux''' OS version 20.04
+
* '''Ubuntu Linux''' OS version 20.04
  
  
−
'''Jmol''' version 14.32.80
+
* '''Jmol''' version 14.32.80
  
  
−
'''Java '''version 11.0.16
+
* '''Java '''version 11.0.16
  
 
|-
 
|-
Line 48: Line 48:
  
  
−
must have knowledge of high school chemistry.
+
* must have knowledge of high school chemistry.
  
  
−
must be familiar with basic operations of '''Jmol'''.  
+
* must be familiar with basic operations of '''Jmol'''.  
  
  
Line 60: Line 60:
  
 
'''Conformations of 1,2-Dichloroethane'''
 
'''Conformations of 1,2-Dichloroethane'''
−
|| The most prominent conformations of''' 1,2- dichloroethane''' are '''anti '''and''' gauche'''
+
|| The most prominent conformations of ''' 1,2- dichloroethane''' are '''anti ''' and ''' gauche'''.
  
  
−
'''Anti conformer''' is more stable when compared to '''gauche'''
+
'''Anti conformer''' is more stable when compared to '''gauche'''.
  
  
−
'''Eclipsed''' conformer is unstable
+
'''Eclipsed''' conformer is unstable.
  
  
−
The conformers are interconvertible by '''C-C''' bond rotation
+
These conformers are interconvertible by '''C-C''' bond rotation.
 +
 
 
|-
 
|-
 
|| Cursor on Jmol interface.
 
|| Cursor on Jmol interface.
 
|| Here I have opened the Jmol Application window.
 
|| Here I have opened the Jmol Application window.
 +
 
|-
 
|-
 
|| Click on the '''model kit'''  menu.
 
|| Click on the '''model kit'''  menu.
−
|| Let us create a model of '''1,2-dichloroethane''' on the Jmol panel.
+
|| 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.
+
Click on the '''model kit menu''' on the toolbar to get the model of ''' methane ''' on the panel.
 +
 
 
|-
 
|-
 
|| Cursor on the  '''modelkit menu ''' options.
 
|| Cursor on the  '''modelkit menu ''' options.
Line 87: Line 90:
  
  
−
Click on one of the hydrogen atoms in the methane model.
+
Click on any one of the hydrogen atoms in the '''methane''' model.
  
−
This creates a model of ethane.
+
This creates a model of '''ethane'''.
 
|-
 
|-
 
|| click on the minimize option from the model it menu.
 
|| 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.
−
|| 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
 
|| In the  '''model kit ''' menu, select the chlorine atom with symbol C.l
Line 111: Line 111:
  
  
−
 
+
|| In the  '''model kit ''' menu, now select the '''chlorine''' atom with symbol '''Cl'''.
−
|| In the  '''model kit ''' menu, now select the '''chlorine''' atom with symbol '''Cl.'''
+
  
  
Line 120: Line 119:
 
Click on the option which shows a question marks.
 
Click on the option which shows a question marks.
  
−
An input box opens. Type the symbol of the element in the input box.
+
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.
+
I will type '''Cl''' for chlorine and click on ''' OK''' in the '''input box'''.
  
 
|-
 
|-
Line 131: Line 132:
 
|-
 
|-
 
|| Click on the molecule and rotate.
 
|| Click on the molecule and rotate.
−
|| Rotate the ethane molecule in such a way that you can see the '''Newman''' projection.
+
|| 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.
 
|| click on the hydrogen atoms that are staggered to each other to get 1,2 dichloroethane.
Line 143: Line 144:
  
  
−
Here is the model of '''anti conformer''' of 1,2 dichloroethane.
+
Here is the model of '''anti conformer''' of '''1,2 dichloroethane'''.
  
  
−
Exit the modelkit menu.
+
Exit the '''modelkit menu'''.
 
|-
 
|-
−
|| Click the file menu. Click on Console from the options.
+
|| Click the '''File''' menu. Click on '''Console''' from the options.
−
|| To view the labeling of atoms, open the '''console '''from the '''File''' menu.  
+
|| To view the labeling of atoms, open the '''console ''' from the '''File''' menu.  
 
|-
 
|-
 
|| At the prompt, type,
 
|| At the prompt, type,
Line 171: Line 172:
  
  
−
and press Enter
+
and press '''Enter'''.
  
  
Line 183: Line 184:
  
  
−
and press Enter
+
and press '''Enter'''.
 
|-
 
|-
 
|| Cursor on the molecule.
 
|| Cursor on the molecule.
Line 224: Line 225:
  
  
−
|| This model is staggered 1,2-dichloroethane.
+
|| This model is '''staggered 1,2-dichloroethane'''.
  
  
−
We will save this model as a mol file.
+
We will save this model as a '''mol''' file.
  
  
Line 236: Line 237:
  
  
−
I will select the '''documents''' folder.
+
I will select the '''Documents''' folder.
  
  
−
Select “'''Files of Type'''” as .mol
+
Select “'''Files of Type'''” as '''.mol'''.
  
−
Name the file as '''Anti-DCE.mol'''
+
Name the file as '''Anti-DCE.mol'''.
  
 
Click on '''Save''' button.
 
Click on '''Save''' button.
 
|-
 
|-
 
|| Click on the model and rotate.
 
|| 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.
 
|| Cursor on the model.
Line 262: Line 262:
  
  
−
Typing Jmol script commands on the '''Console'''.
+
Typing '''Jmol script''' commands on the '''Console'''.
 
|-
 
|-
 
|| Open the modelkit menu, click on the '''rotate bond''' option.
 
|| 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.
  
  
−
Open the '''modelkit '''menu, click on the '''rotate bond''' radio button to activate it.
+
Open the '''modelkit ''' menu, click on the '''rotate bond''' radio button to activate it.
 
|-
 
|-
 
|| Click on the bond connecting C1 and C2 atoms.
 
|| Click on the bond connecting C1 and C2 atoms.
Line 276: Line 276:
  
  
−
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.  
 +
 
 +
'''rotate branch C1 ''' message is displayed on the panel.
  
 
|-
 
|-
−
|| Click on C1 atom and rotate it.
+
|| Click the C1 atom and rotate it.
−
|| Click on 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.
+
Stop rotating when you see the '''dihedral ''' angle between the two chlorine atoms is -60 degrees.
  
  
Line 288: Line 290:
 
|-
 
|-
 
|| Cursor on the panel.
 
|| Cursor on the panel.
−
|| This conformation of 1,2-dichloroethane on the panel is '''gauche.'''
+
|| This conformation of '''1,2-dichloroethane''' on the panel is  
 +
'''gauche.'''
 
|-
 
|-
−
|| Open modelkit menu and choose '''Save file''' option.
+
|| Open '''modelkit''' menu and choose '''Save file''' option.
  
  
Line 300: Line 303:
  
 
Click on '''Save''' button.
 
Click on '''Save''' button.
−
|| Save the model as a mol file using the '''Save file''' option in the modelkit menu.
+
|| Save the model as a '''mol''' file using the '''Save file''' option in the '''modelkit''' menu.
  
  
Line 306: Line 309:
  
  
−
I will select the location as the Documents folder.
+
I will select the location as '''Documents''' folder.
  
  
−
Select '''Files of Type''' as .mol
+
Select '''Files of Type''' as '''.mol'''.
  
  
−
I will type as '''Gauche-DCE.mol''', location as documents folder.
+
I will type the name as '''Gauche-DCE.mol'''.
  
  
Line 318: Line 321:
 
|-
 
|-
 
|| Rotate the model.
 
|| Rotate the model.
−
|| Let us rotate the '''gauche''' conformer to show '''Newman's''' projection.
+
|| Let us rotate the '''gauche''' conformer to show its '''Newman''' projection.
 
|-
 
|-
 
|| Cursor on the model.
 
|| Cursor on the model.
Line 324: Line 327:
  
 
Click on the '''file''' menu and select '''Console''' from the options.
 
Click on the '''file''' menu and select '''Console''' from the options.
−
|| Back to the gauche conformation.  
+
|| Back to the '''gauche''' conformation.  
  
  
−
Let us use script commands and create a model of eclipsed conformation.
+
Let us use script commands and create a model of '''eclipsed''' conformation.
  
  
−
Close the '''modelkit '''menu if it is open.
+
Close the '''modelkit ''' menu if it is open.
  
 
|-
 
|-
−
||  
+
|| At the prompt type,
−
 
+
−
At the prompt type,
+
  
 
'''select connected (C1) and not (C2);'''
 
'''select connected (C1) and not (C2);'''
−
|| Open the '''Console '''window from the File menu.
+
|| Open the '''Console ''' window from the '''File''' menu.
  
  
Line 344: Line 345:
  
  
−
Press Enter key.
+
Press the '''Enter''' key.
 
|-
 
|-
 
|| At the prompt type,
 
|| At the prompt type,
Line 356: Line 357:
  
  
−
The numbers, 60 indicates the angle and 30 is the speed of rotation.
+
The number, 60 indicates the angle and 30 is the speed of rotation.
  
  
−
I will resize the '''Console '''to show the model.
+
I will resize the '''Console ''' to show the model.
  
  
−
Press the Enter key.
+
Press the '''Enter''' key.
  
  
Line 382: Line 383:
  
  
−
|| For more details on script commands please use the following weblinks.
+
|| For more details on script commands please use the following web links.
  
 
|-
 
|-
Line 391: Line 392:
  
 
'''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.
+
|| Please watch the video on '''script commands'''.
  
−
It is available on Spoken Tutorial website in the Jmol Application series
+
It is available on '''Spoken Tutorial website''' in the '''Jmol Application''' series
  
 
|-
 
|-
−
|| Cursor on Jmol Panel.
+
|| Cursor on '''Jmol''' Panel.
−
|| Back to the Jmol panel.
+
|| Back to the '''Jmol''' panel.
  
  
Line 403: Line 404:
  
  
−
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.  
 +
The dihedral angle between two chlorine atoms is 0 degrees.
  
 
|-
 
|-
Line 416: Line 418:
  
 
Click on Save button.
 
Click on Save button.
−
|| Save the model as a mol file. Use the Save file option in the '''model kit''' menu.
+
|| Save the model as a '''mol''' file. Use the Save file option in the '''model kit''' menu.
  
  
Line 422: Line 424:
  
  
−
I will select the location as the Documents folder.
+
I will select the location as the '''Documents''' folder.
  
  
−
Select “'''Files of Type'''” as .mol
+
Select “'''Files of Type'''” as '''.mol'''.
  
  
Line 434: Line 436:
  
  
−
Let us rotate the '''eclipsed '''conformer to show '''Newman's''' projection.
+
Let us rotate the '''eclipsed ''' conformer to show its '''Newman''' projection.
  
  
Line 444: Line 446:
 
|| Let's summarize what we have learnt.
 
|| Let's summarize what we have learnt.
  
−
 
+
In this tutorial, we have:
 
* Used tools in the model-kit menu to rotate bonds.  
 
* Used tools in the model-kit menu to rotate bonds.  
 
* Used script commands to rotate specific bonds in a model
 
* 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 455:
  
 
'''Assignment'''
 
'''Assignment'''
−
|| Explore the rotate command to create models of conformations of n butane.
+
|| As an assignment,
 +
 
 +
Explore the '''rotate''' command to create models of conformations of n-butane.
  
 
|-
 
|-
Line 482: Line 485:
 
||  
 
||  
 
* Please post your timed queries in this forum.
 
* Please post your timed queries in this forum.
−
 
  
 
|-
 
|-
Line 489: Line 491:
  
 
'''Acknowledgement '''
 
'''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 '''
 
|| '''Acknowledgement '''
 
||
 
||
−
* The script for this tutorial is contributed by Snehalatha Kaliappan.
+
* The script for this tutorial is contributed by Snehalatha Kaliappan.
 
* This is Madhuri Ganapathi from IIT Bombay signing off.  
 
* This is Madhuri Ganapathi from IIT Bombay signing off.  
  
−
Thank you for joining.  
+
Thank you for watching.  
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:19, 3 February 2023

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

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