Nancyvarkey at 08:50, 6 May 2016

2016-05-06T08:50:34Z

Madhurig: Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''. |- ||'''Sl..."

2016-04-25T10:20:56Z

Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''. |- ||'''Sl..."

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{| border=1
||'''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 draw two atoms.
||Click on the '''Panel''' and drag 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''' to stop the optimiztion process.
||Click on '''Stop''' to stop the optimiztion 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 '''conformer''' 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 move it to left.

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 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''' to stop the optimization process.
||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''' to stop the optimization process.
||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 attched 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
* Geomertical 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.
|-
|}

Avogadro/C3/Stereoisomerism/English - Revision history

Nancyvarkey at 08:50, 6 May 2016

Madhurig: Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''. |- ||'''Sl..."