Difference between revisions of "GChemPaint/C3/Resonance-Structures/English"

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(Created page with 'Title of the tutorial: '''Analysis Of Compounds ''' Author: '''Madhuri Ganapathi''' Key words:''' Molecular contextual menu,Chemical calculator, Composition, Isotropic pattern,…')
 
 
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−
Title of the tutorial: '''Analysis Of Compounds '''
+
Title of the tutorial: '''Resonance Structures'''
  
 
Author: '''Madhuri Ganapathi'''
 
Author: '''Madhuri Ganapathi'''
  
−
Key words:''' Molecular contextual menu,Chemical calculator, Composition, Isotropic pattern, video tutorial'''
+
Key words: '''Show Electron shift and Resonance Structures, Create a reaction pathway, Create a mesomeric pathway, Build Retrosynthetic Pathway, Video tutorial'''.
  
  
Line 17: Line 17:
 
||Hello everyone.
 
||Hello everyone.
  
−
Welcome to this tutorial on '''Analysis of Compounds''' in '''GChemPaint'''.
+
Welcome to this tutorial on '''Resonance Structures''' in '''GChemPaint'''.
 
|-
 
|-
 
||'''Slide Number 2'''
 
||'''Slide Number 2'''
  
 
'''Learning Objectives'''
 
'''Learning Objectives'''
−
||In this tutorial, we will learn about,
+
||In this tutorial, we will learn to,
  
 +
* Use different types of arrows to represent chemical reactions and
  
 +
* Add charge and electron pairs on an atom
  
 +
|-
 +
||'''Slide Number 3'''
  
 +
'''System Requirement'''
 +
||For this tutorial  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'''.
  
 +
If not, for relevant tutorials, please visit our website.
 +
|-
 +
||Switch to '''GChemPaint''' window.
 +
||I will switch to '''GChemPaint''' window. 
  
 +
I have opened a new '''GChemPaint''' window.
  
 +
Here you can see '''EthylChloride''' and ''' Methylbromide''' structures.
 +
|-
 +
||
 +
||I will show how to obtain a '''Carbo-cation'''.
 +
|-
 +
||Point to '''Chlorine''' atom.
 +
||Let's add a pair of electrons on the '''Chlorine''' atom of '''EthylChloride'''.
 +
|-
 +
||Click on '''Add an electron pair ''' tool>>Click on '''Chlorine''' atom.
 +
||Click on '''Add an electron pair''' tool.
  
 +
Click on '''Chlorine''' atom and observe what happens.
 +
|-
 +
||
 +
||Next, I will show an electron pair shift in the '''Carbon-Chlorine''' bond.
 +
|-
 +
||Click on '''Add a curved arrow to represent an electron pair move'''.
  
 +
Point to the window.
 +
||Click on '''Add a curved arrow to represent an electron pair move''' tool.
  
 +
Property window opens.
 +
|-
 +
||Click on ''' End arrow at center of new bond''' check box.
 +
||Click on '''End arrow at center of new bond''' check box.
  
 +
It moves the electron pair to the correct position.
 +
|-
 +
||Click on Carbon-Chlorine bond.
 +
||Click on '''Carbon-Chlorine''' bond.
 +
|-
 +
||Point to the shift.
 +
||Place the cursor on the curved arrow and observe the electron shift.
 +
|-
 +
||Point to the structure.
 +
||I will make the copy of this structure.
 +
|-
 +
||Click on '''Add on arrow''' >>click between the structures.
 +
||Now, click on '''Add on arrow''' and click between the structures.
 +
|-
 +
||
 +
||Formation of a '''Carbo-cation''' is initialized by a base like '''Sodium Hydroxide(NaOH)'''.
 +
|-
 +
||Click on '''Add or modify a group of atoms''' tool >> click above the arrow.
 +
||Click on '''Add or modify a group of atoms''' tool, click above the arrow.
 +
|-
 +
||Type '''NaOH''' in the green box.
 +
||Type '''NaOH'''.
 +
|-
 +
||Click on '''Selection''' tool>>Click on the text Base to select>>Right-click click on the arrow.
 +
||Click on '''Selection''' tool and select '''NaOH'''.
  
 +
Right-click on the arrow.
 +
|-
 +
||Point to the submenu.
  
 +
Select '''Arrow''' >>click on '''Attach selection to arrow'''.
 +
||In the submenu, select '''Arrow'''.
  
 +
Click on '''Attach selection to arrow'''.
 +
|-
 +
||Point to the dialog box.
 +
||A dialog box with heading '''Arrow associated''' appears.
 +
|-
 +
||Point to drop down.
 +
||In the '''Role''' drop-down, select “Reactant” and click on '''Close'''. <PAUSE>
 +
|-
 +
||
 +
||Now, let's convert second '''EthylChloride''' to '''Ethyl Carbo-cation''' and '''Chloride ions'''.
 +
|-
 +
||Click on '''Eraser''' tool and click on '''Carbon-chlorine'''  bond.
  
 +
Point to products.
 +
||Click on '''Eraser''' tool and click on '''Carbon-chlorine'''  bond.
  
 +
'''Ethane(CH3-CH3''') and '''HCl''' are formed.
 +
|-
 +
||Point to the central carbon.
 +
||When electrons shift from '''Carbon''' to '''Chlorine''', '''Carbon''' gains a positive charge.
 +
|-
 +
||Click on '''Increment the charge''' tool>>Click at the position from where Carbon-chlorine  bond to deleted.
 +
||Click on '''Increment the charge''' tool.
  
 +
Click at the position from where '''Carbon-chlorine'''  bond was deleted.
  
 +
'''Ethyl Carbo-cation(CH3-CH2^+)''' is formed.
 +
|-
 +
||Click on '''Decrement the charge''' tool>>click on '''HCl'''.
 +
||To form Chloride ion, click on '''Decrement  the charge''' tool.
  
 +
Click on '''HCl'''.
  
 +
'''Chloride(Cl^-)''' ion is formed.
 +
<PAUSE>
 +
|-
 +
||
 +
||Now let's move to single electron shift.
 +
|-
 +
||Point to '''Methylbromide'''.
 +
||Let's use the '''Methylbromide''' structure to obtain '''free radicals'''.
 +
|-
 +
||Click on '''Add a curved arrow to represent a single electron move''' tool.
 +
||Click on '''Add a curved arrow to represent a single electron move''' tool.
 +
|-
 +
||Click twice on '''Bromo-methane''' bond.
 +
||Click on '''Methylbromide''' bond to obtain a curved arrow.
  
 +
Shift the '''Pencil''' tool a little on the bond, click again to get second curved arrow.
 +
|-
 +
||Point to the  '''Bromo-methane''' and curved arrows.
 +
||One curved arrow moves to  '''bromo(Br)''' and other moves towards '''methyl(CH3)'''.
  
 +
Both '''Bromo(Br)''' and '''methyl(CH3)''' will get one electron each from the bonded pair of electrons.
 +
|-
 +
||Point to the arrow.
 +
||To show the products, let's add an arrow.
  
 +
Click on '''Add an arrow''', click on '''Display area''' beside '''Methylbromide'''.
 +
|-
 +
||Point to the '''free radicals'''.
 +
||Formation of '''free radicals''' involves heat in the reaction.
 +
|-
 +
||Click on '''Add or modify a text''' tool.
  
 +
Click on the '''Display area''' above the arrow.
  
 +
Type “Heat” in the green box.
 +
||Click on '''Add or modify a text''' tool.
 +
 +
Click on ''' Display area''' above the arrow.
 +
 +
Type “Heat” in the green box.
 +
|-
 +
||Click on '''Selection''' tool>>select “Heat”.
 +
||Click on '''Selection''' tool and select “Heat”
 +
|-
 +
||Right-click on the arrow.
 +
 +
Point to the submenu>> Select '''Arrow''' >>click on '''Attach selection to arrow'''.
 +
||Right-click on the arrow.
 +
 +
In the Submenu select '''Arrow'''.
 +
 +
Click on '''Attach selection to arrow'''.
 +
|-
 +
||Point to the dialog box.
 +
||A dialog box with heading '''Arrow associated''' appears.
 +
|-
 +
||Point to drop down.
 +
||Notice that '''Role''' drop down list has more options.
 +
|-
 +
||Point to '''Role''' drop down.
 +
 +
Select “Temperature”>>Click on Close.
 +
||In the '''Role''' drop-down, select “Temperature” and
 +
 +
click on '''Close'''.
 +
|-
 +
||
 +
||Now let's create the '''free radicals'''.
 +
|-
 +
||Point to the structure.
 +
||I will copy this structure.
 +
|-
 +
||Click on '''Eraser''' tool and click on '''Carbon-bromine'''  bond.
 +
 +
Point to '''CH4''' and''' HBr'''.
 +
||Click on '''Eraser''' tool and click on '''Carbon-bromine''' bond.
 +
 +
'''Methane(CH4)''' and '''Hydrogen-bromide(HBr)''' are formed.
 +
|-
 +
||Click on '''Add an unpaired electron''' tool.
 +
 +
Click on '''CH4''' and '''HBr'''.
 +
||Click on '''Add an unpaired''' electron tool.
 +
 +
Click on '''Methane(CH4)''' and '''Hydrogen-bromide(HBr)'''
 +
 +
'''Methyl(CH3)''' and '''Bromium(Br) free radicals''' are formed.
 +
|-
 +
||Click on '''Selection''' tool.
 +
 +
Drag the cursor over the reaction to select it.
 +
||Click on '''Selection''' tool.
 +
 +
To create a reaction pathway, first select the complete reaction.
 +
|-
 +
||Right-click on the selection.
 +
 +
Point to the Submenu.
 +
||Now, right-click on the selection.
 +
 +
A submenu opens.
 +
|-
 +
||Click on '''Create a new reaction'''.
 +
 +
Point to the previous reaction
 +
||Click on '''Create a new reaction'''.
 +
 +
Reaction path is created.
 +
 +
Drag to see the reaction pathway.
 +
 +
Likewise, I will create the reaction pathway for the previous reaction.
 +
|-
 +
||Right-click on the selection again.
 +
 +
Click on '''Destroy the reaction'''.
 +
||We can also remove the reaction pathway, if we want to. 
 +
 +
To do so, right-click on the reaction again and
 +
 +
click on '''Destroy the reaction'''.
 +
|-
 +
||Point to the reactants and products.
 +
 +
Drag any object.
 +
||This action will remove the reaction pathway.
 +
 +
Drag any of the objects, and you will see that they can be moved individually.
 +
|-
 +
||
 +
||Now we move on to Resonance or Mesomery using '''double headed arrow'''.
 +
|-
 +
||Switch to '''GChempaint'''.
 +
 +
Point to the structure(CH3-NH2).
 +
||I have opened a new '''GChemPaint''' window with structures of '''Nitromethane'''.
 +
|-
 +
||Point to the structures
 +
||I had added curved arrows and charges to show electron shifts within the structures.
 +
|-
 +
||
 +
||Now let's add a double headed arrow.
 +
|-
 +
||Click on '''Add a double headed arrow'''.
 +
 +
Click on '''Display area''' beside '''Nitromethane'''.
 +
||Click on '''Add a double headed arrow'''.
 +
 +
Click on the '''Display area''' in between '''Nitromethanes'''.
 +
|-
 +
||Point to the structures
 +
||The two structures are "Resonance structures" of '''Nitromethane'''..
 +
|-
 +
||Press CTRL+A to select the structures.
 +
 +
Right-click on the selection.
 +
 +
Point to the Submenu.
 +
||Press CTRL+A to select the structures.
 +
 +
Right-click on the selection.
 +
 +
A submenu opens.
 +
|-
 +
||Click on '''Create a new mesomery relationship'''
 +
||Click on '''Create a new mesomery relationship'''.
 +
 +
Drag to see the relationship.
 +
|-
 +
||'''Slide Number'''
 +
 +
'''Resonance structures of Benzene'''
 +
||Here is slide for the resonance structures of ''' Benzene'''.
 +
|-
 +
||
 +
||Now, let's learn to create a '''retro-synthetic''' pathway.
 +
|-
 +
||Point to the window.
 +
||I have opened a new '''GChemPaint''' window with the required structures.
 +
|-
 +
||Point to the final product intermediates and starting material.
 +
||'''Retrosynthetic''' pathway
 +
 +
* starts with the product
 +
 +
* and goes to the reactant
 +
 +
* along with all the intermediates.
 +
|-
 +
||Point to the structures
 +
||In this pathway, the final product is '''Ortho-nitrophenol''' and the starting material is '''Benzene'''.
 +
|-
 +
||
 +
||Let's add a '''retro-synthetic''' arrow, to show the '''retro-synthetic''' pathway.
 +
|-
 +
||Click on '''Add arrow for a retrosynthetic step''' >> Click in between all the compounds.
 +
||Click on '''Add an arrow for a retrosynthetic step'''.
 +
 +
Click between all the compounds.
 +
|-
 +
||Press CTRL+A select all structures.
 +
 +
Right click on the selection.
 +
||Press '''CTRL+A''' to select all structures.
 +
 +
Right click on the selection.
 +
|-
 +
||Point to Submenu.
 +
 +
Click on '''Create a new retrosynthesis pathway'''.
 +
||A sub-menu opens.
 +
 +
Click on '''Create a new retrosynthesis pathway'''.
 +
 +
Drag to see the created pathway.
 +
|-
 +
||
 +
||Let's summarize what we have learnt.
 +
|-
 +
||Slide Number 9
 +
 +
Summary
 +
||In this tutorial we have learnt to
 +
 +
* Show electron shifts using curved arrows
 +
 +
* Attach reaction conditions to reaction arrows.
 +
 +
* Create and destroy reaction pathway using a reaction arrow
 +
 +
* Create a new mesomery relationship using double headed arrow
 +
 +
* Create a retro-synthetic pathway using the retro-synthetic arrow.
 +
|-
 +
||Slide Number 10
 +
 +
Assignment
 +
||As an assignment
 +
 +
Using arrow properties
 +
 +
1. Create a reaction pathway for the reaction of Bromo-Ethane (C2H5Br) and Sodium(Na) with Dry ether as a solvent to obtain Butane(C4H10) and Sodium bromide(NaBr).
 +
 +
2. Add stoichiometric coefficients to the reactants and products.
 +
 +
3. Draw resonance structures of '''Naphthalene, Anthracene''' and '''Carbon-dioxide'''
 +
|-
 +
||Point to the reaction pathway.
 +
 +
Point to the resonance structures
 +
||This is the required reaction pathway.
 +
 +
These are the resonance structures of '''Naphthalene''', '''Anthracene''' and '''Carbon-dioxide'''.
 +
|-
 
||'''Slide Number 10'''
 
||'''Slide Number 10'''
  

Latest revision as of 15:18, 28 October 2020

Title of the tutorial: Resonance Structures

Author: Madhuri Ganapathi

Key words: Show Electron shift and Resonance Structures, Create a reaction pathway, Create a mesomeric pathway, Build Retrosynthetic Pathway, Video tutorial.


Visual Cue Narration

Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Resonance Structures in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to,
  • Use different types of arrows to represent chemical reactions and
  • Add charge and electron pairs on an atom
Slide Number 3

System Requirement

For this tutorial 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.

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

Switch to GChemPaint window. I will switch to GChemPaint window.

I have opened a new GChemPaint window.

Here you can see EthylChloride and Methylbromide structures.

I will show how to obtain a Carbo-cation.
Point to Chlorine atom. Let's add a pair of electrons on the Chlorine atom of EthylChloride.
Click on Add an electron pair tool>>Click on Chlorine atom. Click on Add an electron pair tool.

Click on Chlorine atom and observe what happens.

Next, I will show an electron pair shift in the Carbon-Chlorine bond.
Click on Add a curved arrow to represent an electron pair move.

Point to the window.

Click on Add a curved arrow to represent an electron pair move tool.

Property window opens.

Click on End arrow at center of new bond check box. Click on End arrow at center of new bond check box.

It moves the electron pair to the correct position.

Click on Carbon-Chlorine bond. Click on Carbon-Chlorine bond.
Point to the shift. Place the cursor on the curved arrow and observe the electron shift.
Point to the structure. I will make the copy of this structure.
Click on Add on arrow >>click between the structures. Now, click on Add on arrow and click between the structures.
Formation of a Carbo-cation is initialized by a base like Sodium Hydroxide(NaOH).
Click on Add or modify a group of atoms tool >> click above the arrow. Click on Add or modify a group of atoms tool, click above the arrow.
Type NaOH in the green box. Type NaOH.
Click on Selection tool>>Click on the text Base to select>>Right-click click on the arrow. Click on Selection tool and select NaOH.

Right-click on the arrow.

Point to the submenu.

Select Arrow >>click on Attach selection to arrow.

In the submenu, select Arrow.

Click on Attach selection to arrow.

Point to the dialog box. A dialog box with heading Arrow associated appears.
Point to drop down. In the Role drop-down, select “Reactant” and click on Close. <PAUSE>
Now, let's convert second EthylChloride to Ethyl Carbo-cation and Chloride ions.
Click on Eraser tool and click on Carbon-chlorine bond.

Point to products.

Click on Eraser tool and click on Carbon-chlorine bond.

Ethane(CH3-CH3) and HCl are formed.

Point to the central carbon. When electrons shift from Carbon to Chlorine, Carbon gains a positive charge.
Click on Increment the charge tool>>Click at the position from where Carbon-chlorine bond to deleted. Click on Increment the charge tool.

Click at the position from where Carbon-chlorine bond was deleted.

Ethyl Carbo-cation(CH3-CH2^+) is formed.

Click on Decrement the charge tool>>click on HCl. To form Chloride ion, click on Decrement the charge tool.

Click on HCl.

Chloride(Cl^-) ion is formed. <PAUSE>

Now let's move to single electron shift.
Point to Methylbromide. Let's use the Methylbromide structure to obtain free radicals.
Click on Add a curved arrow to represent a single electron move tool. Click on Add a curved arrow to represent a single electron move tool.
Click twice on Bromo-methane bond. Click on Methylbromide bond to obtain a curved arrow.

Shift the Pencil tool a little on the bond, click again to get second curved arrow.

Point to the Bromo-methane and curved arrows. One curved arrow moves to bromo(Br) and other moves towards methyl(CH3).

Both Bromo(Br) and methyl(CH3) will get one electron each from the bonded pair of electrons.

Point to the arrow. To show the products, let's add an arrow.

Click on Add an arrow, click on Display area beside Methylbromide.

Point to the free radicals. Formation of free radicals involves heat in the reaction.
Click on Add or modify a text tool.

Click on the Display area above the arrow.

Type “Heat” in the green box.

Click on Add or modify a text tool.

Click on Display area above the arrow.

Type “Heat” in the green box.

Click on Selection tool>>select “Heat”. Click on Selection tool and select “Heat”
Right-click on the arrow.

Point to the submenu>> Select Arrow >>click on Attach selection to arrow.

Right-click on the arrow.

In the Submenu select Arrow.

Click on Attach selection to arrow.

Point to the dialog box. A dialog box with heading Arrow associated appears.
Point to drop down. Notice that Role drop down list has more options.
Point to Role drop down.

Select “Temperature”>>Click on Close.

In the Role drop-down, select “Temperature” and

click on Close.

Now let's create the free radicals.
Point to the structure. I will copy this structure.
Click on Eraser tool and click on Carbon-bromine bond.

Point to CH4 and HBr.

Click on Eraser tool and click on Carbon-bromine bond.

Methane(CH4) and Hydrogen-bromide(HBr) are formed.

Click on Add an unpaired electron tool.

Click on CH4 and HBr.

Click on Add an unpaired electron tool.

Click on Methane(CH4) and Hydrogen-bromide(HBr)

Methyl(CH3) and Bromium(Br) free radicals are formed.

Click on Selection tool.

Drag the cursor over the reaction to select it.

Click on Selection tool.

To create a reaction pathway, first select the complete reaction.

Right-click on the selection.

Point to the Submenu.

Now, right-click on the selection.

A submenu opens.

Click on Create a new reaction.

Point to the previous reaction

Click on Create a new reaction.

Reaction path is created.

Drag to see the reaction pathway.

Likewise, I will create the reaction pathway for the previous reaction.

Right-click on the selection again.

Click on Destroy the reaction.

We can also remove the reaction pathway, if we want to.

To do so, right-click on the reaction again and

click on Destroy the reaction.

Point to the reactants and products.

Drag any object.

This action will remove the reaction pathway.

Drag any of the objects, and you will see that they can be moved individually.

Now we move on to Resonance or Mesomery using double headed arrow.
Switch to GChempaint.

Point to the structure(CH3-NH2).

I have opened a new GChemPaint window with structures of Nitromethane.
Point to the structures I had added curved arrows and charges to show electron shifts within the structures.
Now let's add a double headed arrow.
Click on Add a double headed arrow.

Click on Display area beside Nitromethane.

Click on Add a double headed arrow.

Click on the Display area in between Nitromethanes.

Point to the structures The two structures are "Resonance structures" of Nitromethane..
Press CTRL+A to select the structures.

Right-click on the selection.

Point to the Submenu.

Press CTRL+A to select the structures.

Right-click on the selection.

A submenu opens.

Click on Create a new mesomery relationship Click on Create a new mesomery relationship.

Drag to see the relationship.

Slide Number

Resonance structures of Benzene

Here is slide for the resonance structures of Benzene.
Now, let's learn to create a retro-synthetic pathway.
Point to the window. I have opened a new GChemPaint window with the required structures.
Point to the final product intermediates and starting material. Retrosynthetic pathway
  • starts with the product
  • and goes to the reactant
  • along with all the intermediates.
Point to the structures In this pathway, the final product is Ortho-nitrophenol and the starting material is Benzene.
Let's add a retro-synthetic arrow, to show the retro-synthetic pathway.
Click on Add arrow for a retrosynthetic step >> Click in between all the compounds. Click on Add an arrow for a retrosynthetic step.

Click between all the compounds.

Press CTRL+A select all structures.

Right click on the selection.

Press CTRL+A to select all structures.

Right click on the selection.

Point to Submenu.

Click on Create a new retrosynthesis pathway.

A sub-menu opens.

Click on Create a new retrosynthesis pathway.

Drag to see the created pathway.

Let's summarize what we have learnt.
Slide Number 9

Summary

In this tutorial we have learnt to
  • Show electron shifts using curved arrows
  • Attach reaction conditions to reaction arrows.
  • Create and destroy reaction pathway using a reaction arrow
  • Create a new mesomery relationship using double headed arrow
  • Create a retro-synthetic pathway using the retro-synthetic arrow.
Slide Number 10

Assignment

As an assignment

Using arrow properties

1. Create a reaction pathway for the reaction of Bromo-Ethane (C2H5Br) and Sodium(Na) with Dry ether as a solvent to obtain Butane(C4H10) and Sodium bromide(NaBr).

2. Add stoichiometric coefficients to the reactants and products.

3. Draw resonance structures of Naphthalene, Anthracene and Carbon-dioxide

Point to the reaction pathway.

Point to the resonance structures

This is the required reaction pathway.

These are the resonance structures of Naphthalene, Anthracene and Carbon-dioxide.

Slide Number 10

Acknowledgement

Watch the video available at this URL.

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 11 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 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]

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

Contributors and Content Editors

Madhurig, Nancyvarkey, PoojaMoolya

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