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

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{| border=1
+
Title of the tutorial: Aromatic-Molecular-Structures
−
|| VISUAL CUE
+
 
−
|| NARRATION
+
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">
 +
{|border=1
 +
!'''Visual Cue'''
 +
!'''Narration'''
 +
</font>
 
|-
 
|-
 
||'''Slide Number 1'''
 
||'''Slide Number 1'''
Line 8: Line 16:
 
||Hello everyone.
 
||Hello everyone.
  
−
Welcome to this tutorial on Aromatic Molecular Structures in GChemPaint.
+
Welcome to this tutorial on '''Aromatic Molecular Structures''' in '''GChemPaint'''.
 
|-
 
|-
 
||'''Slide Number 2'''
 
||'''Slide Number 2'''
  
 
'''Learning Objectives'''
 
'''Learning Objectives'''
−
||In this tutorial, we will learn to convert
+
||In this tutorial, we will learn to
−
* Cyclohexane to Cyclohexene and
+
  
−
* Cyclohexane to Benzene
+
1. Convert '''Cyclohexane''' to '''Cyclohexene'''
  
−
We will also
+
2. Convert '''Cyclohexene''' to '''Benzene'''
  
−
* Create derivatives of Benzene  
+
3. Substitute '''Hydrogen''' of '''Benzene ring''' with other atoms.
  
−
* Add atoms and group of atoms to Benzene ring and
+
4. Substitute '''Hydrogen''' of '''Benzene ring''' with group of atoms
  
−
* Merge two molecules
+
5. Merge two molecules
 
|-
 
|-
−
||Slide Number 3
+
||'''Slide Number 3'''
−
System Requirement
+
 
 +
'''System Requirement'''
 
||Here I am using
 
||Here I am using
−
Ubuntu Linux OS version. 12.04
 
  
−
GChemPaint version 0.12.10
+
'''Ubuntu Linux''' OS version 12.04.
 +
 
 +
'''GChemPaint''' version 0.12.10.
 +
 
 
|-
 
|-
−
||Slide Number 4
+
||'''Slide Number 4'''
−
Pre-requisites
+
 
−
||To follow this tutorial you should be familiar with,
+
'''Pre-requisites'''
 +
||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.
+
||I have opened a new '''GChemPaint''' application.  
 
|-
 
|-
 
||
 
||
−
||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.
−
||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 57: Line 73:
 
||Click and drag the bonds to proper position.
 
||Click and drag the bonds to proper position.
 
||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.
−
||Let's display carbon atoms at 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 I will add Carbon atoms at all the 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 Hydogen atoms.
+
||Point to the '''Hydrogen''' atoms.
−
||Again, see to it that no two Hydrogen atoms 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 >>Press CTRL+C to copy>>Press CTRL+V and paste
+
||Press '''CTRL+A''' >>'''CTRL+C''' >> '''CTRL+V'''
−
||Press CTRL+A to select the structure.
+
||Press '''CTRL+A''' to select the structure.
−
Press CTRL+C to copy and
+
 
−
Press CTRL+V and paste.   
+
Press '''CTRL+C''' to copy and  
 +
 
 +
'''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 >> 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 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>>
−
||Click on Add a bond or change the multiplicity of the existing one tool.
+
 
−
Then click on alternate bonds of the cycle, between the deleted hydrogen bonds.   
+
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.
 
||Point to the structure.
−
||The obtained structure is Cyclohexene(C6H10)
+
||A double bond is formed.
 +
 
 +
The obtained structure is '''Cyclohexene(C6H10)'''
 
|-
 
|-
−
||Slide Number 5
+
||
−
Assignment
+
||Let us convert '''Cyclohexene''' to '''Cyclohexadiene''' and then to '''Benzene'''.
−
||Here is an assignment.
+
−
* Draw structures of Cyclobutane and Cyclopentane.
+
  
−
* Convert them to Cyclobutadiene and Cyclopentadiene structures.
+
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.
 
Your completed assignment should look like this.
 
|-
 
|-
 
||
 
||
−
||Let's clear the Display area.
+
||Next let us learn about ''' Benzene''' derivatives.
 
|-
 
|-
−
||Press CTRL+A to select the structures >>Press Delete key to delete
+
||'''Slide Number 6'''
−
||Press CTRL+A to select the structures.
+
 
−
Press Delete key on the key board to delete.
+
'''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.
 
|-
 
|-
 
||
 
||
−
||Next let's convert Cyclohexane to Benzene.  
+
||Let us copy and paste the '''Benzene''' structure twice, on the '''Display area.'''
−
Ensure that Current element is Carbon.
+
 
|-
 
|-
−
||Click on Add a six membered cycle tool>>Click on Display area.
+
||Click on '''Select one or more objects''' tool >>select '''Benzene''' structure.
−
||Click on Add a six membered cycle tool.
+
||Click on '''Select one or more objects''' tool to select the '''Benzene''' structure.
−
Click on the Display area.
+
 
|-
 
|-
−
||Click on Add a bond or change the multiplicity of the existing one tool>>Click on alternate bonds of the cycle.
+
||Press '''CTRL+C''' to copy >> '''CTRL+V''' twice to paste.
−
||Click on Add a bond or change the multiplicity of the existing one tool.
+
||Press '''CTRL+C''' to copy and press '''CTRL+V''' twice to paste the structures.
−
Click on the alternate bonds and on all corners of the cycle.
+
 
|-
 
|-
 
||
 
||
−
||Let's add Hydrogen atoms to the bonds.  
+
||Let's Substitute '''Hydrogen''' of the first '''Benzene''' structure with a '''Fluorine(F)''' atom.
 
|-
 
|-
−
||Press H on the keyboard.
+
||Press '''F''' on the keyboard.
−
||Press H on the keyboard.
+
||Press '''F''' 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 Add or modify an atom tool
+
 
−
Click on all the bond positions.
+
Click on '''Hydrogen''' to Substitute it with '''Fluorine(F)'''.
−
|-
+
 
−
||Point to the structure.
+
Point to the structure.
−
||The Obtained  structure is Benzene(C6H6).
+
||Click on '''Add or modify an atom''' tool.
 +
 
 +
Click on '''Hydrogen''' to substitute it with '''Fluorine(F)'''.
 +
 
 +
The obtained structure is '''Fluorobenzene(C6H5F)'''.
 
|-
 
|-
 
||
 
||
−
||Let's now learn about Benzene derivatives.
+
||Next let's substitute the '''Hydrogen''' of the second '''Benzene''' with a group of atoms.
 
|-
 
|-
−
||Slide Number 6
+
||Click on '''Add or modify a group of atoms''' tool>>
−
Benzene Derivatives
+
−
||Various chemical compounds can be derived from Benzene. 
+
  
−
This is done by replacing one or more of its hydrogen atoms with other functional groups.
+
Click on the '''Hydrogen''' atom.
 +
||Click on '''Add or modify a group of atoms''' tool.
  
−
Hydrogen atoms can be replaced by F, Cl, Br, I
+
Click on any one of the '''Hydrogens'''.
−
group of atoms like OH, NO2, CH3 and others.
+
 
|-
 
|-
−
||
+
||Point to enclosed '''Hydrogen'''.
−
||Let's copy and paste the Benzene structure twice on the Display area.
+
||Observe that '''Hydrogen''' is enclosed in  a green box with a blinking cursor.
 
|-
 
|-
−
||Press CTRL+A to select the object.
+
||Remove '''Hydrogen''' and type capital '''C H''' and '''3.'''
−
Press CTRL+C to copy >> Press CTRL+V twice to paste.
+
||Let's substitute '''Hydrogen''' with a '''methyl(CH3)''' group.
−
||Press CTRL+A to select the object.
+
 
−
Press CTRL+C to copy and Press CTRL+V twice to paste.
+
Remove '''Hydrogen''' and type capital '''C H''' and '''3'''
 +
 
 +
Click anywhere on the '''Display area'''.
 +
 
 +
The obtained structure is '''Methyl benzene'''.
 
|-
 
|-
−
||Drag the overlapping structures aside
+
||Click on the '''Hydrogen''' of third Benzene structure.
−
||Position the structures side by side on the Display area.
+
||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 replace Hydrogen atom of the first Benzene structure with F.
+
||Let's see '''Carbon''' positions in the '''Benzene ring'''.
 
|-
 
|-
−
||Press F on the keyboard.
+
||'''Slide Number 7'''
−
||Press F on the keyboard.
+
 
 +
'''Benzene Ring Positions'''
 +
||Six '''Carbon''' atoms are numbered from 1 to 6 in '''Benzene'''.
 +
 
 +
All six positions are equivalent, before '''Hydrogen''' is substituted.
 
|-
 
|-
−
||Click on Add or modify an atom tool>>Click on H to replace it with F.
+
||'''Slide Number 8'''
−
Click on Add or modify an atom tool.
+
 
−
||Click on H to replace it with F.
+
'''Electron Density'''
−
The structure obtained is Fluorobenzene.
+
||'''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'''.
 
|-
 
|-
 
||
 
||
−
||Next let's replace the hydrogen atom of the second Benzene with a group of atoms.
+
||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 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 the second '''Hydrogen''' position of the ring.
 
|-
 
|-
−
||Point to enclosed Hydrogen.
+
||Type CH3 in the green box
−
||Observe that Hydrogen is enclosed in a green box with a blinking cursor.
+
||To substitute '''Hydrogen''' in the green box with '''methyl''' group, type capital '''C H 3'''.
 +
 
 +
The new structure obtained is '''ortho-Xylene'''.
 
|-
 
|-
−
||Delete Hydrogen and type capital CH and 3.
+
||
−
||Delete Hydrogen and type capital CH and 3 and click anywhere on the Display area.
+
||Let's substitute '''Nitrobenzene''' with a '''Carboxy(COOH)'''  group.  
−
The obtained structure is Methyl benzene.
+
 
|-
 
|-
−
||Click on the hydrogen of third Benzene structure.
+
||Click on the '''Hydrogen''' atom.
−
||Likewise let's click on the hydrogen of third Benzene structure.
+
||Click on the fourth '''Hydrogen''' position of the ring.
 
|-
 
|-
−
||Delete Hydrogen and type capital NO and 2 in a green box
+
||Substitute the '''Hydrogen''' in the green box with '''COOH'''
−
||Delete Hydrogen and type capital NO and 2 in a green box
+
||To substitute '''Hydrogen''' in the green box with  '''Carboxy group''', type capital '''C O O H'''
−
The obtained structure is Nitrobenzene.
+
 
 +
The new structure obtained is '''para-Nitrobenzoic acid'''.
 
|-
 
|-
−
||Slide Number 7
+
||Press '''CTRL+Z'''
−
Assignment
+
||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.
 
||Here is an assignment.
−
* Draw six Benzene structures.
+
 
−
* Replace one of the Hydrogen atoms of Benzene with Cl, Br and I atoms.
+
Draw seven '''Benzene''' structures.
−
* Likewise replace one of the Hydrogen atoms with OH, NH2 and C2H5  groups
+
 
 +
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.
 
Your completed assignment should look like this.
 
|-
 
|-
 
||
 
||
−
||Now let's merge two structures.
+
||Now, let's learn to merge two structures.
 
|-
 
|-
−
||Press CTRL+A to select all objects>>Press Delete key
+
||
−
||To clear the Display area.
+
||Let's open a new window.
−
Press CTRL+A to select all objects.
+
 
−
Press Delete key on the Keyboard.
+
Ensure that '''current element''' is ''Carbon''.
 
|-
 
|-
−
||Click on the Add  a four membered cycle tool>>Click on the Display area.
+
||Click on the '''Add  a four membered cycle''' tool>>
−
||Click on the Add a four membered cycle tool.
+
 
−
Press 'C' on your keyboard.
+
Click on the '''Display area''' twice.
−
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 >> select the second structure.
+
||Click on '''Select one or more objects''' tool.
−
||Click on Select one or more objects tool to select the second structure.
+
  
 +
Click on the second structure.
 +
||Click on '''Select one or more objects''' tool.
 +
 +
Click on the second structure.
 
|-
 
|-
−
||Drag the structure and place it close to the first structure>>Press CTRL+A to select structures.
+
||Drag it and place it close to the first structure>>
−
||Drag the structure and place it overlapping the first structure.
+
 
−
Press CTRL+A to select both the structures.
+
'''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
−
Click on Merge two molecules tool to merge the molecules.
+
||'''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.
−
Drag the structure to observe the  merging.
+
||Click on '''Merge two molecules''' tool, to merge the molecules.
 +
 
 +
Drag the structures to observe merging.
 +
 
 
<pause>
 
<pause>
 
|-
 
|-
Line 240: Line 388:
 
||Let's summarize what we have learnt.
 
||Let's summarize what we have learnt.
 
|-
 
|-
−
||Slide Number 8
+
||'''Slide Number 11'''
−
Summary
+
 
−
||In this tutorial we have learnt to
+
'''Summary'''
−
* Convert Cyclohexane to Cyclohexene
+
||In this tutorial, we have learnt to
−
* Convert Cyclohexane to Benzene
+
 
−
* Create derivatives of Benzene
+
1. Convert '''Cyclohexane''' to '''Cyclohexene'''
−
* Add group of atoms to Benzene ring
+
 
−
* Merge two molecules
+
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 9
+
||'''Slide Number 12'''
−
Assignment
+
 
−
||As an assignment
+
'''Assignment'''
−
* Merge two Benzene molecules
+
||Here is an assignment.
−
* Merge two Pentane structures
+
 
−
* Merge Cyclopentane and Cyclohexane   
+
Merge  
−
Your completed assignment should look like this
+
 
 +
1.Two '''Benzene''' molecules
 +
 
 +
2.Two '''Pentane''' structures
 +
 
 +
3.'''Cyclopentane''' and '''Cyclohexane''' molecules.
 +
 
 +
Your completed assignment should look like this.
 
|-
 
|-
−
||Slide Number 10
+
||'''Slide Number 13'''
−
Acknowledgement  
+
 
−
||Watch the video available at this URL.
+
'''Acknowledgement'''
−
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial
+
||Watch the video available at this link.
 +
 
 +
'''http://spoken-tutorial.org/What_is_a_Spoken_Tutorial'''
 +
 
 
It summarizes the Spoken Tutorial project
 
It summarizes the Spoken Tutorial project
 +
 
If you do not have good bandwidth, you can download and watch it  
 
If you do not have good bandwidth, you can download and watch it  
 
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|-
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||Slide Number 11
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||'''Slide Number 14'''
 
||The Spoken Tutorial Project Team:  
 
||The Spoken Tutorial Project Team:  
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Conducts workshops using spoken tutorials
 
Conducts workshops using spoken tutorials
 +
 
Gives certificates to those who pass an on-line test  
 
Gives certificates to those who pass an on-line test  
 +
 
For more details, please write to  
 
For more details, please write to  
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contact@spoken-tutorial.org  
+
 
 +
'''contact@spoken-tutorial.org'''
 
|-
 
|-
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||Slide Number 12
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||'''Slide number 15'''
 
||Spoken Tutorial Project is a part of the Talk to a Teacher project  
 
||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
 
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 ]
+
 
 +
More information on this Mission is available at this link  
 +
 
 +
'''http://spoken-tutorial.org/NMEICT-Intro'''
 
|-
 
|-
 
||
 
||
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||This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.  
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||This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
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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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