Jmol-Application/C2/Interchange-the-Element-in-the-3D-Model/English - Revision history

Snehalathak at 10:16, 26 March 2025

2025-03-26T10:16:38Z

Madhurig at 07:08, 26 March 2025

2025-03-26T07:08:26Z

Snehalathak: 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..."

2025-03-21T10:56:52Z

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..."

New page

{|border=1
|-
! align=center | Visual Cue
! align=center | 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 withBasic operations in '''Jmol''' interface.
*Spoken tutorials on '''Jmol Application''' are available at thiswebsite.
|-
|| 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 the'''methane '''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 modelkit 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.
|-
|}

@@ Line 139: / Line 139: @@
 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.
@@ Line 148: / Line 148: @@
 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.
@@ Line 168: / Line 168: @@
 || 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

@@ Line 8: / Line 8: @@
 '''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'''
@@ Line 20: / Line 20: @@
 '''System Requirement'''
 || Here I am using,
-*'''Ubuntu Linux '''OS version 22.04
+*'''Ubuntu Linux ''' OS version 22.04
 *'''Jmol''' version 16.2.35
 *'''Java''' version 11.0.25
@@ Line 30: / Line 30: @@
 '''https://spoken-tutorial.org'''
 ||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.
 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.
@@ Line 45: / Line 45: @@
 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.
@@ Line 65: / Line 65: @@
 |-
 || 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.
@@ Line 90: / Line 90: @@
 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.
@@ Line 96: / Line 96: @@
 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.
@@ Line 105: / Line 105: @@
 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 .
@@ Line 142: / Line 142: @@
 |-
 || 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.
@@ Line 194: / Line 194: @@
 '''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'''.
 |-
 ||