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

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'''Learning Objectives'''
 
'''Learning Objectives'''
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||In this tutorial, we will learn  
+
||In this tutorial, we will learn to,
  
 
* Add bonds to the existing bond
 
* Add bonds to the existing bond
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||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'''.
 
|-
 
|-
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||Click on  '''Select one or more objects''' tool to select '''Ethane.'''
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||Click on  '''Select one or more objects''' tool click on '''Ethane''' to select
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||Click on  '''Select one or more objects''' tool to select '''Ethane''' structure.
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||Click on  '''Select one or more objects''' tool click on '''Ethane''' structure to select it.
 
|-
 
|-
 
||Press '''CTRL +C''' to copy  the structure
 
||Press '''CTRL +C''' to copy  the structure
  
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Press '''CTRL + V''' to paste the copied structure
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Press '''CTRL + V''' to paste the structures.
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||Press '''CTRL +C''' to copy  the structure.
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||Press '''CTRL +C''' to copy  the structure and
  
−
Press '''CTRL + V''' to paste the copied structure
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Press '''CTRL + V''' to paste the structures.
  
 
Observe that two structures overlap each other.
 
Observe that two structures overlap each other.
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|-
 
|-
 
||
 
||
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||Let's first convert the single bond to a double bond.
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||Let's first convert single bond to a double bond.
 
|-
 
|-
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||Click on '''Add a bond or change the multiplicity of existing one''' tool.
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||Click on '''Add a bond or change the multiplicity of an existing one''' tool.
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||Click on '''Add a bond or change the multiplicity of existing one''' tool.  
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||Click on '''Add a bond or change the multiplicity of an existing one''' tool.  
 
|-
 
|-
 
||Click on the existing bond of the second '''Ethane''' structure.
 
||Click on the existing bond of the second '''Ethane''' structure.
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|-
 
|-
 
||Click on '''Add or modify a text''' tool >>Click below the structures.
 
||Click on '''Add or modify a text''' tool >>Click below the structures.
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||Let's name the structures.
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||Let's write the names of the structures.
  
 
Click on '''Add or modify a text''' tool  
 
Click on '''Add or modify a text''' tool  
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|-
 
|-
 
||Enter the names in green boxes.
 
||Enter the names in green boxes.
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||Enter the names of the structures as  '''Ethane, Ethene''' and '''Ethyne''' in the green boxes.
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||Enter the names of the structures as  '''Ethane, Ethene''' and '''Ethyne'''.  
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 +
||
 +
||
 
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||Slide Number 5
 
||Slide Number 5

Revision as of 12:46, 19 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 to,
  • 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 click on Ethane to select Click on Select one or more objects tool click on Ethane structure to select it.
Press CTRL +C to copy the structure

Press CTRL + V to paste the structures.

Press CTRL +C to copy the structure and

Press CTRL + V to paste the structures.

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 single bond to a double bond.
Click on Add a bond or change the multiplicity of an existing one tool. Click on Add a bond or change the multiplicity of an 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 write the names of 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.
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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