Difference between revisions of "Jmol-Application/C2/Interchange-the-Element-in-the-3D-Model/English"

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(Created page with " {|border=1 |- ! align=center | Visual Cue ! align=center | Narration |- || '''Slide Number 1''' '''Title Slide''' ||Welcome to this Spoken Tutorial on '''Interchange the Ele...")
 
 
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'''Title Slide'''
 
'''Title Slide'''
−
||Welcome to this Spoken Tutorial on '''Interchange the Element In the 3D Model'''
+
||Welcome to this Spoken Tutorial on '''Interchange the Element In the 3D Model'''.
 
|-
 
|-
 
|| '''Slide Number 2'''
 
|| '''Slide Number 2'''
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'''System Requirement'''
 
'''System Requirement'''
 
|| Here I am using,
 
|| Here I am using,
−
*'''Ubuntu Linux '''OS version 22.04
+
*'''Ubuntu Linux ''' OS version 22.04
 
*'''Jmol''' version 16.2.35
 
*'''Jmol''' version 16.2.35
 
*'''Java''' version 11.0.25
 
*'''Java''' version 11.0.25
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'''https://spoken-tutorial.org'''
 
'''https://spoken-tutorial.org'''
 
||To follow this tutorial,
 
||To follow this tutorial,
−
* Learner must be familiar withBasic operations in '''Jmol''' interface.
+
* Learner must be familiar with basic operations in '''Jmol''' interface.
−
*Spoken tutorials on '''Jmol Application''' are available at thiswebsite.
+
*Spoken tutorials on '''Jmol Application''' are available at this website.
 
|-
 
|-
 
|| Click on the model-kit icon.
 
|| Click on the model-kit icon.
  
 
Cursor on Methane model
 
Cursor on Methane model
−
|| I have opened the '''Jmol '''interface.
+
|| I have opened the '''Jmol ''' interface.
  
 
Click on the '''model kit''' menu to open it.
 
Click on the '''model kit''' menu to open it.
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Cursor on the elements menu.
 
Cursor on the elements menu.
−
|| I would like to change the'''methane '''molecule to borane.  
+
|| I would like to change the'''methane '''molecule to '''borane'''.  
  
 
Here, we need to change the central carbon atom to boron.  
 
Here, we need to change the central carbon atom to boron.  
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|-
 
|-
 
|| Cursor on the menu.
 
|| Cursor on the menu.
−
||When you open the '''model'''-'''kit''' menu again, boron is already selected.
+
||When you open the '''model-kit''' menu again, boron is already selected.
 
|-
 
|-
 
|| Click on the central carbon atom in the methane model.
 
|| Click on the central carbon atom in the methane model.
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Click on '''minimize''' in the '''model'''-'''kit''' menu to do energy minimization.
 
Click on '''minimize''' in the '''model'''-'''kit''' menu to do energy minimization.
  
−
Now select '''exit modelkit mode''' to close the model kit menu.
+
Now select '''exit model-kit mode''' to close the model kit menu.
 
|-
 
|-
 
||Double click on any hydrogen atom.  
 
||Double click on any hydrogen atom.  
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Click on the central boron atom.  
 
Click on the central boron atom.  
  
−
Again double-click on the other hydrogen atom .  
+
Again double-click on the other hydrogen atom.  
  
 
Cursor on the measurements on the model.
 
Cursor on the measurements on the model.
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Click on the central boron atom.  
 
Click on the central boron atom.  
  
−
Again double-click on the other hydrogen atom .  
+
Again double-click on the other hydrogen atom.  
  
 
You can see the bond-angle as 120 degrees .  
 
You can see the bond-angle as 120 degrees .  
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Hence the hydrogens are also adjusted automatically to 4.  
 
Hence the hydrogens are also adjusted automatically to 4.  
  
−
This molecule is Silane.
+
This molecule is silane.
 
|-
 
|-
 
|| Click on minimize in the model-kit menu.
 
|| Click on minimize in the model-kit menu.
−
|| Click on '''minimize''' in the '''model'''-'''kit '''menu to do energy minimization.
+
|| Click on '''minimize''' in the '''model-kit '''menu to do energy minimization.
  
 
Now select '''exit modelkit mode''' to close the model kit menu.
 
Now select '''exit modelkit mode''' to close the model kit menu.
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Let us measure the bond angle.
 
Let us measure the bond angle.
 
|-
 
|-
−
|| Click on '''model''' '''kit''' menu. Select Nitrogen from the element list . Click on central silicon atom.
+
|| Click on '''model''' '''kit''' menu. Select nitrogen from the element list . Click on central silicon atom.
−
|| Following the same steps I have converted the Silane model to ammonia.
+
|| Following the same steps I have converted the silane model to ammonia.
  
 
Let us measure the bond angle.
 
Let us measure the bond angle.
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|| As an assignment,
 
|| As an assignment,
  
−
Create models of Phosphine and Hydrogen fluoride from model of methane
+
Create models of Phosphine and hydrogen fluoride from model of methane
  
 
Measure the bond angle
 
Measure the bond angle
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'''Acknowledgement '''
 
'''Acknowledgement '''
−
|| The''' Spoken Tutorial '''project was established at IIT Bombay by the Ministry of Education Govt of '''India.'''
+
|| The''' Spoken Tutorial '''project was established at IIT Bombay by the Ministry of Education Govt of '''India'''.
 
|-
 
|-
 
||  
 
||  

Latest revision as of 15:46, 26 March 2025

Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this Spoken Tutorial on Interchange the Element In the 3D Model.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to,
  • Change the element in the 3D model to create a different molecule.
Slide Number 3

System Requirement

Here I am using,
  • Ubuntu Linux OS version 22.04
  • Jmol version 16.2.35
  • Java version 11.0.25
Slide Number 4

Pre-requisites

https://spoken-tutorial.org

To follow this tutorial,
  • Learner must be familiar with basic operations in Jmol interface.
  • Spoken tutorials on Jmol Application are available at this website.
Click on the model-kit icon.

Cursor on Methane model

I have opened the Jmol interface.

Click on the model kit menu to open it.

We have a model of methane on the screen.

Cursor on the methane molecule.

Cursor on the elements menu.

I would like to change themethane molecule to borane.

Here, we need to change the central carbon atom to boron.

Open the Model kit menu.

In the list of elements boron is not included.

Hence we need to add boron to the list of elements.

Click on the double-question mark icon.

type the symbol for boron as capital “B”. Click on OK.

Click on the double-question mark icon.

In the Element input box, type the symbol for boron as capital “B”.

Click on OK.

Cursor on the menu. When you open the model-kit menu again, boron is already selected.
Click on the central carbon atom in the methane model.

Cursor on the boron atom.

Now click on the central carbon atom in the methane model.

The carbon is now replaced by boron atom.

You can see the change in the color of the atom to pink.

The valency is automatically adjusted to 3.

Hence you will see 3 hydrogens on central boron atom.

Cursor on the borane model.

Click on minimize in the model-kit menu.

Select exit modelkit mode to close the model kit menu.

This molecule is borane.

Click on minimize in the model-kit menu to do energy minimization.

Now select exit model-kit mode to close the model kit menu.

Double click on any hydrogen atom.

Click on the central boron atom.

Again double-click on the other hydrogen atom.

Cursor on the measurements on the model.

Let us measure the bond angle.

Double clicking on any hydrogen atom.

Click on the central boron atom.

Again double-click on the other hydrogen atom.

You can see the bond-angle as 120 degrees .

This corresponds to the sp2 hybridization found in borane.

Cursor on the panel.

Click on the model kit icon.

I would now like to change the central atom to silicon to create Silane.

Open the model kit menu.

Let us add a silicon symbol to the list of elements.

Click on the double-question mark icon.

type the symbol for boron as capital “Si”.

Click on OK.

Type “Si” in the element input box and click OK.
Click on the central boron atom on the panel. Now click on the central boron atom on the panel.

Observe the color change of silicon atom.

It is seen as light brown in color.

Cursor on the panel. The valency of silicon is 4.

Hence the hydrogens are also adjusted automatically to 4.

This molecule is silane.

Click on minimize in the model-kit menu. Click on minimize in the model-kit menu to do energy minimization.

Now select exit modelkit mode to close the model kit menu.

Let us measure the bond angle.

Click on model kit menu. Select nitrogen from the element list . Click on central silicon atom. Following the same steps I have converted the silane model to ammonia.

Let us measure the bond angle.

In this way we can create 3D models of a number of covalent inorganic molecules.

Slide Number 5

Summary

Let's summarize

In this tutorial,

  • We have changed the element of the central atom in the 3D model to create a different molecule.
Slide Number 6

Assignment

As an assignment,

Create models of Phosphine and hydrogen fluoride from model of methane

Measure the bond angle

Slide Number 7

About Spoken Tutorial Project

This video summarizes the Spoken Tutorial project.

Please download and watch it.

Slide Number 8

Spoken tutorial workshops

We conduct workshops using spoken tutorials and give certificates.

For more details, please write to us.

Slide Number 9

Forum

Please post your timed queries in this forum.
Slide Number 10

Acknowledgement

The Spoken Tutorial project was established at IIT Bombay by the Ministry of Education Govt of India.
This tutorial is contributed by Snehalatha Kaliappan and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak

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