Difference between revisions of "Avogadro/C3/Stereoisomerism/English"

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(Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''. |- ||'''Sl...")
 
 
Line 14: Line 14:
 
'''Learning Objectives'''
 
'''Learning Objectives'''
 
||In this tutorial, we will learn about:
 
||In this tutorial, we will learn about:
−
* Conformational isomerism  
+
* '''Conformational isomerism'''
  
−
* Geometrical isomerism and
+
* '''Geometrical isomerism''' and
  
−
* R-S configurations with examples.
+
* '''R-S configurations''' with examples.
 
|-
 
|-
 
||'''Slide Number 3'''
 
||'''Slide Number 3'''
Line 25: Line 25:
 
||Here I am using,
 
||Here I am using,
  
−
* Ubuntu Linux OS version. 14.04
+
* '''Ubuntu Linux''' OS version. 14.04
  
−
*Avogadro version 1.1.1.
+
* '''Avogadro''' version 1.1.1.
 
|-
 
|-
 
||'''Slide Number 4'''
 
||'''Slide Number 4'''
Line 33: Line 33:
 
'''Pre-requisties'''
 
'''Pre-requisties'''
  
−
You should be familiar with:
+
You should be familiar with :
  
−
Avogadro interface.
+
'''Avogadro''' interface.
  
 
For relevant tutorials, visit our website.  
 
For relevant tutorials, visit our website.  
  
 
'''www.spoken-tutorial.org'''.
 
'''www.spoken-tutorial.org'''.
−
||To follow this tutorial, you should be familiar with: Avogadro interface.
+
||To follow this tutorial, you should be familiar with '''Avogadro''' interface.
  
 
If not, for relevant tutorials, please visit our website.
 
If not, for relevant tutorials, please visit our website.
Line 69: Line 69:
 
||It is a form of stereoisomerism.
 
||It is a form of stereoisomerism.
  
−
In this, isomers can be inter-converted by rotation about single bonds.
+
In this, '''isomers''' can be inter-converted by rotation about single bonds.
  
−
Rotation about single bond is restricted by rotational energy barrier.
+
Rotation about single bond is restricted by '''rotational energy barrier.'''
 
|-
 
|-
 
||
 
||
Line 80: Line 80:
 
'''Conformations'''  
 
'''Conformations'''  
 
||'''1,2-dichloroethane''' exists in three '''conformers''' namely:
 
||'''1,2-dichloroethane''' exists in three '''conformers''' namely:
−
* Eclipsed
+
* '''Eclipsed'''
  
−
* Gauche and
+
* '''Gauche''' and
  
−
* Anti
+
* '''Anti'''
 
|-
 
|-
 
||Cursor on the Panel.
 
||Cursor on the Panel.
Line 95: Line 95:
 
||Uncheck '''Adjust Hydrogens''' check box.
 
||Uncheck '''Adjust Hydrogens''' check box.
 
|-
 
|-
−
||Click on the '''Panel''' and drag draw two atoms.
+
||Click on the '''Panel''' and drag to draw two atoms.
−
||Click on the '''Panel''' and drag draw two atoms.
+
||Click on the '''Panel''' and drag to draw two atoms.
 
|-
 
|-
 
||Select '''Chlorine''' from '''Element''' drop down.
 
||Select '''Chlorine''' from '''Element''' drop down.
  
−
Draw a bond on each carbon.
+
Draw a bond on each '''carbon'''.
 
||Select '''Chlorine''' from '''Element''' drop down.
 
||Select '''Chlorine''' from '''Element''' drop down.
  
−
Draw a bond on each carbon.
+
Draw a bond on each '''carbon'''.
 
|-
 
|-
 
||Go to '''Build''' menu, click on '''Add Hydrogens'''.
 
||Go to '''Build''' menu, click on '''Add Hydrogens'''.
Line 118: Line 118:
 
||Click on '''Auto Optimization''' tool.
 
||Click on '''Auto Optimization''' tool.
 
|-
 
|-
−
||In the '''Force Field''' select '''MMFF94''', click on '''Start''' button.
+
||In the '''Force Field''' select '''MMFF94'''>> click on '''Start''' button.
−
||In the '''Force Field''' select '''MMFF94''' and click on '''Start''' button.
+
||In the '''Force Field,''' select '''MMFF94''' and click on '''Start''' button.
 
|-
 
|-
−
||Click on '''Stop''' to stop the optimiztion process.
+
||Click on '''Stop'''
−
||Click on '''Stop''' to stop the optimiztion process.
+
||Click on '''Stop''' to stop the '''optimization''' process.
 
|-
 
|-
 
||Click on '''Navigation''' tool, rotate the structure.
 
||Click on '''Navigation''' tool, rotate the structure.
Line 136: Line 136:
 
|-
 
|-
 
||Click on the bond between two carbon atoms.
 
||Click on the bond between two carbon atoms.
−
||Click on the bond between two carbon atoms.
+
||Click on the bond between two '''carbon''' atoms.
 
|-
 
|-
 
||Point to the planes.
 
||Point to the planes.
Line 147: Line 147:
 
||Place the cursor on '''Chlorine''' atom.
 
||Place the cursor on '''Chlorine''' atom.
  
−
Rotate the bond in clock wise direction.
+
Rotate the bond in clock-wise direction.
  
 
Click on '''Navigation''' tool and rotate the structure.
 
Click on '''Navigation''' tool and rotate the structure.
Line 155: Line 155:
 
||Point to the '''conformer'''.
 
||Point to the '''conformer'''.
  
−
||Again use '''Bondcentric Manipulation''' tool to rotate the C-C bond.
+
||Again use '''Bondcentric Manipulation''' tool to rotate the '''C-C bond'''.
  
 
We have '''Eclipsed conformer''' on the '''Panel'''.
 
We have '''Eclipsed conformer''' on the '''Panel'''.
Line 170: Line 170:
  
 
Uncheck '''Adjust Hydrogens''' check box.
 
Uncheck '''Adjust Hydrogens''' check box.
−
||In '''Draw settings''' menu '''Carbon''' is selected as default element.
+
||In '''Draw settings''' menu, '''Carbon''' is selected as default element.
  
 
Uncheck '''Adjust Hydrogens''' check box.
 
Uncheck '''Adjust Hydrogens''' check box.
Line 187: Line 187:
 
|-
 
|-
 
||Cursor on the  structure.
 
||Cursor on the  structure.
−
||Let us label the '''conformer''' as per our requirement.
+
||Let us label the '''conformers''' as per our requirement.
 
|-
 
|-
 
||Click on '''Selection''' tool>>right click on first carbon atom.
 
||Click on '''Selection''' tool>>right click on first carbon atom.
−
||Click on '''Selection''' tool, then right click on first carbon atom.
+
||Click on '''Selection''' tool, then right-click on first '''carbon''' atom.
 
|-
 
|-
 
||Point to the menu.
 
||Point to the menu.
Line 204: Line 204:
 
|-
 
|-
 
||Type 1, click OK.
 
||Type 1, click OK.
−
||In the '''New Label''' field type 1 and click OK.
+
||In the '''New Label''' field type 1 and click '''OK'''.
 
|-
 
|-
 
||right click on the second atom, change the label as 2.
 
||right click on the second atom, change the label as 2.
  
 
Point to the atoms.
 
Point to the atoms.
−
||Next right click on the second atom and change the label as 2.
+
||Next right-click on the second atom and change the label as 2.
  
−
Similarly I will change the labels of atoms as 3, 4, 5 and 6.  
+
Similarly, I will change the labels of atoms as 3, 4, 5 and 6.  
 
|-
 
|-
 
||Cursor on the Panel.
 
||Cursor on the Panel.
Line 222: Line 222:
 
Click on 5 and drag it upwards.
 
Click on 5 and drag it upwards.
  
−
Click on 3 and move it to left.
+
Click on 3 and drag it upwards.
  
 
Point to the structure.
 
Point to the structure.
Line 242: Line 242:
 
Click on 5 and drag it downwards.
 
Click on 5 and drag it downwards.
  
−
Click on 4 and drag it horizontal position.
+
Click on 4 and drag it to horizontal position.
  
 
Point to the structure.
 
Point to the structure.
Line 251: Line 251:
 
Click on 4 and drag it to horizontal position.
 
Click on 4 and drag it to horizontal position.
  
−
Adjust the positions of all carbon atoms if required to get correct structure.
+
Adjust the positions of all '''carbon''' atoms if required, to get correct structure.
  
 
We have '''half chair''' on the '''Panel'''.
 
We have '''half chair''' on the '''Panel'''.
Line 265: Line 265:
 
Click on 1 and drag it downwards.
 
Click on 1 and drag it downwards.
  
−
Adjust the positions of all carbon atoms if required to get correct structure.
+
Adjust the positions of all '''carbon''' atoms if required, to get correct structure.
  
 
We have '''chair conformer''' on the '''Panel'''.
 
We have '''chair conformer''' on the '''Panel'''.
Line 274: Line 274:
 
||As an assignment,
 
||As an assignment,
  
−
* Draw various  conformers of butane and Cyclopentane.
+
* Draw various  '''conformers''' of '''Butane''' and '''Cyclopentane'''.
 
|-
 
|-
 
||Cursor on the '''Panel'''.
 
||Cursor on the '''Panel'''.
−
||Now I will draw structures to demonstrate '''geometrical isomerism'''.
+
||Now I will draw structures to demonstrate '''geometrical isomerism'''.
 
|-
 
|-
 
||'''Slide Number 9'''
 
||'''Slide Number 9'''
  
 
'''Geometrical isomerism'''  
 
'''Geometrical isomerism'''  
−
||'''Geometrical isomerism''' arises due to: * different spatial arrangement of atoms around a double bond.
+
||'''Geometrical isomerism''' arises due to:  
 +
* different spatial arrangement of atoms around a '''double-bond'''.
  
−
Here rotation of atoms or groups around double bonded carbon is restricted.  
+
Here rotation of atoms or groups around '''double-bonded carbon''' is restricted.  
 
|-
 
|-
 
||Cursor on the Panel.
 
||Cursor on the Panel.
−
||For demonstration I will draw  '''diamminedichloroplatinum(II)''' structure also known as '''cisplatin'''.
+
||For demonstration, I will draw  '''diamminedichloroplatinum(II)''' structure also known as '''cisplatin'''.
 
|-
 
|-
 
||Click on '''New''' button.
 
||Click on '''New''' button.
Line 304: Line 305:
 
||Select '''Platinum(Pt)''' from the table.
 
||Select '''Platinum(Pt)''' from the table.
  
−
Close the '''Periodic''' table window.
+
Close the '''Periodic table''' window.
 
|-
 
|-
 
||Click on the '''Panel'''.
 
||Click on the '''Panel'''.
Line 313: Line 314:
 
|-
 
|-
 
||Click and drag.
 
||Click and drag.
−
||Draw two chlorine bonds on '''Platinum''' atom on the same side.
+
||Draw two '''chlorine bonds''' on '''Platinum''' atom on the same side.
 
|-
 
|-
 
||Select '''Nitrogen''' from '''Element''' drop down.  
 
||Select '''Nitrogen''' from '''Element''' drop down.  
 
||Select '''Nitrogen''' from '''Element''' drop down.  
 
||Select '''Nitrogen''' from '''Element''' drop down.  
  
−
Draw two nitrogen bonds as before.   
+
Draw two '''nitrogen bonds''' as before.   
 
|-
 
|-
 
||Point to Nitrogen atom.
 
||Point to Nitrogen atom.
Line 327: Line 328:
 
|-
 
|-
 
|Click and drag.
 
|Click and drag.
−
||Click on each nitrogen atom to draw the third bond.
+
||Click on each '''nitrogen''' atom to draw the third bond.
 
|-
 
|-
 
||Cursor on the '''Panel'''.
 
||Cursor on the '''Panel'''.
Line 336: Line 337:
 
|-
 
|-
 
||'''Force Field''' select '''UFF''', click on '''Start''' button to optimize.
 
||'''Force Field''' select '''UFF''', click on '''Start''' button to optimize.
−
||In the '''Force Field''' select '''UFF''' and click on '''Start''' button.
+
||In the '''Force Field,''' select '''UFF''' and click on '''Start''' button.
 
|-
 
|-
−
||Click on '''Stop''' to stop the optimization process.
+
||Click on '''Stop'''.
 
||Click on '''Stop''' to stop the optimization process.
 
||Click on '''Stop''' to stop the optimization process.
 
|-
 
|-
Line 344: Line 345:
 
||For demonstration I will require two structures.
 
||For demonstration I will require two structures.
  
−
I will copy and Paste the structures.
+
I will copy and paste the structures.
 
|-
 
|-
 
||Click on '''Selection''' tool.
 
||Click on '''Selection''' tool.
Line 363: Line 364:
  
 
Point to the structures.
 
Point to the structures.
−
||To remove hydrogens go to '''Build''' menu and select '''Remove Hydrogens'''.
+
||To remove '''Hydrogens''', go to '''Build''' menu and select '''Remove Hydrogens'''.
  
 
We have two isomers of '''cisplatin''' on the '''Panel'''.
 
We have two isomers of '''cisplatin''' on the '''Panel'''.
Line 374: Line 375:
 
Click on '''Manipulation''' tool.
 
Click on '''Manipulation''' tool.
 
|-
 
|-
−
||Click and drag Cl4 left.
+
||Click and drag '''Cl4''' left.
  
−
Click and Drag N4 to right.
+
Click and drag '''N4''' to right.
−
||Click and drag Cl4 to  left.
+
||Click and drag '''Cl4''' to  left.
  
−
Click and Drag N4 to right.
+
Click and drag '''N4''' to right.
  
 
Then Adjust the postions of all the bonds to show proper orientation.
 
Then Adjust the postions of all the bonds to show proper orientation.
Line 386: Line 387:
 
||Go to '''Build''' menu and select '''Add Hydrogens'''.
 
||Go to '''Build''' menu and select '''Add Hydrogens'''.
  
−
As before each nitrogen has two atoms attached.
+
As before each '''nitrogen''' has two atoms attached.
  
−
Add the third Hydrogen using Hydrogen from '''Draw''' tool.
+
Add the third '''Hydrogen''' using '''Hydrogen''' from '''Draw''' tool.
 
|-
 
|-
 
||Cursor on the '''Panel'''.
 
||Cursor on the '''Panel'''.
Line 397: Line 398:
 
|-
 
|-
 
|| '''Force Field''' select '''UFF''', click on '''Start''' button to optimize.
 
|| '''Force Field''' select '''UFF''', click on '''Start''' button to optimize.
−
||In the '''Force Field''' select '''UFF''' and click on '''Start''' button.
+
||In the '''Force Field,''' select '''UFF''' and click on '''Start''' button.
 
|-
 
|-
−
||Click on '''Stop''' to stop the optimization process.
+
||Click on '''Stop'''.
 
||Click on '''Stop''' to stop the optimization process.
 
||Click on '''Stop''' to stop the optimization process.
 
|-
 
|-
Line 406: Line 407:
 
|-
 
|-
 
||Point to the structures.
 
||Point to the structures.
−
||Similarly we have the '''geometrical isomers''' of '''diamminetetracyanoferrate(III)ion '''[Fe(NH<sub>3</sub)<sub>2</sub>(CN)<sub>4</sub>]<sup>-</sup>'''.
+
||Similarly, we have the '''geometrical isomers''' of '''diamminetetracyanoferrate(III)ion '''[Fe(NH<sub>3</sub)<sub>2</sub>(CN)<sub>4</sub>]<sup>-</sup>'''.
 
|-
 
|-
 
||
 
||
−
||Next we will discuss about  R-S configuration.
+
||Next we will discuss about  '''R-S configuration'''.
 
|-
 
|-
 
||'''Slide Number 10'''
 
||'''Slide Number 10'''
Line 415: Line 416:
 
'''R-S Configurations'''
 
'''R-S Configurations'''
 
||
 
||
−
* '''R-S configurations''' arise due to the presence of a '''Chiral Centre'''.
+
* '''R-S configurations''' arise due to the presence of a '''Chiral centre'''.
 
* '''Chiral centre''' is an atom connected to four different subsituents
 
* '''Chiral centre''' is an atom connected to four different subsituents
 
* Configurations are '''non-superimposable mirror images''' of each other.
 
* Configurations are '''non-superimposable mirror images''' of each other.
 
|-
 
|-
 
||
 
||
−
||For demonstration of  '''R-S configurations''', I will use '''amino acid, Alanine'''.
+
||For demonstration of  '''R-S configurations''', I will use '''amino acid - Alanine'''.
  
 
Open a new window.
 
Open a new window.
Line 439: Line 440:
 
|-
 
|-
 
||Point to the central atom.
 
||Point to the central atom.
−
||Central carbon atom is '''chiral''', attached to 4 different groups.
+
||Central '''carbon''' atom is '''chiral''', attached to 4 different groups.
 
|-
 
|-
 
||'''Slide Number 11'''
 
||'''Slide Number 11'''
Line 453: Line 454:
 
||Now we see the priority in clockwise direction.
 
||Now we see the priority in clockwise direction.
  
−
In this structure nitrogen is given first priority.
+
In this structure, '''nitrogen''' is given first priority.
  
−
Carbon attached with oxygens is given second priority.
+
'''Carbon''' attached with '''oxygens''' is given second priority.
  
−
And methyl is given third priority.
+
And '''methyl''' is given third priority.
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
Line 473: Line 474:
 
Move carbon attched with oxygens.
 
Move carbon attched with oxygens.
 
||Click on Manipulation tool.  
 
||Click on Manipulation tool.  
−
Move carbon to right side.
+
Move '''carbon''' to right side.
  
−
Move carbon attched to oxygens to left.
+
Move '''carbon''' attached to '''oxygens''' to left.
 
|-
 
|-
 
||Go to '''Build''' menu, select '''Add Hydrogens'''.
 
||Go to '''Build''' menu, select '''Add Hydrogens'''.
Line 484: Line 485:
 
|-
 
|-
 
||Point to the structure and substituents.
 
||Point to the structure and substituents.
−
||Nitrogen has first priority.
+
||'''Nitrogen''' has first priority.
  
−
Carbon attached with oxygen is given second priority.
+
'''Carbon''' attached with '''oxygen''' is given second priority.
−
And methyl is given third priority.
+
And '''Methyl''' is given third priority.
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
Line 493: Line 494:
 
|-
 
|-
 
||Point to the structures.
 
||Point to the structures.
−
||Similarly we have '''R''' and '''S configurations''' of '''Glyceraldehyde''' on the '''Panel'''.
+
||Similarly, we have '''R''' and '''S configurations''' of '''Glyceraldehyde''' on the '''Panel'''.
 
|-
 
|-
 
||
 
||
Line 502: Line 503:
 
'''Summary'''
 
'''Summary'''
 
||In this tutorial we have learnt, to draw:  
 
||In this tutorial we have learnt, to draw:  
−
* Conformations of 1,2-dichloroethane
+
* '''Conformations''' of '''1,2-dichloroethane'''
−
* Conformations of cyclohexane
+
* '''Conformations''' of '''cyclohexane'''
−
* Geomertical isomers of cisplatin
+
* Geometrical '''isomers''' of '''cisplatin'''
−
* R-S configurations of amino acid alanine.
+
* '''R-S configurations''' of '''amino acid Alanine'''.
 
|-
 
|-
 
||'''Slide Number 13'''
 
||'''Slide Number 13'''
Line 511: Line 512:
 
'''Assignment'''
 
'''Assignment'''
 
||As an assignment draw,
 
||As an assignment draw,
−
* Geometrical isomers of 2-butene and 1,2-dichloroethene.
+
* Geometrical '''isomers''' of '''2-butene''' and '''1,2-dichloroethene'''.
−
* R-S configurations of bromochloroiodomethane.
+
* '''R-S configurations''' of '''bromochloroiodomethane'''.
 
|-
 
|-
 
||'''Slide Number 14'''
 
||'''Slide Number 14'''

Latest revision as of 14:20, 6 May 2016

Visual Cue Narration
Slide Number 1

Title Slide

Warm greetings!

Welcome to this tutorial on Stereoisomerism.

Slide Number 2

Learning Objectives

In this tutorial, we will learn about:
  • Conformational isomerism
  • Geometrical isomerism and
  • R-S configurations with examples.
Slide Number 3

System Requirement

Here I am using,
  • Ubuntu Linux OS version. 14.04
  • Avogadro version 1.1.1.
Slide Number 4

Pre-requisties

You should be familiar with :

Avogadro interface.

For relevant tutorials, visit our website.

www.spoken-tutorial.org.

To follow this tutorial, you should be familiar with Avogadro interface.

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

Example files used in this tutorial are provided as code files.

In this tutorial we will learn to build stereoisomers using Avogadro.
Slide Number 5

Stereoiosmersism

I will give a brief introduction about stereoiosmersism.

Stereoisomersism arises due to difference in spatial arrangement of atoms.

Isomers have same structure and hence do not differ much in properties.

Point to the slide. Here is a slide that shows classification of isomers.
I will begin with Conformational isomerism.
Slide Number 6

Conformational Isomerism

It is a form of stereoisomerism.

In this, isomers can be inter-converted by rotation about single bonds.

Rotation about single bond is restricted by rotational energy barrier.

Let's begin with conformers of 1,2-dichloroethane.
Slide Number 7

Conformations

1,2-dichloroethane exists in three conformers namely:
  • Eclipsed
  • Gauche and
  • Anti
Cursor on the Panel. I have opened Avogadro window.
Click on Draw tool. Click on Draw tool.
Uncheck Adjust Hydrogens check box. Uncheck Adjust Hydrogens check box.
Click on the Panel and drag to draw two atoms. Click on the Panel and drag to draw two atoms.
Select Chlorine from Element drop down.

Draw a bond on each carbon.

Select Chlorine from Element drop down.

Draw a bond on each carbon.

Go to Build menu, click on Add Hydrogens.

Point to the structure.

Go to Build menu and click on Add Hydrogens.

1,2-dichloroethane is drawn on the Panel.

Cursor on the Panel. Let's optimize the structure.
Click on Auto Optimaization tool. Click on Auto Optimization tool.
In the Force Field select MMFF94>> click on Start button. In the Force Field, select MMFF94 and click on Start button.
Click on Stop Click on Stop to stop the optimization process.
Click on Navigation tool, rotate the structure. Cick on Navigation tool to rotate the structure for proper orientation.

We have Gauche conformer on the Panel.

Cursor on the Panel. To show conformers of 1,2-dichloroethane, I will fix the plane of rotation.
Click on Bond Centric Manipulation tool. Click on Bond Centric Manipulation tool.
Click on the bond between two carbon atoms. Click on the bond between two carbon atoms.
Point to the planes. Plane between the atoms appears in blue or yellow color.
Cursor on the Panel.


Click on Navigation tool and show the geometry.

Place the cursor on Chlorine atom.

Rotate the bond in clock-wise direction.

Click on Navigation tool and rotate the structure.

We have Anti conformer on the Panel.

Point to the conformer. Again use Bondcentric Manipulation tool to rotate the C-C bond.

We have Eclipsed conformer on the Panel.

Cursor on the Panel.


Point to New button.

Now I will show various conformers of Cyclohexane.

Open a new window.

Point to Draw settings.

Uncheck Adjust Hydrogens check box.

In Draw settings menu, Carbon is selected as default element.

Uncheck Adjust Hydrogens check box.

Cursor on the Panel. Let's draw cyclohexane structure in the boat form.
Click and drag to draw. Click and drag to draw boat conformer of cyclohexane on the Panel.
Click on Label check box in the Display Types menu. To label the atoms, click on Label check box in the Display Types menu.

Please note labeling may not be same all the time.

Cursor on the structure. Let us label the conformers as per our requirement.
Click on Selection tool>>right click on first carbon atom. Click on Selection tool, then right-click on first carbon atom.
Point to the menu.

Select Change label.

Point to the text box.

A menu opens.

Select Change label.

Change label of the atom text box opens.

Type 1, click OK. In the New Label field type 1 and click OK.
right click on the second atom, change the label as 2.

Point to the atoms.

Next right-click on the second atom and change the label as 2.

Similarly, I will change the labels of atoms as 3, 4, 5 and 6.

Cursor on the Panel. We will convert boat to twist boat conformer.
Click on Manipulation Tool.

Click on 2 and drag it upwards.

Click on 5 and drag it upwards.

Click on 3 and drag it upwards.

Point to the structure.

Click on Manipulation Tool.

Click on 2 and drag it upwards.

Click on 5 and drag it upwards.

Click on 3 and drag it upwards.

We have twist boat on the Panel.

Cursor on the Panel. Now we will convert twist boat to half chair conformer.
Click on 2 and drag it downwards.

Click on 5 and drag it downwards.

Click on 4 and drag it to horizontal position.

Point to the structure.

Click on 2 and drag it downwards.

Click on 5 and drag it downwards

Click on 4 and drag it to horizontal position.

Adjust the positions of all carbon atoms if required, to get correct structure.

We have half chair on the Panel.

Cursor on the Panel. Now we will convert half chair to chair conformer.
Click on 4 and drag it downwards.

Point to the structure.

Click on 4 and drag it downwards.

Click on 1 and drag it downwards.

Adjust the positions of all carbon atoms if required, to get correct structure.

We have chair conformer on the Panel.

Slide Number 8

Assignment

As an assignment,
  • Draw various conformers of Butane and Cyclopentane.
Cursor on the Panel. Now I will draw structures to demonstrate geometrical isomerism.
Slide Number 9

Geometrical isomerism

Geometrical isomerism arises due to:
  • different spatial arrangement of atoms around a double-bond.

Here rotation of atoms or groups around double-bonded carbon is restricted.

Cursor on the Panel. For demonstration, I will draw diamminedichloroplatinum(II) structure also known as cisplatin.
Click on New button. Open a new window.
Point to Draw settings menu.

Click on Element drop down and select Other.

In Draw settings menu, click on Element drop down and select Other.

Periodic table window opens.

Select Platinum(Pt) from the table.

Close the Periodic table window.

Select Platinum(Pt) from the table.

Close the Periodic table window.

Click on the Panel. Click on the Panel.
From Element drop down select Chlorine. From Element drop down select Chlorine.
Click and drag. Draw two chlorine bonds on Platinum atom on the same side.
Select Nitrogen from Element drop down. Select Nitrogen from Element drop down.

Draw two nitrogen bonds as before.

Point to Nitrogen atom. To complete the structure we need three attached hydrogens on nitrogen atoms.
Select Hydrogen from Element drop down. Select Hydrogen from Element drop down.
Click and drag. Click on each nitrogen atom to draw the third bond.
Cursor on the Panel. Let's optimize the structure.
Click on Auto Optimization tool. Click on Auto Optimization tool.
Force Field select UFF, click on Start button to optimize. In the Force Field, select UFF and click on Start button.
Click on Stop. Click on Stop to stop the optimization process.
Cursor on the Panel. For demonstration I will require two structures.

I will copy and paste the structures.

Click on Selection tool.

Press CTRL+C to copy and CTRL+V to paste.

Click on Selection tool to select the structure.

Press CTRL+C to copy and CTRL+V to paste.

Drag the pasted structure to right.

Point to Label check box. For convenience I will label the atoms.

Click on Label check box in the Display Types menu.

Go to Build menu and select Remove Hydrogens.

Point to the structures.

To remove Hydrogens, go to Build menu and select Remove Hydrogens.

We have two isomers of cisplatin on the Panel.

Point to the structures.

Click on Manipulation tool.

I will convert the second cis isomer to trans isomer.

Click on Manipulation tool.

Click and drag Cl4 left.

Click and drag N4 to right.

Click and drag Cl4 to left.

Click and drag N4 to right.

Then Adjust the postions of all the bonds to show proper orientation.

Go to Build menu and select Add Hydrogens. Go to Build menu and select Add Hydrogens.

As before each nitrogen has two atoms attached.

Add the third Hydrogen using Hydrogen from Draw tool.

Cursor on the Panel. Let's optimize the structures.
Click on Auto Optimization tool. Click on Auto Optimization tool.
Force Field select UFF, click on Start button to optimize. In the Force Field, select UFF and click on Start button.
Click on Stop. Click on Stop to stop the optimization process.
Point to the structure. We now have two geometrical isomers of diamminedichloroplatinum(II) on the Panel.
Point to the structures. Similarly, we have the geometrical isomers of diamminetetracyanoferrate(III)ion [Fe(NH3</sub)2(CN)4]-.
Next we will discuss about R-S configuration.
Slide Number 10

R-S Configurations

  • R-S configurations arise due to the presence of a Chiral centre.
  • Chiral centre is an atom connected to four different subsituents
  • Configurations are non-superimposable mirror images of each other.
For demonstration of R-S configurations, I will use amino acid - Alanine.

Open a new window.

Point to the structures in the library. I will load Alanine structure from Fragment library.

All the amino acids available in the Fragment library are optically active.

You can load and explore on your own.

Press CTRL+SHIFT+A.

Point to Navigation tool.

Press CTRL+SHIFT and A to deselect he structure.

Using the Navigation tool rotate the structure for proper orientation.

Point to the central atom. Central carbon atom is chiral, attached to 4 different groups.
Slide Number 11

R-S Configurations

R S configuration is based on priority given to the substituent in clockwise or anticlockwise direction.

Priority is based on atomic number of the substituent.

Substituent with higher atomic number gets first priority.

Point to the structure. Now we see the priority in clockwise direction.

In this structure, nitrogen is given first priority.

Carbon attached with oxygens is given second priority.

And methyl is given third priority.

Point to the structure. Structure has R configuration.
Point to the structure. I will change the positions of the attached groups to the chiral carbon.
Go to Build menu, select Remove Hydrogens. Go to Build menu and select Remove Hydrogens.
Click on Manipulation tool.

Move carbon.

Move carbon attched with oxygens.

Click on Manipulation tool.

Move carbon to right side.

Move carbon attached to oxygens to left.

Go to Build menu, select Add Hydrogens. Go to Build menu and select Add Hydrogens.
Point to the structure. Now we will see the priority in anti-clockwise direction.
Point to the structure and substituents. Nitrogen has first priority.

Carbon attached with oxygen is given second priority. And Methyl is given third priority.

Point to the structure. Structure has S configuration.
Point to the structures. Similarly, we have R and S configurations of Glyceraldehyde on the Panel.
Let's summarize.
Slide Number 12

Summary

In this tutorial we have learnt, to draw:
  • Conformations of 1,2-dichloroethane
  • Conformations of cyclohexane
  • Geometrical isomers of cisplatin
  • R-S configurations of amino acid Alanine.
Slide Number 13

Assignment

As an assignment draw,
  • Geometrical isomers of 2-butene and 1,2-dichloroethene.
  • R-S configurations of bromochloroiodomethane.
Slide Number 14

Acknowledgement

Watch the video available at

http://spoken-tutorial.org /What is a Spoken Tutorial

It summarises the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.

This video summarises the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

Slide Number 15

The Spoken Tutorial Project Team

Conducts workshops using spoken tutorials

Gives certificates to those who pass an online test

For more details, please write to

contact@spoken-tutorial.org

We conduct workshops using Spoken Tutorials and give certificates.

Please contact us.

Slide number 16

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

http://spoken-tutorial.org /NMEICT-Intro

The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
This is Madhuri Ganapathi singing off.

Thank you for joining.

Contributors and Content Editors

Madhurig, Nancyvarkey

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