Difference between revisions of "GChemPaint/C3/Aromatic-Molecular-Structures/English"

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Title of the tutorial: Aromatic-Molecular-Structures
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Author: Madhuri Ganapathi
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Key words: Add a six membered cycle, Add a four membered cycle, Add a bond or change the multiplicity of the existing one, Add or modify a group of atoms, Eraser,Merge two molecules, Display symbol, Benzene, fluoro(F), methyl(CH3), nitro(NO2),
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hydroxy(OH), carboxy, Video tutorial.
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<font size="2">
 
<font size="2">
 
{|border=1
 
{|border=1
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||Click on the '''Eraser''' tool.
 
||Click on the '''Eraser''' tool.
  
−
Delete one '''Hydrogen bond'''  from each of the adjacent '''Carbon''' atoms.
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Delete one '''Hydrogen''' bond from each of the adjacent '''Carbon''' atoms.
 
|-
 
|-
 
||Click on '''Add a bond or change the multiplicity of the existing one''' tool
 
||Click on '''Add a bond or change the multiplicity of the existing one''' tool
 
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
 
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
  
−
Then click on the bond between deleted '''Hydrogen bonds'''.   
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Then click on the bond between deleted '''Hydrogen''' bonds.   
 
|-
 
|-
 
||Point to the bond.
 
||Point to the bond.
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'''Functional groups''' that substitute '''Hydrogen''' are  
 
'''Functional groups''' that substitute '''Hydrogen''' are  
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*'''fluoro(F)''',  
 
*'''fluoro(F)''',  
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*'''methyl(CH3)''',  
 
*'''methyl(CH3)''',  
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*'''nitro(NO2)''',  
 
*'''nitro(NO2)''',  
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*'''hydroxy(OH)'''  
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*and others.
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*'''hydroxy(OH)''' and
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* others.
 
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|-
 
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Revision as of 11:03, 19 December 2013

Title of the tutorial: Aromatic-Molecular-Structures

Author: Madhuri Ganapathi

Key words: Add a six membered cycle, Add a four membered cycle, Add a bond or change the multiplicity of the existing one, Add or modify a group of atoms, Eraser,Merge two molecules, Display symbol, Benzene, fluoro(F), methyl(CH3), nitro(NO2),

hydroxy(OH), carboxy, Video tutorial.

Visual Cue Narration

Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Aromatic Molecular Structures in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to

1. Convert Cyclohexane to Cyclohexene

2. Convert Cyclohexene to Benzene

3. Substitute Hydrogen of Benzene ring with other atoms.

4. Substitute Hydrogen of Benzene ring with group of atoms

5. Merge two molecules

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.
Let us first add a six membered cycle to the Display area.
Click on Add a six membered cycle tool >> Click on Display area. Click on Add a six membered cycle tool.

Click on the Display area.

Click on Add a bond or change the multiplicity of the existing one tool.


Add two bonds on every corner of the cycle.

Click on Add a bond or change the multiplicity of the existing one tool.

Add two bonds on every corner of the cycle.

Click and drag the bonds to proper position. Position the bonds in such a way that no two bonds touch each other.

To do so, click and drag the bonds to proper positions.

Point to the corners. Let us display Carbon atoms on all the corners of the cycle.
Right click on any one of the corner>>A Submenu appears Right click on any one of the corners.

A submenu appears.

Select Atom >>click on Display symbol. Select Atom and then click on Display symbol.

Likewise, add Carbon atoms on all corners of the cycle.

Press capital H on the keyboard. To add Hydrogen atoms to the bonds, press H on the keyboard.
Click on Add or modify an atom tool>>Click on all the bond positions. Click on Add or modify an atom tool.

Click on all the bond positions.

Point to the Hydrogen atoms. Again, see to it that no two Hydrogens overlap each other.

The obtained structure is (C6H12) Cyclohexane.

Let's copy and paste the structure.
Press CTRL+A >>CTRL+C >> CTRL+V Press CTRL+A to select the structure.

Press CTRL+C to copy and

CTRL+V to paste the structure.

Point to the structure. Let us convert the second Cyclohexane structure to Cyclohexene.
Click on the Eraser tool >>

delete one of the Hydrogen bonds of the adjacent carbon atoms.

Click on the Eraser tool.

Delete one Hydrogen bond from each of the adjacent carbon atoms.

Click on Add a bond or change the multiplicity of the existing one tool>>

click the bond between deleted Hydrogen bonds.

Click on Add a bond or change the multiplicity of the existing one tool.

Then click on the bond between deleted Hydrogen bonds.

Point to the structure. A double bond is formed.

The obtained structure is Cyclohexene(C6H10)

Let us convert Cyclohexene to Cyclohexadiene and then to Benzene.

Ensure that Current element is Carbon.

Click on the Eraser tool >>

delete one of the Hydrogen bonds of the adjacent Carbon atoms.

Click on the Eraser tool.

Delete one Hydrogen bond from each of the adjacent Carbon atoms.

Click on Add a bond or change the multiplicity of the existing one tool Click on Add a bond or change the multiplicity of the existing one tool.

Then click on the bond between deleted Hydrogen bonds.

Point to the bond. A second double bond is formed.

The obtained structure is Cyclohexadiene(C6H8).

Point to the structure. Likewise let's repeat the process to form the third double bond.

The obtained structure is Benzene(C6H6)

Slide Number 5

Assignment

As an assignment.

Draw the structures of:

  • Cyclobutane and convert to Cyclobutadiene
  • Cyclopentane and convert to Cyclopentadiene

Your completed assignment should look like this.

Next let us learn about Benzene derivatives.
Slide Number 6

Functional groups

Functional groups can substitute Hydrogens in Benzene, to derive various chemical compounds

Functional groups that substitute Hydrogen are

  • fluoro(F),
  • methyl(CH3),
  • nitro(NO2),
  • hydroxy(OH) and
  • others.
Let us copy and paste the Benzene structure twice, on the Display area.
Click on Select one or more objects tool >>select Benzene structure. Click on Select one or more objects tool to select the Benzene structure.
Press CTRL+C to copy >> CTRL+V twice to paste. Press CTRL+C to copy and press CTRL+V twice to paste the structures.
Let's Substitute Hydrogen of the first Benzene structure with a Fluorine(F) atom.
Press F on the keyboard. Press F on the keyboard.
Click on Add or modify an atom tool>>

Click on Hydrogen to Substitute it with Fluorine(F).

Point to the structure.

Click on Add or modify an atom tool.

Click on Hydrogen to substitute it with Fluorine(F).

The obtained structure is Fluorobenzene(C6H5F).

Next let's substitute the Hydrogen of the second Benzene with a group of atoms.
Click on Add or modify a group of atoms tool>>

Click on the Hydrogen atom.

Click on Add or modify a group of atoms tool.

Click on any one of the Hydrogens.

Point to enclosed Hydrogen. Observe that Hydrogen is enclosed in a green box with a blinking cursor.
Remove Hydrogen and type capital C H and 3. Let's substitute Hydrogen with a methyl(CH3) group.

Remove Hydrogen and type capital C H and 3

Click anywhere on the Display area.

The obtained structure is Methyl benzene.

Click on the Hydrogen of third Benzene structure. Let's substitute Hydrogen of the third Benzene with a nitro(NO2) group.

Click on any one of the Hydrogens.

Remove Hydrogen and type capital N O 2 Remove Hydrogen and type capital N O 2

The obtained structure is Nitrobenzene.

Let's see Carbon positions in the Benzene ring.
Slide Number 7

Benzene Ring Positions

Six Carbon atoms are numbered from 1 to 6 in Benzene.

All six positions are equivalent, before Hydrogen is substituted.

Slide Number 8

Electron Density

Electron density of the ring changes, when Hydrogen is substituted by a functional group.

Electron density is dependent on the Substituent.

Slide Number 9

Carbon Positions

A mono-substituted compound of Benzene can be substituted at positions-
  • 1 and 4- as Para.
  • 2 and 6- as Ortho.
  • 3 and 5- as Meta.
Now let's substitute Methylbenzene structure with another methyl group.
Click on Add or modify a group of atoms tool>>

Click on the Hydrogen atom.

Click on Add or modify a group of atoms tool.

Click on the second Hydrogen position of the ring.

Type CH3 in the green box To substitute Hydrogen in the green box with methyl group, type capital C H 3.

The new structure obtained is ortho-Xylene.

Let's substitute Nitrobenzene with a Carboxy(COOH) group.
Click on the Hydrogen atom. Click on the fourth Hydrogen position of the ring.
Substitute the Hydrogen in the green box with COOH To substitute Hydrogen in the green box with Carboxy group, type capital C O O H

The new structure obtained is para-Nitrobenzoic acid.

Press CTRL+Z Press CTRL+Z to undo the process.
Substitute third Hydrogen with a nitro(NO2) group. Substitute third Hydrogen position of Nitrobenzene with a nitro(NO2) group.

Remove Hydrogen and type capital N O 2

The new structure obtained is meta-Dinitrobenzene.

Slide Number 9

Assignment I

Here is an assignment.

Draw seven Benzene structures.

Substitute one of the Hydrogens of:

1)first Benzene with bromo(Br).

2)second Benzene with iodo(I).

3)third Benzene with hydroxy(OH).

4)fourth Benzene with amino(NH2).

5)fifth Benzene with ethyl(C2H5).

Slide Number 10

Assignment II

Also substitute:

6)two of the Hydrogens of the sixth Benzene with Chlorine(Cl) atoms.

2)first and fourth Hydrogen positions of the seventh Benzene with a Carboxy(COOH) groups.

Your completed assignment should look like this.

Now, let's learn to merge two structures.
Let's open a new window.

Ensure that current element is Carbon.

Click on the Add a four membered cycle tool>>

Click on the Display area twice.

Click on Add a four membered cycle tool.

Click on the Display area twice.

Click on Select one or more objects tool.

Click on the second structure.

Click on Select one or more objects tool.

Click on the second structure.

Drag it and place it close to the first structure>>

Press CTRL+A.

Drag it and place it close to the first structure,

such that they touch each other.

Press CTRL+A to select the structures.

Point to the tool Merge two molecules tool becomes active.
Click on Merge two molecules tool to merge the molecules. Click on Merge two molecules tool, to merge the molecules.

Drag the structures to observe merging.

<pause>

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

Summary

In this tutorial, we have learnt to

1. Convert Cyclohexane to Cyclohexene

2. Convert Cyclohexene to Benzene

3. Substitute Hydrogen of Benzene with fluoro(F), methyl(CH3), nitro(NO2) and carboxy(COOH) groups.

4. Merge two four membered cycles.

Slide Number 12

Assignment

Here is an assignment.

Merge

1.Two Benzene molecules

2.Two Pentane structures

3.Cyclopentane and Cyclohexane molecules.

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

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

Contributors and Content Editors

Madhurig, Nancyvarkey

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