Difference between revisions of "Avogadro/C3/Stereoisomerism/English-timed"
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PoojaMoolya (Talk | contribs) (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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||00:06 | ||00:06 | ||
− | ||In this tutorial, we will learn about: '''Conformational isomerism''' | + | ||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 | ||
− | ||Here I am using | + | ||Here, I am using |
− | '''Ubuntu Linux''' OS version. 14.04 | + | '''Ubuntu Linux''' OS version. 14.04, |
'''Avogadro''' version 1.1.1. | '''Avogadro''' version 1.1.1. | ||
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||00:39 | ||00:39 | ||
− | ||Example files used in this tutorial are provided as code files. | + | ||Example files used in this tutorial are provided as '''code files'''. |
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||00:45 | ||00:45 | ||
− | ||In this tutorial we will learn to build '''stereoisomers''' using '''Avogadro'''. | + | ||In this tutorial, we will learn to build '''stereoisomers''' using '''Avogadro'''. |
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||01:09 | ||01:09 | ||
− | ||Here is a slide that shows classification of '''isomers'''. | + | ||Here is a '''slide''' that shows classification of '''isomers'''. |
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||01:23 | ||01:23 | ||
− | ||In this, '''isomers''' can be inter-converted by rotation about single | + | ||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: | ||
− | '''Eclipsed''', '''Gauche''' and '''Anti''' | + | '''Eclipsed''', '''Gauche''' and '''Anti'''. |
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|| 01:59 | || 01:59 | ||
− | ||Click on the ''' | + | ||Click on the '''panel''' and drag to draw two atoms. |
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||02:45 | ||02:45 | ||
− | ||We have '''Gauche conformer''' on the ''' | + | ||We have '''Gauche conformer''' on the '''panel'''. |
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||03:18 | ||03:18 | ||
− | ||We have '''Anti conformer''' on the ''' | + | ||We have '''Anti conformer''' on the '''panel'''. |
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||03:30 | ||03:30 | ||
− | ||Now I will show various '''conformers''' of '''Cyclohexane'''. | + | ||Now, I will show various '''conformers''' of '''Cyclohexane'''. |
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||03:38 | ||03:38 | ||
− | ||In '''Draw settings''' menu, '''Carbon''' is selected as default element. | + | ||In '''Draw settings''' menu, '''Carbon''' is selected as '''default''' element. |
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||04:30 | ||04:30 | ||
− | ||In the '''New Label''' field type 1 and click '''OK'''. | + | ||In the '''New Label''' field, type 1 and click '''OK'''. |
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||05:10 | ||05:10 | ||
− | ||Now we will convert '''twist boat''' to '''half chair conformer'''. | + | ||Now, we will convert '''twist boat''' to '''half chair conformer'''. |
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||05:19 | ||05:19 | ||
− | |Click on 5 and drag it downwards | + | |Click on 5 and drag it downwards. |
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||05:56 | ||05:56 | ||
− | ||As an assignment, | + | ||As an assignment, draw various '''conformers''' of '''Butane''' and '''Cyclopentane'''. |
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||06:09 | ||06:09 | ||
− | ||'''Geometrical isomerism''' arises due to | + | ||'''Geometrical isomerism''' arises due to different spatial arrangement of atoms around a '''double-bond'''. |
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||06:17 | ||06:17 | ||
− | ||Here rotation of atoms or groups around '''double-bonded carbon''' is restricted. | + | ||Here, rotation of atoms or groups around '''double-bonded carbon''' is restricted. |
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||06:53 | ||06:53 | ||
− | ||From '''Element''' drop down select '''Chlorine'''. | + | ||From '''Element''' drop down, select '''Chlorine'''. |
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||07:07 | ||07:07 | ||
− | ||To complete the structure we need three attached hydrogens on nitrogen atoms. | + | ||To complete the structure, we need three attached hydrogens on nitrogen atoms. |
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||07:39 | ||07:39 | ||
− | ||For demonstration I will require two structures. | + | ||For demonstration, I will require two structures. |
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||07:43 | ||07:43 | ||
− | ||I will copy and paste the structures. | + | ||I will '''copy''' and '''paste''' the structures. |
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||07:57 | ||07:57 | ||
− | ||For convenience I will label the atoms. | + | ||For convenience, I will label the atoms. |
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||08:24 | ||08:24 | ||
− | ||Click and drag '''Cl4''' to left.Click and drag '''N4''' to right. | + | ||Click and drag '''Cl4''' to left. Click and drag '''N4''' to right. |
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||08:43 | ||08:43 | ||
− | ||As before each '''nitrogen''' has two atoms attached. | + | ||As before, each '''nitrogen''' has two atoms attached. |
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||09:35 | ||09:35 | ||
− | || '''Chiral centre''' is an atom connected to four different | + | || '''Chiral centre''' is an atom connected to four different substituents. |
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||10:07 | ||10:07 | ||
− | ||You can load and explore on your own. | + | ||You can '''load''' and explore on your own. |
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||10:11 | ||10:11 | ||
− | ||Press '''CTRL+SHIFT''' and '''A''' to deselect | + | ||Press '''CTRL+SHIFT''' and '''A''' to deselect the structure. |
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||10:15 | ||10:15 | ||
− | ||Using the '''Navigation''' tool rotate the structure for proper orientation. | + | ||Using the '''Navigation''' tool, rotate the structure for proper orientation. |
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||10:53 | ||10:53 | ||
− | ||'''Carbon''' attached with '''oxygens''' is given second priority.And '''methyl''' is given third priority. | + | ||'''Carbon''' attached with '''oxygens''' is given second priority. And '''methyl''' is given third priority. |
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||11:15 | ||11:15 | ||
− | ||Click on Manipulation tool. | + | ||Click on '''Manipulation''' tool. |
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||In this tutorial we have learnt, to draw: | ||In this tutorial we have learnt, to draw: | ||
− | '''Conformations''' of '''1,2-dichloroethane''' | + | '''Conformations''' of '''1,2-dichloroethane''', |
− | '''Conformations''' of '''cyclohexane''' | + | '''Conformations''' of '''cyclohexane''', |
− | '''Geometrical | + | '''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 | ||
− | ||As an assignment | + | ||As an assignment, draw Geometrical '''isomers''' of '''2-butene''' and '''1,2-dichloroethene''', '''R-S configurations''' of '''bromochloroiodomethane'''. |
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||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
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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. |