Sandhya.np14 at 10:09, 23 July 2018

2018-07-23T10:09:21Z

Sandhya.np14 at 06:14, 23 July 2018

2018-07-23T06:14:12Z

Sandhya.np14 at 03:55, 23 July 2018

2018-07-23T03:55:35Z

Sandhya.np14 at 16:26, 5 June 2018

2018-06-05T16:26:33Z

Sandhya.np14 at 16:25, 5 June 2018

2018-06-05T16:25:44Z

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PoojaMoolya: Created page with "{| border=1 | Time | Narration |- || 00:01 ||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''. |- ||00:06 ||In this tutori..."

2017-09-14T09:49:46Z

Created page with "{| border=1 | <center>Time</center> | <center>Narration</center> |- || 00:01 ||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''. |- ||00:06 ||In this tutori..."

New page

{| border=1
| <center>Time</center>
| <center>Narration</center>

|-
|| 00:01
||Warm greetings! Welcome to this tutorial on '''Stereoisomerism'''.

|-
||00:06
||In this tutorial, we will learn about: '''Conformational isomerism'''

'''Geometrical isomerism''' and'''R-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'''.

|-
||01:56
||'''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 subsituents.

|-
||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 he 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'''.

|-
||12:29
||This video summarises the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.

|-
||12:37
||We conduct workshops using Spoken Tutorials and give certificates. Please contact us.

|-
||12:44
||The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.

|-
||12:51
||This is Madhuri Ganapathi singing off.

Thank you for joining.
|-
|}

@@ Line 415: / Line 415: @@
 |-
 ||08:32
-||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 15: / Line 15: @@
 |-
 ||00:18
-||Here, I am using
+||Here, I am using:
 '''Ubuntu Linux''' OS version. 14.04,

@@ Line 558: / Line 558: @@
 |-
 ||11:33
-||'''Nitrogen''' has first priority.'''Carbon''' attached with '''oxygen''' is given second priority.
+||'''Nitrogen''' has first priority. '''Carbon''' attached with '''oxygen''' is given second priority.
 And '''Methyl''' is given third priority.
@@ Line 575: / Line 575: @@
 |-
 ||11:57
-||In this tutorial we have learnt, to draw:
+||In this tutorial, we have learnt to draw:
 '''Conformations''' of '''1,2-dichloroethane''',