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

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(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...")
 
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||In this tutorial, we will learn about: '''Conformational isomerism'''  
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||In this tutorial, we will learn about: '''Conformational isomerism''',
  
 
'''Geometrical isomerism''' and'''R-S configurations''' with examples.
 
'''Geometrical isomerism''' and'''R-S configurations''' with examples.
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||00:18
 
||00:18
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||Here I am using,
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||Here, I am using
  
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'''Ubuntu Linux''' OS version. 14.04
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'''Ubuntu Linux''' OS version. 14.04,
  
 
'''Avogadro''' version 1.1.1.
 
'''Avogadro''' version 1.1.1.
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||00:39
 
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||Example files used in this tutorial are provided as code files.  
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||Example files used in this tutorial are provided as '''code files'''.  
  
 
|-
 
|-
 
||00:45
 
||00:45
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||In this tutorial we will learn to build '''stereoisomers''' using '''Avogadro'''.
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||In this tutorial, we will learn to build '''stereoisomers''' using '''Avogadro'''.
  
 
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||01:09
 
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||Here is a slide that shows classification of '''isomers'''.  
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||Here is a '''slide''' that shows classification of '''isomers'''.  
  
 
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||01:23
 
||01:23
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||In this, '''isomers''' can be inter-converted by rotation about single bonds.
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||In this, '''isomers''' can be inter-converted by rotation about single '''bond'''s.
  
 
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||'''1,2-dichloroethane''' exists in three '''conformers''' namely:
 
||'''1,2-dichloroethane''' exists in three '''conformers''' namely:
  
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'''Eclipsed''', '''Gauche''' and '''Anti'''
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'''Eclipsed''', '''Gauche''' and '''Anti'''.
  
 
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|| 01:59
 
|| 01:59
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||Click on the '''Panel''' and drag to draw two atoms.
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||Click on the '''panel''' and drag to draw two atoms.
  
 
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||02:45
 
||02:45
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||We have '''Gauche conformer''' on the '''Panel'''.
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||We have '''Gauche conformer''' on the '''panel'''.
  
 
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||03:18
 
||03:18
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||We have  '''Anti conformer''' on the '''Panel'''.
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||We have  '''Anti conformer''' on the '''panel'''.
  
 
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||03:30
 
||03:30
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||Now I will show various '''conformers''' of '''Cyclohexane'''.
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||Now, I will show various '''conformers''' of '''Cyclohexane'''.
  
 
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||03:38
 
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||In '''Draw settings''' menu, '''Carbon''' is selected as default element.
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||In '''Draw settings''' menu, '''Carbon''' is selected as '''default''' element.
  
 
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||04:30
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||In the '''New Label''' field type 1 and click '''OK'''.
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||In the '''New Label''' field, type 1 and click '''OK'''.
  
 
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||05:10
 
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||Now we will convert '''twist boat''' to '''half chair conformer'''.
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||Now, we will convert '''twist boat''' to '''half chair conformer'''.
  
 
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|Click on 5 and drag it downwards  
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|Click on 5 and drag it downwards.
  
 
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||05:56
 
||05:56
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||As an assignment,  Draw various  '''conformers''' of '''Butane''' and '''Cyclopentane'''.
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||As an assignment,  draw various  '''conformers''' of '''Butane''' and '''Cyclopentane'''.
  
 
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||06:09
 
||06:09
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||'''Geometrical isomerism''' arises due to:  different spatial arrangement of atoms around a '''double-bond'''.
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||'''Geometrical isomerism''' arises due to different spatial arrangement of atoms around a '''double-bond'''.
  
 
|-
 
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||06:17
 
||06:17
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||Here rotation of atoms or groups around '''double-bonded carbon''' is restricted.  
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||Here, rotation of atoms or groups around '''double-bonded carbon''' is restricted.  
  
 
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||06:53
 
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||From '''Element''' drop down select '''Chlorine'''.
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||From '''Element''' drop down, select '''Chlorine'''.
  
 
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||To complete the structure we need three attached hydrogens on nitrogen atoms.
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||To complete the structure, we need three attached hydrogens on nitrogen atoms.
  
 
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||07:39
 
||07:39
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||For demonstration I will require two structures.
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||For demonstration, I will require two structures.
  
 
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||07:43
 
||07:43
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||I will copy and paste the structures.
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||I will '''copy''' and '''paste''' the structures.
  
 
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||07:57
 
||07:57
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||For convenience I will label the atoms.
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||For convenience, I will label the atoms.
  
 
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||08:24
 
||08:24
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||Click and drag '''Cl4''' to  left.Click and drag '''N4''' to right.
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||Click and drag '''Cl4''' to  left. Click and drag '''N4''' to right.
  
 
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||08:43
 
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||As before each '''nitrogen''' has two atoms attached.
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||As before, each '''nitrogen''' has two atoms attached.
  
 
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||09:35
 
||09:35
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|| '''Chiral centre''' is an atom connected to four different subsituents.
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|| '''Chiral centre''' is an atom connected to four different substituents.
  
 
  |-
 
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||10:07
 
||10:07
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||You can load and explore on your own.
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||You can '''load''' and explore on your own.
  
 
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||10:11
 
||10:11
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||Press '''CTRL+SHIFT''' and '''A''' to deselect he structure.
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||Press '''CTRL+SHIFT''' and '''A''' to deselect the structure.
  
 
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||10:15
 
||10:15
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||Using the '''Navigation''' tool rotate the structure for proper orientation.
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||Using the '''Navigation''' tool, rotate the structure for proper orientation.
  
 
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||10:53
 
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||'''Carbon''' attached with '''oxygens''' is given second priority.And '''methyl''' is given third priority.
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||'''Carbon''' attached with '''oxygens''' is given second priority. And '''methyl''' is given third priority.
  
 
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||11:15
 
||11:15
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||Click on Manipulation tool.  
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||Click on '''Manipulation''' tool.  
  
 
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|-
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||In this tutorial we have learnt, to draw:  
 
||In this tutorial we have learnt, to draw:  
  
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'''Conformations''' of '''1,2-dichloroethane'''
+
'''Conformations''' of '''1,2-dichloroethane''',
  
−
'''Conformations''' of '''cyclohexane'''
+
'''Conformations''' of '''cyclohexane''',
  
−
'''Geometrical '''isomers''' of '''cisplatin'''
+
'''Geometrical isomers''' of '''cisplatin''',
  
 
'''R-S configurations''' of '''amino acid Alanine'''.
 
'''R-S configurations''' of '''amino acid Alanine'''.
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|-
 
|-
 
||12:15
 
||12:15
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||As an assignment draw, Geometrical '''isomers''' of '''2-butene''' and '''1,2-dichloroethene'''. '''R-S configurations''' of '''bromochloroiodomethane'''.
+
||As an assignment, draw Geometrical '''isomers''' of '''2-butene''' and '''1,2-dichloroethene''', '''R-S configurations''' of '''bromochloroiodomethane'''.
  
 
|-
 
|-
 
||12:29
 
||12:29
−
||This video 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.
  
 
|-
 
|-

Revision as of 21:55, 5 June 2018

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.
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 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.
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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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