GChemPaint/C3/Analysis-of-compounds/English-timed

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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.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 and 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 file name 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 with Alcoholic Potassium hydroxide and Aqueous Potassium hydroxide to yield Ethene and Ethanol 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.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 attachment 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 the option Open with Molecules viewer.
10:02 Likewise, I will open all the files with Molecules viewer.
10:07 Observe the compounds in 3D.
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: 1) Propene (C3H6)(C3H6) and Bromine(Br-Br) molecule with Carbon tetra chloride(CCl4) as a catalyst.
10:51 2) 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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11:41 This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Sandhya.np14