Avogadro/C3/Stereoisomerism/English-timed

Time	Narration
00:01	Warm greetings! Welcome to this tutorial on Stereoisomerism.
00:06	In this tutorial, we will learn about: Conformational isomerism, Geometrical isomerism andR-S configurations with examples.
00:18	Here, I am using: Ubuntu Linux OS version. 14.04, Avogadro version 1.1.1.
00:28	To follow this tutorial, you should be familiar with Avogadro interface. If not, for relevant tutorials, please visit our website.
00:39	Example files used in this tutorial are provided as code files.
00:45	In this tutorial, we will learn to build stereoisomers using Avogadro.
00:51	I will give a brief introduction about stereoiosmersism.
00:56	Stereoisomersism arises due to difference in spatial arrangement of atoms.
01:03	Isomers have same structure and hence do not differ much in properties.
01:09	Here is a slide that shows classification of isomers.
01:16	I will begin with Conformational isomerism.
01:21	It is a form of stereoisomerism.
01:23	In this, isomers can be inter-converted by rotation about single bonds.
01:30	Rotation about single bond is restricted by rotational energy barrier.
01:36	Let's begin with conformers of 1,2-dichloroethane.
01:41	1,2-dichloroethane exists in three conformers namely: Eclipsed, Gauche and Anti.
01:50	I have opened Avogadro window.
01:53	Click on Draw tool.
01:55	Uncheck Adjust Hydrogens check box.
01:59	Click on the panel and drag to draw two atoms.
02:04	Select Chlorine from Element drop down.
02:08	Draw a bond on each carbon.
02:11	Go to Build menu and click on Add Hydrogens.
02:15	1,2-dichloroethane is drawn on the Panel.
02:19	Let's optimize the structure.
02:22	Click on Auto Optimization tool.
02:25	In the Force Field, select MMFF94 and click on Start button.
02:35	Click on Stop to stop the optimization process.
02:40	Cick on Navigation tool to rotate the structure for proper orientation.
02:45	We have Gauche conformer on the panel.
02:49	To show conformers of 1,2-dichloroethane, I will fix the plane of rotation.
02:55	Click on Bond Centric Manipulation tool.
02:59	Click on the bond between two carbon atoms.
03:03	Plane between the atoms appears in blue or yellow color.
03:08	Place the cursor on Chlorine atom.
03:10	Rotate the bond in clock-wise direction.
03:14	Click on Navigation tool and rotate the structure.
03:18	We have Anti conformer on the panel.
03:21	Again use Bondcentric Manipulation tool to rotate the C-C bond.
03:25	We have Eclipsed conformer on the Panel.
03:30	Now, I will show various conformers of Cyclohexane.
03:35	Open a new window.
03:38	In Draw settings menu, Carbon is selected as default element.
03:44	Uncheck Adjust Hydrogens check box.
03:48	Let's draw cyclohexane structure in the boat form.
03:53	Click and drag to draw boat conformer of cyclohexane on the Panel.
04:01	To label the atoms, click on Label check box in the Display Types menu.
04:07	Please note labeling may not be same all the time.
04:11	Let us label the conformers as per our requirement.
04:16	Click on Selection tool, then right-click on first carbon atom.
04:21	A menu opens. Select Change label.
04:25	Change label of the atom text box opens.
04:30	In the New Label field, type 1 and click OK.
04:35	Next right-click on the second atom and change the label as 2.
04:41	Similarly, I will change the labels of atoms as 3, 4, 5 and 6.
04:50	We will convert boat to twist boat conformer.
04:54	Click on Manipulation Tool. Click on 2 and drag it upwards.
04:57	Click on 5 and drag it upwards. Click on 3 and drag it upwards.
05:08	We have twist boat on the Panel.
05:10	Now, we will convert twist boat to half chair conformer.
05:16	Click on 2 and drag it downwards.
05:19	Click on 5 and drag it downwards.
05:23	Click on 4 and drag it to horizontal position.
05:27	Adjust the positions of all carbon atoms if required, to get correct structure.
05:33	We have half chair on the Panel.
05:36	Now we will convert half chair to chair conformer.
05:41	Click on 4 and drag it downwards.
05:44	Click on 1 and drag it downwards.
05:47	Adjust the positions of all carbon atoms if required, to get correct structure.
05:53	We have chair conformer on the Panel.
05:56	As an assignment, draw various conformers of Butane and Cyclopentane.
06:03	Now I will draw structures to demonstrate geometrical isomerism.
06:09	Geometrical isomerism arises due to different spatial arrangement of atoms around a double-bond.
06:17	Here, rotation of atoms or groups around double-bonded carbon is restricted.
06:24	For demonstration, I will draw diamminedichloroplatinum(II) structure also known as cisplatin.
06:33	Open a new window.
06:36	In Draw settings menu, click on Element drop down and select Other. Periodic table window opens.
06:44	Select Platinum(Pt) from the table. Close the Periodic table window.
06:50	Click on the Panel.
06:53	From Element drop down, select Chlorine.
06:55	Draw two chlorine bonds on Platinum atom on the same side.
07:00	Select Nitrogen from Element drop down. Draw two nitrogen bonds as before.
07:07	To complete the structure, we need three attached hydrogens on nitrogen atoms.
07:13	Select Hydrogen from Element drop down.
07:16	Click on each nitrogen atom to draw the third bond.
07:21	Let's optimize the structure.
07:24	Click on Auto Optimization tool.
07:27	In the Force Field, select UFF and click on Start button.
07:35	Click on Stop to stop the optimization process.
07:39	For demonstration, I will require two structures.
07:43	I will copy and paste the structures.
07:46	Click on Selection tool to select the structure.
07:50	Press CTRL+C to copy and CTRL+V to paste. Drag the pasted structure to right.
07:57	For convenience, I will label the atoms.
08:00	Click on Label check box in the Display Types menu.
08:05	To remove Hydrogens, go to Build menu and select Remove Hydrogens.
08:11	We have two isomers of cisplatin on the Panel.
08:16	I will convert the second cis isomer to trans isomer.
08:21	Click on Manipulation tool.
08:24	Click and drag Cl4 to left. Click and drag N4 to right.
08:32	Then Adjust the postions of all the bonds to show proper orientation.
08:38	Go to Build menu and select Add Hydrogens.
08:43	As before, each nitrogen has two atoms attached.
08:48	Add the third Hydrogen using Hydrogen from Draw tool.
08:53	Let's optimize the structures.
08:55	Click on Auto Optimization tool.
08:59	In the Force Field, select UFF and click on Start button.
09:05	Click on Stop to stop the optimization process.
09:09	We now have two geometrical isomers of diamminedichloroplatinum(II) on the Panel.
09:17	Similarly, we have the geometrical isomers of diamminetetracyanoferrate(III)ion [Fe(NH3</sub)2(CN)4]-.
09:25	Next we will discuss about R-S configuration.
09:29	R-S configurations arise due to the presence of a Chiral centre.
09:35	Chiral centre is an atom connected to four different substituents.
09:41	Configurations are non-superimposable mirror images of each other.
09:47	For demonstration of R-S configurations, I will use amino acid - Alanine.
09:53	Open a new window.
09:56	I will load Alanine structure from Fragment library.
10:01	All the amino acids available in the Fragment library are optically active.
10:07	You can load and explore on your own.
10:11	Press CTRL+SHIFT and A to deselect the structure.
10:15	Using the Navigation tool, rotate the structure for proper orientation.
10:22	Central carbon atom is chiral, attached to 4 different groups.
10:26	R S configuration is based on priority given to the substituent in clockwise or anticlockwise direction.
10:35	Priority is based on atomic number of the substituent.
10:40	Substituent with higher atomic number gets first priority.
10:45	Now we see the priority in clockwise direction.
10:49	In this structure, nitrogen is given first priority.
10:53	Carbon attached with oxygens is given second priority. And methyl is given third priority.
11:02	Structure has R configuration.
11:05	I will change the positions of the attached groups to the chiral carbon.
11:10	Go to Build menu and select Remove Hydrogens.
11:15	Click on Manipulation tool.
11:17	Move carbon to right side.
11:20	Move carbon attached to oxygens to left.
11:25	Go to Build menu and select Add Hydrogens.
11:29	Now we will see the priority in anti-clockwise direction.
11:33	Nitrogen has first priority.Carbon attached with oxygen is given second priority. And Methyl is given third priority.
11:45	Structure has S configuration.
11:48	Similarly, we have R and S configurations of Glyceraldehyde on the Panel.
11:55	Let's summarize.
11:57	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.
12:15	As an assignment, draw Geometrical isomers of 2-butene and 1,2-dichloroethene, R-S configurations of bromochloroiodomethane.
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Contributors and Content Editors

PoojaMoolya, Sandhya.np14