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

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Title of the tutorial: Formation-of-Bonds
 +
 +
Author: Madhuri Ganapathi
 +
 +
Key words: Video tutorial, Add bonds to the existing bond, Orient bonds, Add Stereochemical bonds and Inverse wedge hashes
 +
GChemPaint tools- Add a bond or change the multiplicity of an existing one, Add a wedge bond, Add a hash bond, Add a squiggle bond and  Add a fore bond.
 +
 
{|border=1
 
{|border=1
 
!'''Visual Cue'''
 
!'''Visual Cue'''
Line 13: Line 20:
  
 
'''Learning Objectives'''
 
'''Learning Objectives'''
−
||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
Line 19: Line 26:
 
* Orient the bonds
 
* Orient the bonds
  
−
* Add Stereochemical bonds  
+
* Add Stereochemical bonds and
  
 
* Inverse wedge hashes
 
* Inverse wedge hashes
Line 50: Line 57:
 
||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 click on '''Ethane''' to select it.
−
||Click on  '''Select one or more objects''' tool to select '''Ethane''' structure.
+
||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
  
−
Press '''CTRL + V''' to paste the copied structure
+
Press '''CTRL + V''' to paste the structures.
−
||Press '''CTRL +C''' to copy  the structure.
+
||Press '''CTRL +C''' to copy  the structure and
  
−
Press '''CTRL + V''' to paste the copied structure
+
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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|-
 
|-
 
||
 
||
−
||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.
 
|-
 
|-
−
||Click on '''Add a bond or change the multiplicity of existing one''' tool.
+
||Click on '''Add a bond or change the multiplicity of an 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 an existing one''' tool.  
 
|-
 
|-
 
||Click on the existing bond of the second '''Ethane''' structure.
 
||Click on the existing bond of the second '''Ethane''' structure.
Line 89: Line 96:
 
|-
 
|-
 
||
 
||
−
||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.
Line 104: Line 111:
 
|-
 
|-
 
||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 write the names of the structures.
  
 
Click on '''Add or modify a text''' tool  
 
Click on '''Add or modify a text''' tool  
Line 110: Line 117:
 
Click below the structures.
 
Click below the structures.
 
|-
 
|-
−
||Enter the names in green boxes.
+
||Enter the names.
−
||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'''.  
 
|-
 
|-
−
||Slide Number 5
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||
−
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.
+
|-
 +
||Press '''CTRL+A''' to select all objects>>
 +
 
 +
Click on '''Select one or more objects''' tool and drag the structures.
 +
||Let's move the structures to a side.
 +
 
 +
Press '''CTRL+A''' to select all objects.
 +
 
 +
Click on '''Select one or more objects''' tool and drag the structures.
 +
|-
 +
||'''Slide Number 5'''
 +
 
 +
Show slide on  '''Tetrahedral Methane''' structure.
 +
||Here is a slide for the '''Tetrahedral Methane''' structure.
 +
 
 +
All the bond lengths are equal to 1.09 '''angstrom'''.
 +
|-
 +
||'''Tetrahedral structure'''(animation)
 +
||In  '''Tetrahedral methane''' structure,
 +
 
 +
all the bond angles are equal to 109.5 degree.
 
|-
 
|-
 
||
 
||
−
||Now, let's draw ''' Ethane''' structure.  
+
||Now, let's draw '''Tetrahedral'''  ''' 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.
 +
 
 +
Click on the '''Display area.'''
  
 
Orient the bond in horizontal direction.  
 
Orient the bond in horizontal direction.  
 
|-
 
|-
 
||Point to the bond
 
||Point to the bond
−
||On the edge of each bond let's draw three bonds.
+
||On each edge of the 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.
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||Click on each edge>>orient the three bonds in different directions.
−
||Click on one edge.
+
||Click on each edge.
  
 
Then orient the three bonds in different directions.
 
Then orient the three bonds in different directions.
  
−
Likewise let's draw for the other edge.
+
Likewise let's draw on the other edge.
 
|-
 
|-
 
||
 
||
 
||Let's attach hydrogen atoms at the ends.
 
||Let's attach hydrogen atoms at the ends.
 
|-
 
|-
−
||Press capital H >>a '''Submenu''' opens select H
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||Press capital H >>a '''Submenu''' opens select '''H'''
  
−
To attach hydrogen atoms to the ends,  
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||To attach '''Hydrogen''' atoms to the ends,  
−
||Press capital H.
+
Press capital '''H.'''
  
−
A submenu opens in which we will select H.
+
A submenu opens in which we will select '''H'''.
  
−
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 '''hydrogen''' atoms.
 
||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 '''hydrogen''' atoms.
 
|-
 
|-
 
||
 
||
−
||Let's now add '''Stereochemical''' bonds to '''Ethane''' structure.
+
||Now let's add '''Stereochemical''' bonds to '''Ethane''' structure.
 
|-
 
|-
 
||Point to the '''Stereochemical''' bonds-
 
||Point to the '''Stereochemical''' bonds-
−
'''Add a wedge bond''',
 
  
−
'''Add a hash bond''',  
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* '''Add a wedge bond''',  
  
−
'''Add a squiggle bond''' and
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* '''Add a hash bond''',
  
−
'''Add a fore bond.'''
+
* '''Add a squiggle bond''' and
 +
 
 +
* '''Add a fore bond.'''
 
||'''Stereochemical''' bonds available in the tool box are,
 
||'''Stereochemical''' bonds available in the tool box are,
−
'''Add a wedge bond,'''
 
  
−
'''Add a hash bond,'''  
+
* '''Add a wedge bond,'''
 +
 
 +
* '''Add a hash bond,'''  
  
−
'''Add a squiggle bond''' and  
+
* '''Add a squiggle bond''' and  
  
−
'''Add a fore bond'''.
+
* '''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'''.
Line 186: Line 216:
 
Click on  '''Add a wedge bond'''.
 
Click on  '''Add a wedge bond'''.
  
−
Click on all the bonds.
+
Then click on all the bonds.
  
 
Observe the changes.
 
Observe the changes.
 +
|-
 +
||Click on '''Add a hash bond'''>>click on the Display area.
 +
||Click on '''Add a hash bond''' and
 +
then click on the '''Display area'''.
 
|-
 
|-
 
||
 
||
−
||
+
||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 '''Invert wedge hashes''' checkbox.
−
||Click on '''Inverse wedge hashes''' checkbox.
+
||Click on '''Invert 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 and broad end at the other end.
  
 
This helps to visualize the bond correctly.
 
This helps to visualize the bond correctly.
  
−
Default convention in GChemPaint is inverse, because it is more consistent with perspective rules.
+
Default convention in '''GChemPaint''' is inverse, because it is more consistent with the perspective rules.
 +
|-
 +
||Click on '''Close''' button to close the window.
 +
||Let's click on '''Close''' button to close the window.  
 
|-
 
|-
 
||
 
||
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Click on all the bonds.
 
Click on all the bonds.
−
 
−
Observe the changes.
 
 
|-
 
|-
 
||
 
||
−
||Let's save and close the file.
+
||Let's now save the file.
 
|-
 
|-
 
||Click on '''Save the current file''' icon on the toolbar.
 
||Click on '''Save the current file''' icon on the toolbar.
Line 234: Line 269:
 
||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.
 
 
|-
 
|-
 
||
 
||
−
||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 to,
  
 
* Add bonds to the existing bond
 
* Add bonds to the existing bond
Line 251: Line 282:
 
* Orient the bonds
 
* Orient the bonds
  
−
* Add Stereochemical bonds  
+
* Add Stereochemical bonds and
  
 
* Inverse wedge hashes
 
* Inverse wedge hashes
Line 258: Line 289:
  
 
'''Assignment'''  
 
'''Assignment'''  
−
||''' Assignment'''
+
||As an assignment,
  
 
* Convert Propane to Propyne
 
* Convert Propane to Propyne
  
−
* Draw Propane and butane structures and
+
* Draw Propane and butane structures  
  
−
*Show the stereochemical bonds.
+
* Show the stereochemical bonds.
  
−
Output of the assignment should look like this.
+
Your completed assignment should look like this.
  
 
|-
 
|-

Latest revision as of 17:52, 18 December 2013

Title of the tutorial: Formation-of-Bonds

Author: Madhuri Ganapathi

Key words: Video tutorial, Add bonds to the existing bond, Orient bonds, Add Stereochemical bonds and Inverse wedge hashes GChemPaint tools- Add a bond or change the multiplicity of an existing one, Add a wedge bond, Add a hash bond, Add a squiggle bond and Add a fore bond.

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 and
  • 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 it. 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. Enter the names of the structures as Ethane, Ethene and Ethyne.
Next, let's learn about Tetrahedral geometry.
Press CTRL+A to select all objects>>

Click on Select one or more objects tool and drag the structures.

Let's move the structures to a side.

Press CTRL+A to select all objects.

Click on Select one or more objects tool and drag the structures.

Slide Number 5

Show slide on Tetrahedral Methane structure.

Here is a slide for the Tetrahedral Methane structure.

All the bond lengths are equal to 1.09 angstrom.

Tetrahedral structure(animation) In Tetrahedral methane structure,

all the bond angles are equal to 109.5 degree.

Now, let's draw Tetrahedral 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.

Click on the Display area.

Orient the bond in horizontal direction.

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

Orient the bonds to form a Tetrahedral geometry.

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

Then orient the three bonds in different directions.

Likewise let's draw on 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 hydrogen atoms.

Click on Add or modify an atom tool.

Click on all the positions to add hydrogen atoms.

Now let's 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.

Then click on all the bonds.

Observe the changes.

Click on Add a hash bond>>click on the Display area. Click on Add a hash bond and

then click on the Display area.

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 Invert wedge hashes checkbox. Click on Invert 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 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 the perspective rules.

Click on Close button to close the window. Let's click on Close button to close the window.
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.

Let's now save 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.
Let's summarise.
Slide Number 6

Summary

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

Assignment

As an assignment,
  • Convert Propane to Propyne
  • Draw Propane and butane structures
  • Show the stereochemical bonds.

Your completed 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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