Difference between revisions of "GChemPaint/C2/Formation-of-Bonds/English"

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Line 47: Line 47:
 
||Let's learn to convert '''Saturated Hydrocarbons''' to '''Unsaturated Hydrocarbons'''.
 
||Let's learn to convert '''Saturated Hydrocarbons''' to '''Unsaturated Hydrocarbons'''.
 
|-
 
|-
−
||Point to the Ethane structure.
+
||Point to the ''' Ethane''' structure.
−
||Let's copy Ethane structure and paste it twice on the Display area.
+
||Let's copy '''Ethane''' structure and paste it twice on the '''Display area'''.
 
|-
 
|-
−
||Click on  Select one or more objects tool to select Ethane.
+
||Click on  '''Select one or more objects''' tool to select '''Ethane.'''
−
||Click on  Select one or more objects tool to select Ethane structure.
+
||Click on  '''Select one or more objects''' tool to select '''Ethane''' structure.
 
|-
 
|-
−
||Press CTRL +C to copy  the structure
+
||Press '''CTRL +C''' to copy  the structure
−
Press CTRL + V to paste the copied structure
+
 
−
||Press CTRL +C to copy  the structure.
+
Press '''CTRL + V''' to paste the copied structure
−
Press CTRL + V to paste the copied structure
+
||Press '''CTRL +C''' to copy  the structure.
 +
 
 +
Press '''CTRL + V''' to paste the copied structure
  
 
Observe that two structures overlap each other.
 
Observe that two structures overlap each other.
 
|-
 
|-
−
||
+
||Place the cursor on  the structure >>drag it with the mouse.   
−
Place the cursor on  the structure >>drag it with the mouse.   
+
 
||Let's move the second overlapping structure aside.
 
||Let's move the second overlapping structure aside.
  
Line 72: Line 73:
 
||Let's first convert the single bond to a double bond.
 
||Let's first convert the single bond to a double bond.
 
|-
 
|-
−
||Click on Add a bond or change the multiplicity of existing one tool.
+
||Click on '''Add a bond or change the multiplicity of existing one''' tool.
−
||Click on Add a bond or change the multiplicity of existing one tool.  
+
||Click on '''Add a bond or change the multiplicity of existing one''' tool.  
 
|-
 
|-
−
||Click on the existing bond of the second ethane structure.
+
||Click on the existing bond of the second '''Ethane''' structure.
−
||Click on the existing bond of the second Ethane structure.
+
||Click on the existing bond of the second ''' Ethane''' structure.
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
 +
 
Point to the hydrogen atoms.
 
Point to the hydrogen atoms.
 
||Observe that 1) Single bond is converted to a double bond.
 
||Observe that 1) Single bond is converted to a double bond.
−
2)Number of hydrogen atoms reduced from 6 to 4.
+
 
−
The new structure is Ethene.
+
2)Number of '''Hydrogen''' atoms reduced from 6 to 4.
 +
 
 +
The new structure is '''Ethene'''.
 
|-
 
|-
 
||
 
||
 
||Next let's convert  the single bond to a triple bond.
 
||Next let's convert  the single bond to a triple bond.
 
|-
 
|-
−
||Click on the existing bond of the third ethane structure twice.
+
||Click on the existing bond of the third '''Ethane''' structure twice.
−
||Click on the existing bond of the third Ethane structure twice.
+
||Click on the existing bond of the third '''Ethane''' structure twice.
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
−
Point to the hydrogen atoms.
+
 
 +
Point to the '''Hydrogen''' atoms.
 
||Observe that 1) Single bond is converted to a triple bond.
 
||Observe that 1) Single bond is converted to a triple bond.
 +
 
2)Number of hydrogen atoms reduced from 6 to 2.
 
2)Number of hydrogen atoms reduced from 6 to 2.
−
The new structure is Ethyne.
+
 
 +
The new structure is '''Ethyne'''.
 
|-
 
|-
−
||Click on Add or modify a text tool >>Click below the structures.
+
||Click on '''Add or modify a text''' tool >>Click below the structures.
 
||Let's name the structures.
 
||Let's name the structures.
−
Click on Add or modify a text tool  
+
 
 +
Click on '''Add or modify a text''' tool  
 +
 
 
Click below the structures.
 
Click below the structures.
 
|-
 
|-
 
||Enter the names in green boxes.
 
||Enter the names in green boxes.
−
||Enter the names of the structures as  Ethane, Ethene and Ethyne  in the green boxes.
+
||Enter the names of the structures as  '''Ethane, Ethene''' and '''Ethyne''' in the green boxes.
 
|-
 
|-
 
||Slide Number 5
 
||Slide Number 5
−
Show slide on  Tetrahedral Methane structure.
+
Show slide on  '''Tetrahedral Methane''' structure.
−
||Next, let's learn about Tetrahedral geometry.
+
||Next, let's learn about '''Tetrahedral geometry'''.
−
Here is a slide for the Tetrahedral Methane structure.
+
Here is a slide for the '''Tetrahedral Methane''' structure.
 
|-
 
|-
 
||
 
||
−
||Now, let's draw Ethane structure.  
+
||Now, let's draw ''' Ethane''' structure.  
 
|-
 
|-
−
||Click on Add a bond or change the multiplicity of existing one tool>>Orient the bond in horizontal direction.  
+
||Click on '''Add a bond or change the multiplicity of existing one''' tool>>Orient the bond in horizontal direction.  
−
||Click on Add a bond or change the multiplicity of existing one tool
+
||Click on '''Add a bond or change the multiplicity of existing one''' tool
  
 
Orient the bond in horizontal direction.  
 
Orient the bond in horizontal direction.  
Line 119: Line 128:
 
||Point to the bond
 
||Point to the bond
 
||On the edge of each bond let's draw three bonds.
 
||On the edge of each bond let's draw three bonds.
−
Orient the bonds to form a tetrahedral geometry.
+
 
 +
Orient the bonds to form a '''Tetrahedral geometry'''.
 
|-
 
|-
 
||Click on one edge>>orient the three bonds in different directions.
 
||Click on one edge>>orient the three bonds in different directions.
 
||Click on one edge.
 
||Click on one edge.
 +
 
Then orient the three bonds in different directions.
 
Then orient the three bonds in different directions.
  
Line 130: Line 141:
 
||Let's attach hydrogen atoms at the ends.
 
||Let's attach hydrogen atoms at the ends.
 
|-
 
|-
−
||Press capital H >>a Submenu opens select H
+
||Press capital H >>a '''Submenu''' opens select H
 +
 
 
To attach hydrogen atoms to the ends,  
 
To attach hydrogen atoms to the ends,  
 
||Press capital H.
 
||Press capital H.
Line 138: Line 150:
 
Observe that Hydrogen atom appears in the tool box.
 
Observe that Hydrogen atom appears in the tool box.
 
|-
 
|-
−
||Click on Add or modify an atom tool
+
||Click on '''Add or modify an atom''' tool
 +
 
 
Click on all the positions to add hydrogens.
 
Click on all the positions to add hydrogens.
−
||Click on Add or modify an atom tool.  
+
||Click on '''Add or modify an atom''' tool.  
 +
 
 
Click on all the positions to add hydrogens.
 
Click on all the positions to add hydrogens.
 
|-
 
|-
 
||
 
||
−
||Let's now add stereochemical bonds to Ethane structure.
+
||Let's now add '''Stereochemical''' bonds to '''Ethane''' structure.
 
|-
 
|-
−
||Point to the stereochemical bonds Add a wedge bond, Add a hash bond, Add a squiggle bond and Add a fore bond.
+
||Point to the '''Stereochemical''' bonds-
−
||Stereochemical bonds available in the tool box are,
+
'''Add a wedge bond''',  
−
Add a wedge bond,  
+
 
−
Add a hash bond,  
+
'''Add a hash bond''',  
−
Add a squiggle bond and  
+
 
−
Add a fore bond.
+
'''Add a squiggle bond''' and  
 +
 
 +
'''Add a fore bond.'''
 +
||'''Stereochemical''' bonds available in the tool box are,
 +
'''Add a wedge bond,'''
 +
 
 +
'''Add a hash bond,'''
 +
 
 +
'''Add a squiggle bond''' and  
 +
 
 +
'''Add a fore bond'''.
 
|-
 
|-
 
||
 
||
 
||Let's use Add a wedge bond to convert Ethane to a  stereochemical structure.
 
||Let's use Add a wedge bond to convert Ethane to a  stereochemical structure.
 
|-
 
|-
−
||Click on  Add a wedge bond.
+
||Click on  '''Add a wedge bond'''.
 +
 
 
Click on all the bonds.
 
Click on all the bonds.
 
||
 
||
−
Click on  Add a wedge bond.
+
Click on  '''Add a wedge bond'''.
 +
 
 
Click on all the bonds.
 
Click on all the bonds.
  
Line 168: Line 194:
 
Now I will explain about Invert wedge hashes.
 
Now I will explain about Invert wedge hashes.
 
|-
 
|-
−
||Go Edit menu, navigate to Preferences and click on it>> GChemPaint Preferences window opens.  
+
||Go '''Edit''' menu, navigate to '''Preferences''' and click on it>> '''GChemPaint''' '''Preferences''' window opens.  
−
||Go Edit menu, navigate to Preferences and click on it.
+
||Go '''Edit''' menu, navigate to '''Preferences''' and click on it.
−
GChemPaint Preferences window opens.  
+
'''GChemPaint Preferences''' window opens.  
 
|-
 
|-
−
||Click on Inverse wedge hashes checkbox.
+
||Click on '''Inverse wedge hashes''' checkbox.
−
||Click on Inverse wedge hashes checkbox.
+
||Click on '''Inverse wedge hashes''' checkbox.
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
 
||If set, the wedge hashes bonds will follow the usual convention.
 
||If set, the wedge hashes bonds will follow the usual convention.
 +
 
Narrow end is at the start of the bond(centre of the structure) and broad end at the other end.
 
Narrow end is at the start of the bond(centre of the structure) and broad end at the other end.
  
Line 184: Line 211:
 
|-
 
|-
 
||
 
||
−
||Let's change the bonds to  Add a hash bond  in the Ethane structure.
+
||Let's change the bonds to  '''Add a hash bond''' in the '''Ethane''' structure.
 
|-
 
|-
−
||Click on  Add a hash bond.
+
||Click on  '''Add a hash bond'''.
 +
 
 
Click on all the bonds.
 
Click on all the bonds.
 
||
 
||
−
Click on  Add a hash bond  
+
Click on  '''Add a hash bond'''
 +
 
 
Click on all the bonds.
 
Click on all the bonds.
 +
 
Observe the changes.
 
Observe the changes.
 
|-
 
|-
Line 196: Line 226:
 
||Let's save and close the file.
 
||Let's save and close the file.
 
|-
 
|-
−
||Click on Save the current file icon on the toolbar.
+
||Click on '''Save the current file''' icon on the toolbar.
−
||Click on Save the current file icon on the toolbar
+
||Click on '''Save the current file''' icon on the toolbar
 
|-
 
|-
−
||Save as dialog box opens
+
||'''Save as''' dialog box opens.
−
||Save as dialog box opens
+
||'''Save as''' dialog box opens.
 
|-
 
|-
−
||Enter the file name as Formation of  bond >>click on Save button.
+
||Enter the file name as '''Formation of  bond''' >>click on Save button.
 
||Enter the file name as Formation of  bond and then click on Save button.
 
||Enter the file name as Formation of  bond and then click on Save button.
 
|-
 
|-
−
||Click on Close to close the file.
+
||Click on '''Close''' to close the file.
 
||Click on Close to close the file.
 
||Click on Close to close the file.
 
|-
 
|-
 
||
 
||
−
||
+
||With this, we come to the end of this tutorial.
−
With this, we come to the end of this tutorial.
+
 
Let's summarise.
 
Let's summarise.
 
|-
 
|-
−
||Slide Number 6
+
||'''Slide Number 6'''
−
Summary
+
 
 +
'''Summary'''
 
||In this tutorial we have learnt,
 
||In this tutorial we have learnt,
−
Add bonds to the existing bond
+
 
−
Orient the bonds
+
* Add bonds to the existing bond
−
Add Stereochemical bonds  
+
 
−
Inverse wedge hashes
+
* Orient the bonds
 +
 
 +
* Add Stereochemical bonds  
 +
 
 +
* Inverse wedge hashes
 
|-
 
|-
−
||Slide Number 7
+
||'''Slide Number 7'''
−
Assignment  
+
 
−
|| Assignment  
+
'''Assignment'''
−
Convert Propane to Propyne
+
||''' Assignment'''
−
Draw Propane and butane structures and
+
 
−
Show the stereochemical bonds.
+
* Convert Propane to Propyne
 +
 
 +
* Draw Propane and butane structures and
 +
 
 +
*Show the stereochemical bonds.
  
 
Output of the assignment should look like this.
 
Output of the assignment should look like this.
  
 
|-
 
|-
−
||Slide Number 8
+
||'''Slide Number 8'''
−
Acknowledgement  
+
 
 +
'''Acknowledgement'''
 
||Watch the video available at this URL.
 
||Watch the video available at this URL.
−
http://spoken-tutorial.org /What_a_Spoken_Tutorial
+
 
 +
'''http://spoken-tutorial.org /What_a_Spoken_Tutorial'''
  
 
It summarises the Spoken Tutorial project
 
It summarises the Spoken Tutorial project
Line 240: Line 280:
 
If you do not have good bandwidth, you can download and watch it  
 
If you do not have good bandwidth, you can download and watch it  
 
|-
 
|-
−
||Slide Number 11
+
||'''Slide Number 11'''
 
||The Spoken Tutorial Project Team:  
 
||The Spoken Tutorial Project Team:  
 +
 
Conducts workshops using spoken tutorials
 
Conducts workshops using spoken tutorials
 +
 
Gives certificates to those who pass an online test  
 
Gives certificates to those who pass an online test  
 +
 
For more details, please write to  
 
For more details, please write to  
−
contact@spoken-tutorial.org  
+
 
 +
'''contact@spoken-tutorial.org'''
 
|-
 
|-
−
||Slide number 12
+
||'''Slide number 12'''
 
||Spoken Tutorial Project is a part of the Talk to a Teacher project  
 
||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 ]
 
  
−
Animation is done by Udhaya Chandrika.
+
It is supported by the National Mission on Education through ICT, MHRD,
−
This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining.  
+
Government of India
 +
 
 +
More information on this Mission is available at this link
 +
 
 +
'''http://spoken-tutorial.org/NMEICT-Intro'''
 +
 
 +
Animation is done by '''Udhaya Chandrika.'''
 +
 
 +
This is '''Madhuri Ganpathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
 
|-
 
|-

Revision as of 12:22, 4 July 2013

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome the tutorial on Formation of bonds in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn
  • Add bonds to the existing bond
  • Orient the bonds
  • Add Stereochemical bonds
  • Inverse wedge hashes
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.

Switch to GChemPaint application. I have opened a new GChemPaint application with Ethane structure.
Let's learn to convert Saturated Hydrocarbons to Unsaturated Hydrocarbons.
Point to the Ethane structure. Let's copy Ethane structure and paste it twice on the Display area.
Click on Select one or more objects tool to select Ethane. Click on Select one or more objects tool to select Ethane structure.
Press CTRL +C to copy the structure

Press CTRL + V to paste the copied structure

Press CTRL +C to copy the structure.

Press CTRL + V to paste the copied structure

Observe that two structures overlap each other.

Place the cursor on the structure >>drag it with the mouse. Let's move the second overlapping structure aside.

Place the cursor on the structure and drag it with the mouse.

Point to the bonds. Observe the single bond between the carbon atoms in the structures.
Let's first convert the single bond to a double bond.
Click on Add a bond or change the multiplicity of existing one tool. Click on Add a bond or change the multiplicity of existing one tool.
Click on the existing bond of the second Ethane structure. Click on the existing bond of the second Ethane structure.
Point to the structure.

Point to the hydrogen atoms.

Observe that 1) Single bond is converted to a double bond.

2)Number of Hydrogen atoms reduced from 6 to 4.

The new structure is Ethene.

Next let's convert the single bond to a triple bond.
Click on the existing bond of the third Ethane structure twice. Click on the existing bond of the third Ethane structure twice.
Point to the structure.

Point to the Hydrogen atoms.

Observe that 1) Single bond is converted to a triple bond.

2)Number of hydrogen atoms reduced from 6 to 2.

The new structure is Ethyne.

Click on Add or modify a text tool >>Click below the structures. Let's name the structures.

Click on Add or modify a text tool

Click below the structures.

Enter the names in green boxes. Enter the names of the structures as Ethane, Ethene and Ethyne in the green boxes.
Slide Number 5

Show slide on Tetrahedral Methane structure.

Next, let's learn about Tetrahedral geometry.

Here is a slide for the Tetrahedral Methane structure.

Now, let's draw Ethane structure.
Click on Add a bond or change the multiplicity of existing one tool>>Orient the bond in horizontal direction. Click on Add a bond or change the multiplicity of existing one tool

Orient the bond in horizontal direction.

Point to the bond On the edge of each bond let's draw three bonds.

Orient the bonds to form a Tetrahedral geometry.

Click on one edge>>orient the three bonds in different directions. Click on one edge.

Then orient the three bonds in different directions.

Likewise let's draw for the other edge.

Let's attach hydrogen atoms at the ends.
Press capital H >>a Submenu opens select H

To attach hydrogen atoms to the ends,

Press capital H.

A submenu opens in which we will select H.

Observe that Hydrogen atom appears in the tool box.

Click on Add or modify an atom tool

Click on all the positions to add hydrogens.

Click on Add or modify an atom tool.

Click on all the positions to add hydrogens.

Let's now add Stereochemical bonds to Ethane structure.
Point to the Stereochemical bonds-

Add a wedge bond,

Add a hash bond,

Add a squiggle bond and

Add a fore bond.

Stereochemical bonds available in the tool box are,

Add a wedge bond,

Add a hash bond,

Add a squiggle bond and

Add a fore bond.

Let's use Add a wedge bond to convert Ethane to a stereochemical structure.
Click on Add a wedge bond.

Click on all the bonds.

Click on Add a wedge bond.

Click on all the bonds.

Observe the changes.

Now I will explain about Invert wedge hashes.

Go Edit menu, navigate to Preferences and click on it>> GChemPaint Preferences window opens. Go Edit menu, navigate to Preferences and click on it.

GChemPaint Preferences window opens.

Click on Inverse wedge hashes checkbox. Click on Inverse wedge hashes checkbox.
Point to the structure. If set, the wedge hashes bonds will follow the usual convention.

Narrow end is at the start of the bond(centre of the structure) and broad end at the other end.

This helps to visualize the bond correctly.

Default convention in GChemPaint is inverse, because it is more consistent with perspective rules.

Let's change the bonds to Add a hash bond in the Ethane structure.
Click on Add a hash bond.

Click on all the bonds.

Click on Add a hash bond

Click on all the bonds.

Observe the changes.

Let's save and close the file.
Click on Save the current file icon on the toolbar. Click on Save the current file icon on the toolbar
Save as dialog box opens. Save as dialog box opens.
Enter the file name as Formation of bond >>click on Save button. Enter the file name as Formation of bond and then click on Save button.
Click on Close to close the file. Click on Close to close the file.
With this, we come to the end of this tutorial.

Let's summarise.

Slide Number 6

Summary

In this tutorial we have learnt,
  • Add bonds to the existing bond
  • Orient the bonds
  • Add Stereochemical bonds
  • Inverse wedge hashes
Slide Number 7

Assignment

Assignment
  • Convert Propane to Propyne
  • Draw Propane and butane structures and
  • Show the stereochemical bonds.

Output of the assignment should look like this.

Slide Number 8

Acknowledgement

Watch the video available at this URL.

http://spoken-tutorial.org /What_a_Spoken_Tutorial

It summarises the Spoken Tutorial project

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

Slide Number 11 The Spoken Tutorial Project Team:

Conducts workshops using spoken tutorials

Gives certificates to those who pass an online test

For more details, please write to

contact@spoken-tutorial.org

Slide number 12 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

Animation is done by Udhaya Chandrika.

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

Contributors and Content Editors

Madhurig

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