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

From Script | Spoken-Tutorial
Jump to: navigation, search
Line 21: Line 21:
 
2. Convert '''Cyclohexene''' to '''Benzene'''  
 
2. Convert '''Cyclohexene''' to '''Benzene'''  
  
−
3. Substitute Hydrogen of '''Benzene ring''' with other atoms  
+
3. Substitute Hydrogen of '''Benzene ring''' with other atoms.
  
 
4. Substitute Hydrogen of '''Benzene ring''' with group of atoms  
 
4. Substitute Hydrogen of '''Benzene ring''' with group of atoms  
Line 32: Line 32:
 
||Here I am using
 
||Here I am using
  
−
'''Ubuntu Linux''' OS version. 12.04
+
'''Ubuntu Linux''' OS version 12.04.
  
−
'''GChemPaint''' version 0.12.10
+
'''GChemPaint''' version 0.12.10.
  
 
|-
 
|-
Line 42: Line 42:
 
||To follow this tutorial you should be familiar with,
 
||To follow this tutorial you should be familiar with,
  
−
GChemPaint chemical structure editor.
+
'''GChemPaint''' chemical structure editor.
  
 
If not, for relevant tutorials,  please visit our website.  
 
If not, for relevant tutorials,  please visit our website.  
 
|-
 
|-
 
||Switch to '''GChemPaint''' application.
 
||Switch to '''GChemPaint''' application.
−
||I have opened a new '''GChemPaint''' application.  Switch to '''GChemPaint''' application.
+
||I have opened a new '''GChemPaint''' application.  
 
|-
 
|-
 
||
 
||
−
||Let's first add a six membered cycle to the Display area.
+
||Let's 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 '''Display area'''.
Line 57: Line 57:
 
Click on the '''Display area'''.
 
Click on the '''Display area'''.
 
|-
 
|-
−
||Click on Add a bond or change the multiplicy of the existing one tool
+
||Click on '''Add a bond or change the multiplicy of the existing one''' tool
−
||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.
 
Add two bonds on every corner of the cycle.
Line 67: Line 70:
 
To do so, click and drag the bonds to proper position.
 
To do so, click and drag the bonds to proper position.
 
|-
 
|-
−
||
+
||Point to the corners.
−
||Let's display '''Carbon''' atoms at the corners of the cycle.
+
||Let's display '''Carbon''' atoms at all the corners of the cycle.
 
|-
 
|-
 
||Right click on any one of the corner>>A '''Submenu''' appears  
 
||Right click on any one of the corner>>A '''Submenu''' appears  
Line 77: Line 80:
 
||Select '''Atom''' and then click on '''Display symbol'''.
 
||Select '''Atom''' and then click on '''Display symbol'''.
  
−
Likewise add '''Carbon''' atoms at all corners of the cycle.
+
Likewise add '''Carbon''' atoms on all corners of the cycle.
 
|-
 
|-
 
||Press capital H on the keyboard.
 
||Press capital H on the keyboard.
Line 89: Line 92:
 
Click on all the bond positions.
 
Click on all the bond positions.
 
|-
 
|-
−
||Point to the Hydogen atoms.
+
||Point to the Hydrogen atoms.
 
||Again, see to it that no two Hydrogens overlap each other.
 
||Again, see to it that no two Hydrogens overlap each other.
  
Line 97: Line 100:
 
||Let's copy and paste the structure
 
||Let's copy and paste the structure
 
|-
 
|-
−
||Press '''CTRL+A''' to select the structure >>Press '''CTRL+C'''  to copy>>Press '''CTRL+V''' and paste  
+
||Press '''CTRL+A''' to select the structure >>'''CTRL+C'''  to copy>> '''CTRL+V''' to paste.
 
||Press '''CTRL+A''' to select the structure.
 
||Press '''CTRL+A''' to select the structure.
  
−
Press '''CTRL+C'''  to copy and
+
'''CTRL+C'''  to copy and
  
−
Press '''CTRL+V''' and paste.   
+
'''CTRL+V''' to paste the structure.   
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
Line 133: Line 136:
 
||Click on the '''Eraser''' tool >>  
 
||Click on the '''Eraser''' tool >>  
  
−
delete one of the hydrogen bonds of the adjacent carbon atoms.
+
delete one of the hydrogen bonds of the adjacent '''Carbon''' atoms.
 
||Click on the '''Eraser''' tool.
 
||Click on the '''Eraser''' tool.
  
−
Delete one hydrogen bond from each of the adjacent carbon atoms.
+
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
Line 148: Line 151:
 
The obtained structure is '''Cyclohexadiene(C6H8)'''.
 
The obtained structure is '''Cyclohexadiene(C6H8)'''.
 
|-
 
|-
−
||
+
||Point to the structure.
 
||Likewise let's repeat the process to form the third double bond.
 
||Likewise let's repeat the process to form the third double bond.
−
The obtained structure is '''Cyclohexatriene''' or '''Benzene(C6H6)'''
+
 
 +
The obtained structure is '''Benzene(C6H6)'''
 
|-
 
|-
 
||'''Slide Number 5'''
 
||'''Slide Number 5'''
Line 166: Line 170:
 
|-
 
|-
 
||
 
||
−
||Let's now learn about''' Benzene''' derivatives.
+
||Next let's learn about''' Benzene''' derivatives.
 
|-
 
|-
 
||'''Slide Number 6'''
 
||'''Slide Number 6'''
Line 173: Line 177:
 
||'''Functional groups''' can substitute hydrogens in '''Benzene''' to derive various chemical compounds
 
||'''Functional groups''' can substitute hydrogens in '''Benzene''' to derive various chemical compounds
  
−
Functional groups that can substitute Hydrogen of Benzene are''' F, Cl, Br''', '''I''' or '''OH, NO2, CH3'''.
+
Functional groups that can substitute Hydrogen of ''Benzene'' are ''' F, Cl, Br, I''' or '''OH, NO2, CH3''' and others.
 
|-
 
|-
 
||
 
||
Line 181: Line 185:
 
||Click on '''Select one or more objects''' tool to select '''Benzene''' structure.
 
||Click on '''Select one or more objects''' tool to select '''Benzene''' structure.
 
|-
 
|-
−
||Press '''CTRL+C''' to copy >> Press '''CTRL+V''' twice to paste.
+
||Press '''CTRL+C''' to copy >> '''CTRL+V''' twice to paste.
−
||Press '''CTRL+C''' to copy and Press '''CTRL+V''' twice to paste.
+
||Press '''CTRL+C''' to copy and '''CTRL+V''' twice to paste the structure.
−
|-
+
−
||Drag the overlapping structures aside
+
−
||Position the structures side by side on the Display area.
+
 
|-
 
|-
 
||
 
||
Line 195: Line 196:
 
||Click on '''Add or modify an atom''' tool>>
 
||Click on '''Add or modify an atom''' tool>>
  
−
Click on H to Substitute it with F.
+
Click on Hydrogen to Substitute it with F.
 +
 
 +
Point to the structure.
 
||Click on Add or modify an atom tool.
 
||Click on Add or modify an atom tool.
  
−
Click on H to Substitute it with F.
+
Click on Hydrogen to Substitute it with F.
  
 
The structure obtained is '''Fluorobenzene'''.
 
The structure obtained is '''Fluorobenzene'''.
Line 215: Line 218:
 
||Observe that Hydrogen is enclosed in  a green box with a blinking cursor.
 
||Observe that Hydrogen is enclosed in  a green box with a blinking cursor.
 
|-
 
|-
−
||Delete Hydrogen and type capital CH and 3.
+
||Remove Hydrogen and type capital CH and 3.
−
||Remove Hydrogen and type capital CH and 3 and click anywhere on the Display area.
+
||Remove Hydrogen and type capital CH and 3 and click anywhere on the ''Display area''.
  
−
The obtained structure is Methyl benzene.
+
The obtained structure is '''Methyl benzene'''.
 
|-
 
|-
 
||Click on the hydrogen of third Benzene structure.
 
||Click on the hydrogen of third Benzene structure.
−
||Likewise let's click one of the hydrogens of third Benzene structure.
+
||Likewise let's click one of the hydrogens of third '''Benzene''' structure.
 
|-
 
|-
−
||Delete Hydrogen and type capital NO and 2 in  a green box
+
||Remove ''Hydrogen'' and type capital NO 2  
−
||Remove Hydrogen and type capital NO and 2 in  a green box
+
||Remove ''Hydrogen'' and type capital NO 2
  
−
The obtained structure is Nitrobenzene.
+
The obtained structure is '''Nitrobenzene'''.
 +
|-
 +
||
 +
||Let's now see '''Carbon''' positions in the '''Benzene ring'''.
 
|-
 
|-
 
||'''Slide Number 7'''  
 
||'''Slide Number 7'''  
  
 
'''Benzene Ring Positions'''
 
'''Benzene Ring Positions'''
−
||
+
||Six '''Carbon''' atoms are numbered from 1 to 6 in '''Benzene'''.
−
Let's now see '''Carbon''' positions in the '''Benzene ring'''.
+
−
 
+
−
Six '''Carbon''' atoms are numbered from 1 to 6 in '''Benzene'''.
+
  
−
All the six positions are equivalent before Hydrogen is substituted.
+
All six positions are equivalent before ''Hydrogen'' is substituted.
 
|-
 
|-
 
||'''Slide Number 8'''
 
||'''Slide Number 8'''
Line 243: Line 246:
 
||Electron density of ring changes, when Hydrogen is substituted by a functional group.
 
||Electron density of ring changes, when Hydrogen is substituted by a functional group.
  
−
'''Electron density''' of the ring is dependent on the '''Substituent'''.
+
'''Electron density''' is dependent on the '''Substituent'''.
 
|-
 
|-
 
||'''Slide Number 9'''
 
||'''Slide Number 9'''
  
 
'''Carbon Positions'''
 
'''Carbon Positions'''
−
||A '''mono-substituted''' compound of '''Benzene''' can be substituted at-
+
||A '''mono-substituted''' compound of '''Benzene''' can be substituted at positions-
  
−
1 & 4- called as '''Para''' positions
+
1 & 4- as '''Para'''.
  
−
2 & 6- called as '''Ortho''' positions
+
2 & 6- as '''Ortho'''.
  
−
3 & 5- called as '''Meta''' positions.
+
3 & 5- as '''Meta'''.
 
|-
 
|-
 
||
 
||
Line 281: Line 284:
 
Click on the  fourth Hydrogen position of the ring.
 
Click on the  fourth Hydrogen position of the ring.
 
|-
 
|-
−
||Substitute the Hydrogen in the green box  with '''COOH'''
+
||Substitute the ''Hydrogen'' in the green box  with '''COOH'''
−
||Substitute Hydrogen in the green box with '''COOH'''
+
||Substitute ''Hydrogen'' in the green box with '''COOH'''
  
 
The new structure obtained is '''para-Nitrobenzoic acid'''.
 
The new structure obtained is '''para-Nitrobenzoic acid'''.
Line 316: Line 319:
 
||Also Substitute:
 
||Also Substitute:
  
−
1)two of the '''Hydrogens''' of the 6th '''Benzene''' with  '''Cl''' atoms.  
+
1)two of the '''Hydrogens''' of the sixth '''Benzene''' with  '''Cl''' atoms.  
  
−
2)1 and 4 '''Hydrogen''' positions of the 7th '''Benzene''' with '''COOH'''  group.
+
2)1 and 4 '''Hydrogen''' positions of the seventh '''Benzene''' with '''COOH'''  group.
  
 
Your completed assignment should look like this.
 
Your completed assignment should look like this.
Line 325: Line 328:
 
||Now let's learn to merge two structures.
 
||Now let's learn to merge two structures.
 
|-
 
|-
−
||Click on '''Create  a new file''' icon on the toolbar.
+
||
 
||Let's open a new window.
 
||Let's open a new window.
  
−
Click on '''Create  a new file''' icon on the toolbar.
+
Ensure that current element is ''Carbon''.
 
|-
 
|-
 
||Click on the '''Add  a four membered cycle''' tool>>
 
||Click on the '''Add  a four membered cycle''' tool>>
  
−
Click on the '''Display area'''.
+
Click on the '''Display area''' twice.
 
||Click on '''Add a four membered cycle''' tool.
 
||Click on '''Add a four membered cycle''' tool.
  
 
Click on the '''Display area''' twice.
 
Click on the '''Display area''' twice.
 
|-
 
|-
−
||Click on '''Select one or more objects''' tool >>
+
||Click on '''Select one or more objects''' tool.
 +
 
 +
Click on the second structure.
 +
||Click on '''Select one or more objects''' tool.
  
−
select the second structure.
+
Click on the second structure.
−
||Click on '''Select one or more objects''' tool to select the second structure.
+
 
|-
 
|-
−
||Drag the structure and place it close to the first structure>>
+
||Drag it and place it close to the first structure>>
  
 
Press CTRL+A to select structures.
 
Press CTRL+A to select structures.
−
||Drag the structure and
+
||Drag it and place it close to the first structure,
  
−
place it close to the first structure such that they touch each other.
+
such that they touch each other.
  
 
Press '''CTRL+A''' to select the structures.
 
Press '''CTRL+A''' to select the structures.
Line 375: Line 380:
 
3. Substitute Hydrogen of Benzene ring with F
 
3. Substitute Hydrogen of Benzene ring with F
  
−
4. Substitute Hydrogen of Benzene ring with CH_3, NO_2.
+
4. Substitute Hydrogen of Benzene ring with CH_3, NO_2 and COOH groups.
  
 
5. Merge two four membered cycles
 
5. Merge two four membered cycles
Line 382: Line 387:
  
 
'''Assignment'''
 
'''Assignment'''
−
||As an assignment  
+
||Here is an assignment.
 +
 
 +
Merge
  
−
1. Merge two Benzene molecules
+
1.Two Benzene molecules
  
−
2. Merge two Pentane structures
+
2.Two Pentane structures
  
−
3. Merge Cyclopentane and Cyclohexane   
+
3.Cyclopentane and Cyclohexane   
  
 
Your completed assignment should look like this
 
Your completed assignment should look like this

Revision as of 13:19, 18 November 2013

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's 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 multiplicy 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 position.

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

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 Cyclohexane(C6H12).

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

CTRL+C to copy and

CTRL+V to paste the structure.

Point to the structure. Let's 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's 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

Here is an assignment.

Draw the structures of:

1.Cyclobutane and Convert to Cyclobutadiene

2.Cyclopentane and Convert to Cyclopentadiene.

Your completed assignment should look like this.

Next let's learn about Benzene derivatives.
Slide Number 6

Benzene Derivatives

Functional groups can substitute hydrogens in Benzene to derive various chemical compounds

Functional groups that can substitute Hydrogen of Benzene are F, Cl, Br, I or OH, NO2, CH3 and others.

Let's 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 Benzene structure.
Press CTRL+C to copy >> CTRL+V twice to paste. Press CTRL+C to copy and CTRL+V twice to paste the structure.
Let's Substitute Hydrogen atom of the first Benzene structure with F.
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 F.

Point to the structure.

Click on Add or modify an atom tool.

Click on Hydrogen to Substitute it with F.

The structure obtained is Fluorobenzene.

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 Hydrogen atom.

Point to enclosed Hydrogen. Observe that Hydrogen is enclosed in a green box with a blinking cursor.
Remove Hydrogen and type capital CH and 3. Remove Hydrogen and type capital CH and 3 and click anywhere on the Display area.

The obtained structure is Methyl benzene.

Click on the hydrogen of third Benzene structure. Likewise let's click one of the hydrogens of third Benzene structure.
Remove Hydrogen and type capital NO 2 Remove Hydrogen and type capital NO 2

The obtained structure is Nitrobenzene.

Let's now 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 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 & 4- as Para.

2 & 6- as Ortho.

3 & 5- as Meta.

Let's now 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 Substitute Hydrogen in the green box with CH3.

The new structure obtained is ortho-Xylene.

Let's substitute Nitrobenzene with a Carboxylic(COOH) 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 fourth Hydrogen position of the ring.

Substitute the Hydrogen in the green box with COOH Substitute Hydrogen in the green box with COOH

The new structure obtained is para-Nitrobenzoic acid.

Press CTRL+Z Press CTRL+Z to undo the process.
Likewise Substitute third Hydrogen position with NO_2 to get meta-Dinitrobenzene.
Slide Number 9

Assignment

Here is an assignment.

Draw seven Benzene structures.

Substitute one of the Hydrogens of:

1)first Benzene with Br.

2)second Benzene with I.

3)third Benzene with OH.

4)fourth Benzene with NH2.

5)fifth Benzene with C2H5.

Slide Number 10

Assignment

Also Substitute:

1)two of the Hydrogens of the sixth Benzene with Cl atoms.

2)1 and 4 Hydrogen positions of the seventh Benzene with COOH group.

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 to select structures.

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 structure to observe the 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 ring with F

4. Substitute Hydrogen of Benzene ring with CH_3, NO_2 and COOH groups.

5. 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

Your completed assignment should look like this

Slide Number 13

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 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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=GChemPaint/C3/Aromatic-Molecular-Structures/English&oldid=7215"