Avogadro/C3/Stereoisomerism/English-timed
From Script | Spoken-Tutorial
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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. |
| 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. |
| 12:29 | This video summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
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| 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. |
