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

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 +
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.
 +
 
<font size="2">
 
<font size="2">
 
{|border=1
 
{|border=1
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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  
  
 
5. Merge two molecules
 
5. Merge two molecules
Line 40: Line 46:
  
 
'''Pre-requisites'''
 
'''Pre-requisites'''
−
||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.
Line 50: Line 56:
 
|-
 
|-
 
||
 
||
−
||Let's first add a six membered cycle to the '''Display area'''.
+
||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 '''Display area'''.
 
||Click on '''Add a six membered cycle''' tool.
 
||Click on '''Add a six membered cycle''' tool.
  
 
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 multiplicity of the existing one''' tool.
  
  
Line 68: Line 74:
 
||Position the bonds in such a way that no two bonds touch each other.
 
||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.
+
To do so, click and drag the bonds to proper positions.
 
|-
 
|-
 
||Point to the corners.
 
||Point to the corners.
−
||Let's display '''Carbon''' atoms at all the corners of the cycle.
+
||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 corner>>A '''Submenu''' appears  
−
||Right click on any one of the corner,
+
||Right click on any one of the corners.
−
A '''Submenu''' appears.  
+
 
 +
A '''submenu''' appears.  
 
|-
 
|-
 
||Select '''Atom''' >>click on Display symbol.
 
||Select '''Atom''' >>click on Display symbol.
 
||Select '''Atom''' and then click on '''Display symbol'''.
 
||Select '''Atom''' and then click on '''Display symbol'''.
  
−
Likewise add '''Carbon''' atoms on 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.
−
||To add Hydrogen atoms to the bonds,  
+
||To add '''Hydrogen''' atoms to the bonds, press '''H''' on the keyboard.
−
 
+
−
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.
−
||Click on '''Add or modify an atom''' tool
+
||Click on '''Add or modify an atom''' tool.
  
 
Click on all the bond positions.
 
Click on all the bond positions.
 
|-
 
|-
−
||Point to the Hydrogen 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.
  
−
The obtained structure is '''Cyclohexane(C6H12)'''.
+
The obtained structure is '''(C6H12) Cyclohexane'''.
 
|-
 
|-
 
||
 
||
−
||Let's copy and paste the structure
+
||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''' >>'''CTRL+C''' >> '''CTRL+V'''  
 
||Press '''CTRL+A''' to select the structure.
 
||Press '''CTRL+A''' to select the structure.
  
−
'''CTRL+C''' to copy and
+
Press '''CTRL+C''' to copy and  
  
 
'''CTRL+V''' to paste the structure.   
 
'''CTRL+V''' to paste the structure.   
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
−
||Let's convert the second '''Cyclohexane''' structure to  '''Cyclohexene'''.
+
||Let us convert the second '''Cyclohexane''' structure to  '''Cyclohexene'''.
 
|-
 
|-
 
||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>>
  
−
click the bond between deleted hydrogen bonds.   
+
click the bond between deleted '''Hydrogen bonds'''.   
 
||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.   
+
Then click on the bond between deleted '''Hydrogen bonds'''.   
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
Line 130: Line 135:
 
|-
 
|-
 
||
 
||
−
||Let's convert '''Cyclohexene''' to '''Cyclohexadiene''' and then to '''Benzene'''.
+
||Let us convert '''Cyclohexene''' to '''Cyclohexadiene''' and then to '''Benzene'''.
  
−
Ensure that Current element is '''Carbon'''.
+
Ensure that '''Current element''' is '''Carbon'''.
 
|-
 
|-
 
||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
 
||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.   
+
Then click on the bond between deleted '''Hydrogen''' bonds.   
 
|-
 
|-
 
||Point to the bond.
 
||Point to the bond.
Line 159: Line 164:
  
 
'''Assignment'''
 
'''Assignment'''
−
||Here is an assignment.
+
||As an assignment.
  
 
Draw the structures of:  
 
Draw the structures of:  
  
−
1.'''Cyclobutane''' and Convert to '''Cyclobutadiene'''  
+
*'''Cyclobutane''' and convert to '''Cyclobutadiene'''  
  
−
2.'''Cyclopentane''' and Convert to  '''Cyclopentadiene'''.
+
*'''Cyclopentane''' and convert to  '''Cyclopentadiene'''
  
 
Your completed assignment should look like this.
 
Your completed assignment should look like this.
 
|-
 
|-
 
||
 
||
−
||Next let's learn about''' Benzene''' derivatives.
+
||Next let us learn about ''' Benzene''' derivatives.
 
|-
 
|-
 
||'''Slide Number 6'''
 
||'''Slide Number 6'''
  
−
'''Benzene Derivatives'''
+
'''Functional groups'''
−
||'''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 substitute '''Hydrogen''' are
 +
 
 +
*'''fluoro(F)''',
 +
 
 +
*'''methyl(CH3)''',
 +
 
 +
*'''nitro(NO2)''',
 +
 
 +
*'''hydroxy(OH)''' and
  
−
Functional groups that can substitute Hydrogen of ''Benzene'' are ''' F, Cl, Br, I''' or '''OH, NO2, CH3''' and others.
+
* others.
 
|-
 
|-
 
||
 
||
−
||Let's copy and paste the Benzene structure twice on the Display area.
+
||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 >>select '''Benzene''' structure.
−
||Click on '''Select one or more objects''' tool to 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 >> '''CTRL+V''' twice to paste.
−
||Press '''CTRL+C''' to copy and '''CTRL+V''' twice to paste the structure.
+
||Press '''CTRL+C''' to copy and press '''CTRL+V''' twice to paste the structures.
 
|-
 
|-
 
||
 
||
−
||Let's Substitute '''Hydrogen''' atom of the first '''Benzene''' structure with F.
+
||Let's Substitute '''Hydrogen''' of the first '''Benzene''' structure with a '''Fluorine(F)''' atom.
 
|-
 
|-
−
||Press F on the keyboard.
+
||Press '''F''' on the keyboard.
−
||Press F on the keyboard.
+
||Press '''F''' on the keyboard.
 
|-
 
|-
 
||Click on '''Add or modify an atom''' tool>>
 
||Click on '''Add or modify an atom''' tool>>
  
−
Click on Hydrogen to Substitute it with F.
+
Click on '''Hydrogen''' to Substitute it with '''Fluorine(F)'''.
  
 
Point to the structure.
 
Point to the structure.
−
||Click on Add or modify an atom tool.
+
||Click on '''Add or modify an atom''' tool.
  
−
Click on Hydrogen to Substitute it with F.
+
Click on '''Hydrogen''' to substitute it with '''Fluorine(F)'''.
  
−
The structure obtained is '''Fluorobenzene'''.
+
The obtained structure  is '''Fluorobenzene(C6H5F)'''.
 
|-
 
|-
 
||
 
||
−
||Next let's Substitute the hydrogen of the second '''Benzene''' with a group of atoms.
+
||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 '''Add or modify a group of atoms''' tool>>
  
−
Click on the Hydrogen atom.
+
Click on the '''Hydrogen''' atom.
 
||Click on '''Add or modify a group of atoms''' tool.
 
||Click on '''Add or modify a group of atoms''' tool.
  
−
Click on any one of the Hydrogen atom.
+
Click on any one of the '''Hydrogens'''.
 
|-
 
|-
−
||Point to enclosed Hydrogen.
+
||Point to enclosed '''Hydrogen'''.
−
||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.
 
|-
 
|-
−
||Remove Hydrogen and type capital CH and 3.
+
||Remove '''Hydrogen''' and type capital '''C H''' and '''3.'''
−
||Remove Hydrogen and type capital CH and 3 and click anywhere on the ''Display area''.
+
||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'''.
 
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.
+
||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 NO 2  
+
||Remove '''Hydrogen''' and type capital '''N O 2'''
−
||Remove ''Hydrogen'' and type capital NO 2
+
||Remove '''Hydrogen''' and type capital '''N O 2'''
  
 
The obtained structure is '''Nitrobenzene'''.
 
The obtained structure is '''Nitrobenzene'''.
 
|-
 
|-
 
||
 
||
−
||Let's now see '''Carbon''' positions in the '''Benzene ring'''.
+
||Let's see '''Carbon''' positions in the '''Benzene ring'''.
 
|-
 
|-
 
||'''Slide Number 7'''  
 
||'''Slide Number 7'''  
Line 239: Line 260:
 
||Six '''Carbon''' atoms are numbered from 1 to 6 in '''Benzene'''.
 
||Six '''Carbon''' atoms are numbered from 1 to 6 in '''Benzene'''.
  
−
All six positions are equivalent before ''Hydrogen'' is substituted.
+
All six positions are equivalent, before '''Hydrogen''' is substituted.
 
|-
 
|-
 
||'''Slide Number 8'''
 
||'''Slide Number 8'''
  
 
'''Electron Density'''
 
'''Electron Density'''
−
||Electron density of ring changes, when Hydrogen is substituted by a functional group.
+
||'''Electron density''' of the ring changes, when '''Hydrogen''' is substituted by a functional group.
  
 
'''Electron density''' is dependent on the '''Substituent'''.
 
'''Electron density''' is dependent on the '''Substituent'''.
Line 253: Line 274:
 
||A '''mono-substituted''' compound of '''Benzene''' can be substituted at positions-
 
||A '''mono-substituted''' compound of '''Benzene''' can be substituted at positions-
  
−
1 & 4- as '''Para'''.
+
* 1 and 4- as '''Para'''.
−
 
+
* 2 and 6- as '''Ortho'''.
−
2 & 6- as '''Ortho'''.
+
* 3 and  5- as '''Meta'''.
−
 
+
−
3 & 5- as '''Meta'''.
+
 
|-
 
|-
 
||
 
||
−
||Let's now substitute '''Methylbenzene''' structure with another '''Methyl''' group.   
+
||Now let's substitute '''Methylbenzene''' structure with another '''methyl''' group.   
 
|-
 
|-
 
||Click on '''Add or modify a group of atoms''' tool>>
 
||Click on '''Add or modify a group of atoms''' tool>>
  
−
Click on the Hydrogen atom.   
+
Click on the '''Hydrogen''' atom.   
 
||Click on '''Add or modify a group of atoms''' tool.
 
||Click on '''Add or modify a group of atoms''' tool.
  
−
Click on the  second Hydrogen position of the ring.
+
Click on the  second '''Hydrogen''' position of the ring.
 
|-
 
|-
 
||Type CH3 in the green box
 
||Type CH3 in the green box
−
||Substitute Hydrogen in the green box  with '''CH3'''.
+
||To substitute '''Hydrogen''' in the green box  with '''methyl''' group, type capital '''C H 3'''.
  
 
The new structure obtained is '''ortho-Xylene'''.
 
The new structure obtained is '''ortho-Xylene'''.
 
|-
 
|-
 
||
 
||
−
||Let's substitute '''Nitrobenzene''' with a '''Carboxylic(COOH)'''  group.  
+
||Let's substitute '''Nitrobenzene''' with a '''Carboxy(COOH)'''  group.  
 
|-
 
|-
−
||Click on '''Add or modify a group of atoms''' tool>>
+
||Click on the '''Hydrogen''' atom.
−
 
+
||Click on the  fourth '''Hydrogen''' position of the ring.
−
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 the '''Hydrogen''' in the green box  with '''COOH'''
−
||Substitute ''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'''.
 
The new structure obtained is '''para-Nitrobenzoic acid'''.
Line 292: Line 307:
 
||Press '''CTRL+Z''' to undo the process.
 
||Press '''CTRL+Z''' to undo the process.
 
|-
 
|-
−
||
+
||Substitute third '''Hydrogen''' with a '''nitro(NO2)''' group.
−
||Likewise Substitute third Hydrogen position with '''NO_2''' to get '''meta-Dinitrobenzene'''.
+
||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'''
 
||'''Slide Number 9'''
  
−
'''Assignment'''
+
'''Assignment I'''
 
||Here is an assignment.
 
||Here is an assignment.
  
−
Draw seven Benzene structures.
+
Draw seven '''Benzene''' structures.
  
−
Substitute one of the Hydrogens  of:
+
Substitute one of the '''Hydrogens''' of:
  
−
1)first '''Benzene''' with '''Br'''.
+
1)first '''Benzene''' with '''bromo(Br)'''.
  
−
2)second '''Benzene''' with '''I'''.
+
2)second '''Benzene''' with '''iodo(I)'''.
  
−
3)third '''Benzene''' with  '''OH'''.
+
3)third '''Benzene''' with  '''hydroxy(OH)'''.
  
−
4)fourth '''Benzene''' with '''NH2'''.
+
4)fourth '''Benzene''' with '''amino(NH2)'''.
  
−
5)fifth '''Benzene''' with '''C2H5'''.
+
5)fifth '''Benzene''' with '''ethyl(C2H5)'''.
 
|-
 
|-
 
||'''Slide Number 10'''
 
||'''Slide Number 10'''
  
−
'''Assignment'''
+
'''Assignment II'''
−
||Also Substitute:
+
||Also substitute:
  
−
1)two of the '''Hydrogens''' of the sixth '''Benzene''' with  '''Cl''' atoms.  
+
6)two of the '''Hydrogens''' of the sixth '''Benzene''' with  '''Chlorine(Cl)''' atoms.  
  
−
2)1 and 4 '''Hydrogen''' positions of the seventh '''Benzene''' with '''COOH'''  group.
+
2)first and fourth '''Hydrogen''' positions of the seventh '''Benzene''' with a '''Carboxy(COOH)'''  groups.
  
 
Your completed assignment should look like this.
 
Your completed assignment should look like this.
 
|-
 
|-
 
||
 
||
−
||Now let's learn to merge two structures.
+
||Now, let's learn to merge two structures.
 
|-
 
|-
 
||
 
||
 
||Let's open a new window.
 
||Let's open a new window.
  
−
Ensure that current element is ''Carbon''.
+
Ensure that '''current element''' is ''Carbon''.
 
|-
 
|-
 
||Click on the '''Add  a four membered cycle''' tool>>
 
||Click on the '''Add  a four membered cycle''' tool>>
Line 349: Line 368:
 
||Drag it 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'''.
 
||Drag it and place it close to the first structure,
 
||Drag it and place it close to the first structure,
  
Line 357: Line 376:
 
|-
 
|-
 
||Point to the tool
 
||Point to the tool
−
||Merge two molecules tool becomes active.
+
||'''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.
−
||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.
+
Drag the structures to observe merging.
  
 
<pause>
 
<pause>
Line 372: Line 391:
  
 
'''Summary'''
 
'''Summary'''
−
||In this tutorial we have learnt to
+
||In this tutorial, we have learnt to
  
 
1. Convert '''Cyclohexane''' to '''Cyclohexene'''
 
1. Convert '''Cyclohexane''' to '''Cyclohexene'''
  
−
2. Convert '''Cyclohexene''' to Benzene  
+
2. Convert '''Cyclohexene''' to '''Benzene'''
  
−
3. Substitute Hydrogen of Benzene ring with F
+
3. Substitute '''Hydrogen''' of '''Benzene'''  with '''fluoro(F), methyl(CH3), nitro(NO2)''' and '''carboxy(COOH)''' groups.
  
−
4. Substitute Hydrogen of Benzene ring with CH_3, NO_2 and COOH groups.
+
4. Merge two four membered cycles.
−
 
+
−
5. Merge two four membered cycles
+
 
|-
 
|-
 
||'''Slide Number 12'''
 
||'''Slide Number 12'''
Line 391: Line 408:
 
Merge  
 
Merge  
  
−
1.Two Benzene molecules
+
1.Two '''Benzene''' molecules
  
−
2.Two Pentane structures
+
2.Two '''Pentane''' structures
  
−
3.Cyclopentane and Cyclohexane   
+
3.'''Cyclopentane''' and '''Cyclohexane''' molecules.
  
−
Your completed assignment should look like this
+
Your completed assignment should look like this.
 
|-
 
|-
 
||'''Slide Number 13'''
 
||'''Slide Number 13'''
  
 
'''Acknowledgement'''  
 
'''Acknowledgement'''  
−
||Watch the video available at this URL.
+
||Watch the video available at this link.
  
−
'''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''
+
'''http://spoken-tutorial.org/What_is_a_Spoken_Tutorial'''
  
 
It summarizes the Spoken Tutorial project
 
It summarizes the Spoken Tutorial project
Line 428: Line 445:
 
More information on this Mission is available at this link  
 
More information on this Mission is available at this link  
  
−
'''http://spoken-tutorial.org/NMEICT-Intro ]'''  
+
'''http://spoken-tutorial.org/NMEICT-Intro'''  
 
|-
 
|-
 
||
 
||
 
||This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
 
||This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
 
|}
 
|}

Latest 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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