GChemPaint/C3/Analysis-of-compounds/English-timed
From Script | Spoken-Tutorial
| Time | Narration |
| 00:01 | Hello everyone. Welcome to this tutorial on Analysis of Compounds in GChemPaint. |
| 00:07 | In this tutorial, we will learn about, |
| 00:10 | * Molecular contextual menu |
| 00:12 | * Save the molecule in .mol format |
| 00:15 | * Add and edit a reaction |
| 00:18 | * Add reaction conditions and reagents on the reaction arrow |
| 00:22 | * Convert reaction molecules into 3D |
| 00:26 | For this tutorial I am using |
| 00:28 | Ubuntu Linux OS version 12.04. |
| 00:32 | GChemPaint version 0.12.10. |
| 00:37 | You will also require Internet connectivity. |
| 00:41 | To follow this tutorial, you should be familiar with GChemPaint. |
| 00:46 | If not, for relevant tutorials, please visit our website. |
| 00:52 | I have opened a new GChemPaint window. |
| 00:55 | Click on Use or manage templates tool. |
| 00:59 | Templates tool property page opens below. |
| 01:02 | Click on Amino Acids on Templates drop down button. |
| 01:07 | Select Alanine from the list. |
| 01:11 | Structure of Alanine is loaded onto the Templates property page. |
| 01:16 | Click on the structure and click on Display area to load it. |
| 01:21 | I will explain about contextual menu of Alanine molecule. |
| 01:26 | Right click on the molecule. |
| 01:29 | A sub-menu opens. |
| 01:31 | Select Molecule; a contextual menu opens alongside. |
| 01:36 | Contextual menu contains different menu items, of which, I will discuss about- |
| 01:43 | * NIST WebBook page for this molecule |
| 01:46 | * PubChem page for this molecule |
| 01:48 | * Open in Calculator |
| 01:51 | Click on NIST Web page for this molecule |
| 01:55 | Alanine's NIST webpage opens. |
| 01:59 | Webpage shows all the details about Alanine. |
| 02:03 | Come back to GChemPaint editor. |
| 02:06 | Right click on Alanine to open the PubChem page for this molecule. |
| 02:12 | Click on Alanine structure on this webpage. |
| 02:16 | A new web-page with 2D Structure and 3D Conformer tabs, is seen. |
| 02:22 | Click on 3D Conformer tab to view Alanine in 3 dimensions. |
| 02:28 | Click on the displayed 3D structure. |
| 02:31 | This opens the structure in a separate window with some controls on the top and on the left. |
| 02:37 | Click on the Rotation icon to rotate the structure in various directions. |
| 02:43 | On the same page, click on H icon to show hydrogens. |
| 02:48 | These are the Hydrogens. |
| 02:51 | Let us switch to GChemPaint window again. |
| 02:53 | Right click on Alanine; choose the option Open in Calculator. |
| 03:00 | Chemical calculator window opens. |
| 03:03 | If not, please install the same, using Synaptic Package Manager, as in the Overview tutorial. |
| 03:10 | This Window has two tabs at the bottom - Composition and Isotopic Pattern. |
| 03:16 | Composition tab has the following components- |
| 03:19 | * Formula |
| 03:21 | * Raw formula |
| 03:23 | * Molecular weight in g.mol-1 ( gram.mole-inverse) |
| 03:26 | * Compound's elemental mass percentage(%) analysis. |
| 03:32 | Click on the Isotropic Pattern tab. |
| 03:35 | It shows a graph of mass spectrum with a peak at Molecular weight of the compound. |
| 03:42 | As an assignment |
| 03:43 | 1. Select other Amino Acids from Templates list. |
| 03:46 | 2. Obtain their Composition and Isotropic pattern. |
| 03:51 | I have opened a new GChemPaint window. |
| 03:54 | Let us draw 1,3-butadiene structure. |
| 03:58 | Click on Add a chain tool. |
| 04:01 | Click and drag the chain to 4 carbons. |
| 04:04 | Click on Add a bond tool and click on first and third bonds positions, to form double bonds. |
| 04:13 | Right click at each position to show atoms. |
| 04:17 | Click on Atom then click on Display symbol. |
| 04:22 | To convert 1,3-butadiene 2D structure to 3D structure, click on the Save icon on the tool bar. |
| 04:30 | Save as dialog box opens. |
| 04:33 | In the File type field, select MDL Molfile Format. |
| 04:39 | Type the filename as 1,3-butadiene. |
| 04:42 | Select Desktop to save the file on Desktop. |
| 04:47 | Then click on Save button. |
| 04:50 | Alternatively, you can also save the file with extension .mol or .mdl directly. |
| 04:56 | For example, type the filename as 1,3butadiene.mol or .mdl |
| 05:06 | Click on Save button. |
| 05:09 | To view the structure in 3D, right click on the molecule. |
| 05:12 | Select the option Open With Molecules viewer. |
| 05:17 | This is 1,3butadiene in 3D. |
| 05:20 | Please note, we cannot make changes in the structure. |
| 05:23 | To rotate the structure, place the cursor on the structure, hold and drag the mouse. |
| 05:31 | As an assignment,
Convert Benzene structure from 2D to 3D. |
| 05:36 | Now let's learn to draw chemical reactions and reaction conditions. |
| 05:41 | This is a chemical reaction of Ethyl chloride (C2H5Cl) with Alcoholic Potassium hydroxide(Alc.KOH) and Aqueous Potassium hydroxide(Aq.KOH) to yield Ethene(C2H4) and Ethanol(C2H5OH) respectively. |
| 05:52 | I have opened a new GChemPaint window. |
| 05:55 | Let us first draw structure of Ethyl chloride. |
| 05:59 | Click on Add a chain tool. |
| 06:01 | Click on the Display area. |
| 06:04 | Right click on the chain to display atoms on first and second bond positions. |
| 06:10 | Click on Current element drop down arrow button. |
| 06:13 | Select Cl from table. |
| 06:16 | Click on Add or modify an atom tool. |
| 06:20 | Click on the third bond position. |
| 06:23 | Structure of Ethyl chloride is drawn. |
| 06:26 | Click on Add or modify a group of atoms tool. |
| 06:31 | Click on the Display area. Type Alc.KOH. |
| 06:37 | Click again and type Aq.KOH |
| 06:42 | Click on Add an arrow for an irreversible reaction tool. |
| 06:47 | You can change the Arrow length using the scroller here. |
| 06:51 | I will increase the arrow length to 280. |
| 06:54 | Click on the Display area, beside Ethyl Chloride. |
| 06:58 | Click below Ethyl Chloride. |
| 07:01 | Hold the mouse and rotate the arrow to point downwards. |
| 07:05 | Click on the Selection tool. |
| 07:08 | Position Alcoholic Potassium Hydroxide (Alc.KOH) above first arrow. |
| 07:13 | Position Aqueous Potassium Hydroxide (Aq.KOH) close to second arrow. |
| 07:18 | Select Alcoholic Potassium hydroxide(Alc.KOH). |
| 07:22 | Right click on the arrow. |
| 07:23 | A sub-menu opens. |
| 07:25 | Select Arrow and click on Attach selection to arrow. |
| 07:29 | A dialog box with heading Arrow associated opens. |
| 07:34 | Click on Role drop down list. |
| 07:37 | Select Catalyst from the list. Click on Close. |
| 07:42 | Drag arrow to check if Alcoholic Potassium Hydroxide (Alc.KOH) attaches to the arrow, as a catalyst. |
| 07:49 | Let's repeat the process for Aqueous Potassium Hydroxide(Aq.KOH). |
| 07:58 | Drag to see the attachement as a catalyst. |
| 08:02 | Click on Selection tool to select Ethyl chloride structure. |
| 08:06 | Press CTRL + C to copy and CTRL+V twice to paste the structures. |
| 08:11 | Place the structures at proper positions by dragging. |
| 08:15 | In the reactions Ethyl chloride reacts with Alcoholic potassium Hyroxide to give Ethene. |
| 08:21 | Ethyl chloride reacts with Aqueous Potassium Hydroxide to give Ethanol. |
| 08:27 | To obtain Ethene, click on Eraser tool and delete Cl bond of Ethyl chloride. |
| 08:34 | Ethane is formed. |
| 08:37 | In the Tool box, ensure that Current element is Carbon. |
| 08:42 | Click on Add a bond tool and click on the bond to obtain a double bond. |
| 08:48 | Ethene is formed. |
| 08:50 | To obtain Ethanol, press O on the keyboard. |
| 08:54 | Click on Add or modify an atom tool |
| 08:58 | and then click on Cl of Ethyl chloride. |
| 09:02 | Now let's convert the reactants and products from 2D to 3D. |
| 09:07 | Open a new file, copy Ethyl Chloride and paste it into new file. |
| 09:15 | Click on Save button. |
| 09:17 | Save as dialog box opens. |
| 09:20 | Type the file name as Ethyl Chloride.mol |
| 09:24 | Click on Desktop to save your file on your Desktop. |
| 09:28 | Click on Save button. |
| 09:31 | Likewise copy Ethene into a new file. |
| 09:34 | Save as Ethene.mol. |
| 09:37 | Copy Ethanol into a new file. |
| 09:39 | Save as Ethanol.mol |
| 09:42 | I had already saved the files on my Desktop. |
| 09:46 | I will minimize the current window. |
| 09:49 | And I will go to Desktop folder where I had saved my files. |
| 09:54 | To view the compound in 3D, right click on the file, choose Open with Molecules viewer. |
| 10:02 | Likewise, I will open all the files with Molecules viewer |
| 10:07 | Observe the compounds in 3D. <Pause> |
| 10:11 | Let's summarize what we have learnt. |
| 10:14 | In this tutorial we have learnt |
| 10:16 | * NIST WebBook page for this molecule. |
| 10:19 | * Pub-Chem page for the molecule |
| 10:22 | * Find molecular weight of the compound using Chemical calculator. |
| 10:25 | * Obtain graph of mass spectrum of a molecule |
| 10:29 | * Save the molecule in .mol format |
| 10:32 | * Add reaction conditions and reagents on the reaction arrow |
| 10:36 | * Add and edit a reaction |
| 10:39 | * Convert reaction molecules into 3D structures |
| 10:42 | As an assignment |
| 10:44 | Draw chemical reaction of: Propene (C3H6)(C3H6) and Bromine(Br-Br) molecule with Carbon tetra chloride(CCl4) as a catalyst. |
| 10:51 | Benzene and Chlorine(Cl-Cl) molecule with Anhydrous Aluminum Chloride(AlCl3) as a catalyst. |
| 10:57 | Your completed assignment should look like this. |
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| 11:36 | More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro |
| 11:41 | This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining. s |
