Avogadro/C3/Stereoisomerism/English

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.
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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