Difference between revisions of "GChemPaint/C3/Orbital-Overlap/English"

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If not, for relevant tutorials,  please visit our website.  
 
If not, for relevant tutorials,  please visit our website.  
 
|-
 
|-
−
||Switch to '''GChemPaint''' application.
+
||'''Slide Number 5'''
−
||I have opened a new '''GChemPaint''' application.
+
−
|-
+
−
||
+
−
'''Slide Number 5'''
+
  
 
'''Atomic Orbital'''
 
'''Atomic Orbital'''
−
||
+
||Let's first see what an '''atomic orbital''' is.  
−
 
+
−
Let's first see what an '''atomic orbital''' is.  
+
  
 
An '''atomic orbital''' is a mathematical function.  
 
An '''atomic orbital''' is a mathematical function.  
Line 66: Line 60:
 
An '''orbital''' is a region of space with maximum probability of finding an electron.
 
An '''orbital''' is a region of space with maximum probability of finding an electron.
 
|-
 
|-
−
||Slide Numbers 6
+
||'''Slide Numbers 6'''
  
 
'''‘s’ and ‘p’ Orbitals'''
 
'''‘s’ and ‘p’ Orbitals'''
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'p' orbitals are '''"dumb-bell"''' shaped.
 
'p' orbitals are '''"dumb-bell"''' shaped.
 
|-
 
|-
−
||‘d’ Orbitals
+
||'''Slide Numbers  7'''
 +
 
 +
'''‘d’ Orbitals'''
 
||Next, we have 'd' orbitals in different axes.
 
||Next, we have 'd' orbitals in different axes.
  
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|-
 
|-
 
||Point to the properties window.
 
||Point to the properties window.
−
||The '''Orbital''' property window opens.
+
||'''Orbital''' property window opens.
 
|-
 
|-
 
||Point to the properties.
 
||Point to the properties.
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Notice the different orbital shapes displayed alongside.
 
Notice the different orbital shapes displayed alongside.
 
|-
 
|-
−
||Point to  Coefficient and Rotation
+
||Point to  '''Coefficient''' and '''Rotation'''
 
||Next let's check the '''Coefficient''' and '''Rotation''' properties.
 
||Next let's check the '''Coefficient''' and '''Rotation''' properties.
 
|-
 
|-
Line 120: Line 116:
 
||'''Coefficient''' property has values from -1.00 to 1.00.
 
||'''Coefficient''' property has values from -1.00 to 1.00.
 
|-
 
|-
−
||Press the down arrow continuously till it reaches 0.6 or so.
+
||Press the down arrow continuously.
 
||Using '''Coefficient''' field values, we can vary the size of the '''orbital'''.
 
||Using '''Coefficient''' field values, we can vary the size of the '''orbital'''.
  
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|-
 
|-
 
||Cursor on the value box.
 
||Cursor on the value box.
−
||'''Rotation''' property has values from -180 to 180.  
+
||'''Rotation''' property has values from -180(minus) to 180.  
 
|-
 
|-
−
||Press the down arrow continuously till it reaches 35 and then press the up arrow  continuously till it reaches -35
+
||Press the down arrow continuously.
 
||We can rotate the orbitals clockwise or anticlockwise.  
 
||We can rotate the orbitals clockwise or anticlockwise.  
  
Line 143: Line 139:
 
Here is a slide for '''Positive overlap''' of different orbitals.
 
Here is a slide for '''Positive overlap''' of different orbitals.
  
−
's-s'(ss), 's-p'(sp), 'p-p'(pp) end-on overlaps and 'p-p'(pp) side-wise overlap.
+
's-s'overlap, 's-p'overlap, 'p-p'overlap and 'p-p' side-wise overlap.
 
|-
 
|-
 
||Switch to '''GChemPaint''' window.
 
||Switch to '''GChemPaint''' window.
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||Set '''Co-efficient''' value to one.
 
||Set '''Co-efficient''' value to one.
 
|-
 
|-
−
 
 
||Click on '''Add or modify a atom''' tool.
 
||Click on '''Add or modify a atom''' tool.
−
Click on '''Add or modify a atom''' tool.
+
||Click on '''Add or modify a atom''' tool.
 
|-
 
|-
 
||Click '''Add a bond''' tool.
 
||Click '''Add a bond''' tool.
−
Click '''Add a bond''' tool.
+
||Click '''Add a bond''' tool.
  
 
Ensure that bond length is around 130.
 
Ensure that bond length is around 130.
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||Click on 's' orbital,  
 
||Click on 's' orbital,  
  
−
then click on '''Hydrogen''' atoms of '''Hydrogen''' molecule.
+
Then click on '''Hydrogen''' atoms of '''Hydrogen''' molecule.
  
 
Observe 's-s' end-on overlap.
 
Observe 's-s' end-on overlap.
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Point to the molecule.
 
Point to the molecule.
 
||Click '''Add a bond''' tool.
 
||Click '''Add a bond''' tool.
 +
 +
Ensure that bond length is around 200.
  
 
Click on '''Display area'''.
 
Click on '''Display area'''.
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||Click on 'p' orbital.
 
||Click on 'p' orbital.
 
|-
 
|-
−
||
+
||Point to 'p' orbital
 
||To form 'p-p' end-on overlap, we need 'p' orbitals in horizontal direction.
 
||To form 'p-p' end-on overlap, we need 'p' orbitals in horizontal direction.
 
|-
 
|-
 
||Click and hold the up arrow triangle
 
||Click and hold the up arrow triangle
 
||Let's increase the '''Rotation''' value to 90.
 
||Let's increase the '''Rotation''' value to 90.
−
 
−
To do this, click and hold the up arrow triangle.
 
 
|-
 
|-
 
||Click on the horizontal p orbital>> Click on '''Fluorine''' atom.
 
||Click on the horizontal p orbital>> Click on '''Fluorine''' atom.
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Click on '''Close''' button
 
Click on '''Close''' button
−
observe the 'p-p' end-on overlap.
 
 
|-
 
|-
−
||
+
||Point to the overlap
 +
||I will repeat the process for the other orbital 
 +
 
 +
Observe 'p-p' end-on overlap.
 +
|-
 +
||Point to 'dz^2' orbital
 
||Now to 'd-d' end-on overlap using  'dz^2' orbital.
 
||Now to 'd-d' end-on overlap using  'dz^2' orbital.
 
|-
 
|-
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|-
 
|-
 
||Point to the arrow triangles.
 
||Point to the arrow triangles.
−
||Rotate the ''''dz^2'''' orbital to horizontal direction.
+
||For proper overlap, decrease the '''Coefficient''' value to around 0.8.  
−
 
+
−
Also, for proper overlap, decrease the '''Coefficient''' value to around 0.8 or so.
+
 
|-
 
|-
 
||Click on the bonded iron atoms to overlap '''dz^2''' orbitals.  
 
||Click on the bonded iron atoms to overlap '''dz^2''' orbitals.  
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||Click on '''Add a bond''' tool.
 
||Click on '''Add a bond''' tool.
  
−
Ensure '''Bond length''' is close to 90 and click on the '''Display area'''.
+
Ensure '''Bond length''' is close to 90.
 +
 
 +
Click on the '''Display area'''.
 
|-
 
|-
 
||Click on '''Add or modify an atomic orbital''' tool.  
 
||Click on '''Add or modify an atomic orbital''' tool.  
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Click on the edges of the bonds.
 
Click on the edges of the bonds.
−
 
−
 
−
 
−
Point to the overlap.
 
 
||Click on 'p' orbital radio button.
 
||Click on 'p' orbital radio button.
−
||Rotate the orbital to vertical position if it is in horizontal position.
+
Rotate the orbital to vertical position if it is in horizontal position.
  
 
Click on the edges of the bonds.
 
Click on the edges of the bonds.
 +
|-
 +
||Point to the overlap.
 +
||Observe the 'p-p' side-wise overlap.
 
    
 
    
−
In this type of overlap, lobes are of same sign.
+
In this type of overlap, lobes of orbitals are of same sign.
−
 
+
−
Observe the 'p-p' side-wise overlap.
+
 
|-
 
|-
 
||
 
||
−
||
+
||Next, we will move to negative and zero overlaps.
−
Next, we will move to negative and zero overlaps.
+
 
|-
 
|-
 
||'''Slide Number 9'''
 
||'''Slide Number 9'''
  
 
'''Negative overlaps'''
 
'''Negative overlaps'''
−
||Here is a slide with different types of negative overlaps.  
+
||Here is a slide for '''negative''' overlaps.
 +
|-
 +
||Switch to '''GChemPaint''' window.
 +
||I have opened a new '''GChempaint''' window.
 
|-
 
|-
 
||
 
||
 
||Now, I will demonstrate how to draw a negative overlap.
 
||Now, I will demonstrate how to draw a negative overlap.
−
|-
 
−
||Switch to '''GChemPaint''' window.
 
−
||I have opened a new '''GChempaint''' window.
 
 
|-
 
|-
 
||Click on '''Add a bond''' tool >>Click on the '''Display area'''.
 
||Click on '''Add a bond''' tool >>Click on the '''Display area'''.
 
||Click on '''Add a bond''' tool.
 
||Click on '''Add a bond''' tool.
 +
 +
Ensure Bond length is around 90.
  
 
Click on the '''Display area'''.
 
Click on the '''Display area'''.
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|-
 
|-
 
||Cursor on '''Rotation''' arrow triangle.
 
||Cursor on '''Rotation''' arrow triangle.
 +
 +
Click on the other edge of the bond.
 
||Rotate 'p' orbital to 180 degree to flip it upside down.
 
||Rotate 'p' orbital to 180 degree to flip it upside down.
−
|-
 
−
||Click on the other edge of the bond.
 
  
−
Point to the overlap.
+
Then click other edge of the bond.
−
||Click on the other edge of the bond and observe the negative overlap.
+
|-
 +
||Point to the overlap.
 +
||Observe negative overlap.
  
−
In this type of overlap, lobes of orbitals are of opposite sign.
+
In this type of overlap, lobes of orbitals are of opposite sign.
 
|-
 
|-
 
||
 
||
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||Click on '''Add or modify an atomic orbital''' tool.  
 
||Click on '''Add or modify an atomic orbital''' tool.  
 
|-
 
|-
−
||Click on '''Add or modify an atomic orbital''' tool.
 
−
||Click on '''Add or modify an atomic orbital''' tool.
 
−
|-
 
−
||Click on the 'p' orbital radio button>> click on one edge of the bond.
 
−
||Click on 'p' orbital radio button and then click on one edge of the bond.
 
  
−
Ensure that 'p' orbital is vertical.
+
||Click on the 'p' >>Rotate the 'p' orbital to original position>>
 +
 
 +
Click on one edge of the bond.
 +
||Click on the 'p' orbital.
 +
 
 +
Rotate the 'p' orbital to original position.
 +
 
 +
Click on one edge of the bond.
 
|-
 
|-
−
||Click on the 's' orbital radio button >>click on one edge of the bond.
+
||Click on the 's' orbital >>click on one edge of the bond.
−
||Click on 's' orbital radio button and then click on other edge of the bond.
+
||Click on 's' orbital and then click on other edge of the bond.
 
|-
 
|-
 
||Point to the overlap
 
||Point to the overlap
 
||Observe zero overlap.
 
||Observe zero overlap.
  
−
In this overlap, orientation of the orbitals is not same.  
+
In this type of overlap, orientation of the orbitals is not same.  
 
|-
 
|-
 
||
 
||

Revision as of 13:16, 10 February 2014

Title of the tutorial: Orbital overlap

Author: Madhuri Ganapathi

Key words: Atomic orbital, Add or modify an atomic orbital tool, rotation and resize of orbitals, positive, negative overlaps and zero overlap, Video tutorial


Visual Cue Narration

Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Orbital Overlap in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn
  • About different types of orbitals
  • Rotation and resize of orbitals
  • Types of orbital overlaps
Slide Number 3

System Requirement

Here I am using

Ubuntu Linux OS version 12.04.

GChemPaint version 0.12.10.

Slide Number 4

Pre-requisites

To follow this tutorial, you should be familiar with

GChemPaint chemical structure editor.

If not, for relevant tutorials, please visit our website.

Slide Number 5

Atomic Orbital

Let's first see what an atomic orbital is.

An atomic orbital is a mathematical function.

It describes the wave-like behavior of an electron in an atom.

An orbital is a region of space with maximum probability of finding an electron.

Slide Numbers 6

‘s’ and ‘p’ Orbitals

Point to the orbitals

This is an 's' orbital.

It has spherical shape.

Here are 'p' orbitals in different axes.

'p' orbitals are "dumb-bell" shaped.

Slide Numbers 7

‘d’ Orbitals

Next, we have 'd' orbitals in different axes.

'd' orbitals are double "dumb-bell" shaped.

Switch to GChemPaint application. I have opened a new GChemPaint application.
Let's first learn about orbitals.
Click on Add or modify an atomic orbital tool Click on Add or modify an atomic orbital tool.
Point to the properties window. Orbital property window opens.
Point to the properties. This window contains fields like- Coefficient, Rotation and Type.
Point to Type field. First, I will begin with Type.
Point to 's' By default, 's' orbital is selected.
Click on p, dxy and dz^2 radio buttons.


Point to the orbital shapes.

Let's click on p, d xy and d z square orbital radio buttons.

Notice the different orbital shapes displayed alongside.

Point to Coefficient and Rotation Next let's check the Coefficient and Rotation properties.
Cursor on the value box Coefficient property has values from -1.00 to 1.00.
Press the down arrow continuously. Using Coefficient field values, we can vary the size of the orbital.

Notice that size of the orbital alongside, has changed.

Cursor on the value box. Rotation property has values from -180(minus) to 180.
Press the down arrow continuously. We can rotate the orbitals clockwise or anticlockwise.

Values can be changed using the up and down arrows.

Let's see how to use orbitals to show different types of positive overlaps.
Slide Number 8

Positive Overlaps

Here is a slide for Positive overlap of different orbitals.

's-s'overlap, 's-p'overlap, 'p-p'overlap and 'p-p' side-wise overlap.

Switch to GChemPaint window. Let's draw Hydrogen molecule on the Display area.
Press H on the Key board. Press H on the keyboard.
Set Co-efficient value to 1. Set Co-efficient value to one.
Click on Add or modify a atom tool. Click on Add or modify a atom tool.
Click Add a bond tool. Click Add a bond tool.

Ensure that bond length is around 130.

Click on the Display area. Click on the Display area.

Hydrogen molecule is formed.

Let's start with 's-s' end-on overlap.
Click on Add or modify an atomic orbital tool. Click on Add or modify an atomic orbital tool.
Click on 's' orbital>>click on the Hydrogen atoms of Hydrogen molecule.

Point to the s-s end on overlap.

Click on 's' orbital,

Then click on Hydrogen atoms of Hydrogen molecule.

Observe 's-s' end-on overlap.

Now to 'p-p' end-on overlap.
Press F on the keyboard Press F on the keyboard.
Click on Add or modify an atom tool. Click on Add or modify an atom tool.
Click Add a bond tool.

Point to the molecule.

Click Add a bond tool.

Ensure that bond length is around 200.

Click on Display area.

Fluorine molecule is formed.

Click on Add or modify an atomic orbital tool Click on Add or modify an atomic orbital tool.
Click on 'p' orbital. Click on 'p' orbital.
Point to 'p' orbital To form 'p-p' end-on overlap, we need 'p' orbitals in horizontal direction.
Click and hold the up arrow triangle Let's increase the Rotation value to 90.
Click on the horizontal p orbital>> Click on Fluorine atom. Click on horizontal 'p' orbital.

Click on one Fluorine atom.

Click on the other Fluorine atom. Likewise, repeat the process and rotate the 'p' orbital to '-90'(minus90).

Click on the other Fluorine atom.

Right click on the orbital>> select Orbital >> click on Properties. In case you are not able to view the overlap clearly, you can resize the orbital.

To do so, we have to change the Coefficient value.

Right click on the orbital, select Orbital then click on Properties.

Orbital properties dialogue box opens. Orbital properties dialog box opens.
Point to 'p-p' end-on overlap. Reduce the Coefficient value till you see a proper overlap.

Click on Close button

Point to the overlap I will repeat the process for the other orbital

Observe 'p-p' end-on overlap.

Point to 'dz^2' orbital Now to 'd-d' end-on overlap using 'dz^2' orbital.
Press capital F on the keyboard.

Point to the list.

Come to the Display Area and press capital F on the keyboard.

Select Fe from the list.

Click on Add or modify an atom tool>>Click on the Display area. Click on Add or modify an atom tool.

Click on the Display area.

Click on Add a bond tool>>Click on Display area. Click on Add a bond tool.

Click on iron atom(Fe) to draw a bond.

Click on Add or modify an atomic orbital tool>>Select dz^2 orbital. Click on Add or modify an atomic orbital tool.

Select 'dz^2' orbital radio button.

Point to the arrow triangles. For proper overlap, decrease the Coefficient value to around 0.8.
Click on the bonded iron atoms to overlap dz^2 orbitals. Click on the bonded Iron atoms to overlap "dz^2" orbitals.
Now let's learn about side-wise overlap of 'p' orbitals.

Ensure that current element is Carbon.

Click on Add a bond tool. Click on Add a bond tool.

Ensure Bond length is close to 90.

Click on the Display area.

Click on Add or modify an atomic orbital tool. Click on Add or modify an atomic orbital tool.
Click on 'p' orbital radio button>>

Click on the edges of the bonds.

Click on 'p' orbital radio button.

Rotate the orbital to vertical position if it is in horizontal position.

Click on the edges of the bonds.

Point to the overlap. Observe the 'p-p' side-wise overlap.

In this type of overlap, lobes of orbitals are of same sign.

Next, we will move to negative and zero overlaps.
Slide Number 9

Negative overlaps

Here is a slide for negative overlaps.
Switch to GChemPaint window. I have opened a new GChempaint window.
Now, I will demonstrate how to draw a negative overlap.
Click on Add a bond tool >>Click on the Display area. Click on Add a bond tool.

Ensure Bond length is around 90.

Click on the Display area.

Click on Add or modify an atomic orbital tool. Click on Add or modify an atomic orbital tool.
Click on the p orbital radio button >>click on one edge of the bond. Click on 'p' orbital radio button then click on one edge of the bond.
Cursor on Rotation arrow triangle.

Click on the other edge of the bond.

Rotate 'p' orbital to 180 degree to flip it upside down.

Then click other edge of the bond.

Point to the overlap. Observe negative overlap.

In this type of overlap, lobes of orbitals are of opposite sign.

Now, let's learn how to create a zero overlap.
Slide Number 10

Zero Overlap

Here is a slide for zero overlap.
Click on Add a bond tool>>

Click on the Display area.

Click on Add a bond tool.

Click on the Display area.

Click on Add or modify an atomic orbital tool. Click on Add or modify an atomic orbital tool.
Click on the 'p' >>Rotate the 'p' orbital to original position>>

Click on one edge of the bond.

Click on the 'p' orbital.

Rotate the 'p' orbital to original position.

Click on one edge of the bond.

Click on the 's' orbital >>click on one edge of the bond. Click on 's' orbital and then click on other edge of the bond.
Point to the overlap Observe zero overlap.

In this type of overlap, orientation of the orbitals is not same.

Let's summarize what we have learnt.
Slide Number 11

Summary

In this tutorial we have learnt ,
  • About different types of orbitals
  • End-on and side-wise overlaps
  • Rotation and resize of orbitals
  • Positive, negative and zero overlap.
Slide Number 12

Assignment

Here is an assignment.
  • Draw 's-p' end-on overlap with Hydrogen chloride(H-Cl) molecule
  • Draw side-wise overlap of 'dxy-dxy' orbitals
  • Draw other negative and zero overlaps.
  • Hint: Rotate and resize the orbitals for proper overlap.

Your completed assignment should look like this.

Slide Number 13

Acknowledgement

Watch the video available at this link.

http://spoken-tutorial.org/What_is_a_Spoken_Tutorial

It summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it

Slide Number 14 The Spoken Tutorial Project Team:

Conducts workshops using spoken tutorials

Gives certificates to those who pass an on-line test

For more details, please write to contact@spoken-tutorial.org

Slide number 15 Spoken Tutorial Project is a part of the Talk to a Teacher project

It is supported by the National Mission on Education through ICT, MHRD, Government of India.

More information on this Mission is available at this link

http://spoken-tutorial.org/NMEICT-Intro

Drawings are contributed by Arathi

This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, PoojaMoolya

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