View source for GChemPaint/C3/Analysis-of-compounds/English-timed

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|'''Time'''
|'''Narration'''

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|00:01
|Hello everyone. Welcome to this tutorial on '''Analysis of Compounds''' in '''GChemPaint'''.

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|00:07
|In this tutorial, we will learn about,

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|00:10
|* Molecular contextual menu

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|00:12
|* Save the molecule in '''.mol''' format 

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|00:15
|* Add and edit a reaction

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|00:18
|* Add reaction conditions and reagents on the reaction arrow

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|00:22
|* Convert reaction molecules into 3D 

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|00:26
|For this tutorial  I am using

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|00:28
|'''Ubuntu Linux''' OS version 12.04.

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|00:32
|'''GChemPaint''' version 0.12.10. 

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|00:37
|You will also require '''Internet connectivity'''.

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|00:41
|To follow this tutorial, you should be familiar with '''GChemPaint.'''

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|00:46
|If not, for relevant tutorials, please visit our website.

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|00:52
|I have opened a new '''GChemPaint''' window.

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|00:55
|Click on '''Use or manage templates''' tool.

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|00:59
|'''Templates''' tool property page opens below.

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|01:02
|Click on '''Amino Acids''' on '''Templates''' drop down button.

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|01:07
|Select '''Alanine''' from the list. 

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|01:11
|Structure of '''Alanine''' is loaded onto the '''Templates''' property page.

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|01:16
|Click on the structure and click on  '''Display area''' to load it. 

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|01:21
|I will explain about contextual menu of '''Alanine''' molecule.

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|01:26
|Right click on the molecule.

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|01:29
|A sub-menu opens.

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|01:31
|Select '''Molecule'''; a contextual menu opens alongside.

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|01:36
|Contextual menu contains different menu items, of which, I will discuss about-

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|01:43
|* '''NIST WebBook page for this molecule'''

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|01:46
|*''' PubChem page for this molecule''' 

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|* '''Open in Calculator'''

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|01:51
|Click on '''NIST Web page for this molecule'''

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|01:55
|'''Alanine's NIST''' webpage opens.

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|01:59
|Webpage shows all the details about '''Alanine'''.

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|02:03
|Come back to '''GChemPaint''' editor.

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|02:06
|Right click on '''Alanine''' to open the '''PubChem page for this molecule'''.

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|02:12
|Click on '''Alanine''' structure on this webpage.

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|02:16
|A new web-page with '''2D Structure''' and '''3D Conformer''' tabs, is seen.

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|02:22
|Click on '''3D Conformer''' tab to view '''Alanine'''  in 3 dimensions. 

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|02:28
|Click on the displayed 3D structure.

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|02:31
|This opens the structure in a separate window with some controls on the top and on the left.

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|02:37
|Click on the '''Rotation''' icon to rotate the structure in various directions.

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|02:43
|On the same page, click on '''H''' icon to show '''hydrogens'''.

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|02:48
|These are the '''Hydrogens'''.

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|02:51
|Let us switch to '''GChemPaint''' window again.

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|02:53
|Right click on '''Alanine''';  choose the option '''Open in Calculator'''. 

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|03:00
|'''Chemical calculator''' window opens.

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|03:03
|If not, please install the same, using '''Synaptic Package Manager''', as in the '''Overview''' tutorial.

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|03:10
|This Window has two tabs at the bottom - '''Composition''' and '''Isotopic Pattern.'''

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|'''Composition''' tab has the following components-

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|03:19
|* '''Formula''' 

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|03:21
|* '''Raw formula'''

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|03:23
|* '''Molecular weight in g.mol-1''' ( gram.mole-inverse)

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|03:26
|* '''Compound's elemental mass percentage(%) analysis'''.

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|03:32
|Click on the '''Isotropic Pattern''' tab.

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|03:35
|It shows a graph of '''mass spectrum''' with a peak at '''Molecular weight''' of the compound.

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|03:42
|As an assignment
 
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|03:43
|1. Select other '''Amino Acids''' from '''Templates''' list.

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|03:46
|2. Obtain their '''Composition''' and '''Isotropic pattern'''. 

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|03:51
|I have opened a new '''GChemPaint''' window.

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|03:54
|Let us draw '''1,3-butadiene''' structure.

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|03:58
|Click on '''Add a chain''' tool.

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|04:01
|Click and drag the chain to 4 carbons.

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|04:04
|Click on '''Add a bond''' tool and click on first and third bonds positions, to form double bonds. 

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|04:13
|Right click at each position to show atoms. 

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|04:17
|Click on '''Atom''' then click on '''Display symbol'''. 

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|04:22
|To convert '''1,3-butadiene''' 2D structure to 3D structure, click on the '''Save''' icon on the tool bar.

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|04:30
|'''Save as''' dialog box opens.

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|In the '''File type''' field, select '''MDL Molfile Format.'''

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|04:39
|Type the filename as '''1,3-butadiene'''. 

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|04:42
|Select '''Desktop''' to save the file on '''Desktop'''.

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|04:47
|Then click on '''Save''' button.

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|04:50
|Alternatively, you can also save the file with extension ''.mol'' or ''.mdl'' directly.

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|04:56
|For example, type the filename as '''1,3butadiene.mol''' or '''.mdl'''

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|05:06
|Click on '''Save''' button.

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|05:09
|To view the structure in 3D, right click on the molecule.

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|05:12
|Select the option '''Open With Molecules viewer'''.

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|05:17
|This is''' 1,3butadiene''' in 3D.

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|05:20
|Please note, we cannot make changes in the structure.

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|05:23
|To rotate the structure, place the cursor on the structure, hold and drag the mouse. 

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|05:31
|As an assignment, 
 Convert '''Benzene''' structure from 2D to 3D.

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|05:36
|Now let's learn to draw chemical reactions and reaction conditions.

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|05:41
|This is a chemical reaction of '''Ethyl chloride'''  ('''C<sub>2</sub>H<sub>5</sub>Cl''') with '''Alcoholic Potassium hydroxide(Alc.KOH)''' and '''Aqueous Potassium hydroxide(Aq.KOH)''' to yield '''Ethene(C<sub>2</sub>H<sub>4</sub>)''' and '''Ethanol(C<sub>2</sub>H<sub>5</sub>OH)''' respectively. 

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|05:52
|I have opened a new '''GChemPaint''' window.

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|05:55
|Let us first draw structure of '''Ethyl chloride.''' 

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|Click on '''Add a chain''' tool.

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|06:01
|Click on the '''Display area'''.

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|Right click on the chain to display atoms on first and second bond positions.

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|Click on '''Current element''' drop down arrow button.

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|06:13
|Select '''Cl''' from table.

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|Click on '''Add or modify an atom''' tool.

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|Click on the third bond position.

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|06:23
|Structure  of '''Ethyl chloride''' is drawn.

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|Click on '''Add or modify a group of atoms''' tool. 

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|Click on the '''Display area'''. Type '''Alc.KOH'''. 

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|06:37
|Click again and type '''Aq.KOH''' 

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|06:42
|Click on '''Add an arrow for an irreversible reaction''' tool.

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|06:47
|You can change the '''Arrow length''' using the scroller here.  

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|06:51
|I will increase the arrow length to 280.

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|06:54
|Click on the '''Display area''',  beside '''Ethyl Chloride'''.  

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|06:58
|Click below '''Ethyl Chloride'''. 

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|07:01
|Hold the mouse and rotate the arrow to point downwards.

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|07:05
|Click on the '''Selection''' tool. 

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|07:08
|Position '''Alcoholic Potassium Hydroxide (Alc.KOH)''' above first arrow.

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|07:13
|Position '''Aqueous Potassium Hydroxide (Aq.KOH)''' close to second arrow.

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|07:18
|Select '''Alcoholic Potassium hydroxide(Alc.KOH)'''.

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|Right click on the arrow.

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|A sub-menu opens.

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|Select '''Arrow''' and click on '''Attach selection to arrow'''.

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|07:29
|A dialog box with heading '''Arrow associated''' opens.

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|Click on '''Role''' drop down list. 

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|07:37
|Select '''Catalyst''' from the list. Click on '''Close'''.

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|07:42
|Drag arrow to check if '''Alcoholic Potassium Hydroxide (Alc.KOH)''' attaches to the arrow, as a '''catalyst'''.

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|07:49
|Let's repeat the process for '''Aqueous Potassium Hydroxide(Aq.KOH)'''.

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|07:58
|Drag to see the attachement as a '''catalyst'''.

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|08:02
|Click on '''Selection''' tool to select '''Ethyl chloride''' structure.

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|08:06
|Press '''CTRL + C''' to copy and '''CTRL+V''' twice to paste the structures.

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|08:11
|Place the structures at proper positions by dragging.

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|08:15
|In the reactions '''Ethyl chloride''' reacts with '''Alcoholic potassium Hyroxide''' to give '''Ethene'''.

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|08:21
|'''Ethyl chloride''' reacts with '''Aqueous Potassium Hydroxide''' to give '''Ethanol'''.

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|08:27
|To obtain '''Ethene''', click on '''Eraser''' tool and delete '''Cl''' bond of  '''Ethyl chloride'''. 

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|08:34
|'''Ethane''' is formed.

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|08:37
|In the Tool box, ensure that '''Current element''' is '''Carbon'''.

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|08:42
|Click on '''Add a bond''' tool and click on the bond to obtain a double bond.

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|'''Ethene''' is formed.

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|To obtain '''Ethanol''', press '''O''' on the keyboard. 

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|Click on '''Add or modify an atom''' tool 

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|08:58
|and then click on '''Cl''' of  '''Ethyl chloride'''. 

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|09:02
|Now let's convert the reactants and products from 2D to 3D. 

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|09:07
|Open a new file,  copy '''Ethyl Chloride''' and paste it into new file.

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|09:15
|Click on '''Save ''' button.

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|09:17
|'''Save as''' dialog box opens.

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|09:20
|Type the file name as '''Ethyl Chloride.mol''' 

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|09:24
|Click on '''Desktop''' to save your file on your '''Desktop'''. 

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|09:28
|Click on '''Save''' button.

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|09:31
|Likewise copy '''Ethene''' into a new file. 

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|09:34
|Save as '''Ethene.mol'''. 

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|09:37
|Copy '''Ethanol''' into a new file.

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|09:39
|Save as '''Ethanol.mol'''

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|09:42
|I had already saved the files on my '''Desktop'''.

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|09:46
|I will minimize the current  window.

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|09:49
|And I will go to '''Desktop''' folder where I had saved my files.

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|09:54
|To view the compound in 3D, right click on the file, choose '''Open with Molecules viewer'''.

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|10:02
|Likewise, I will open all the files with '''Molecules viewer'''

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|10:07
|Observe the compounds in 3D.  <Pause>

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|10:11
|Let's summarize what we have learnt.

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|10:14
|In this tutorial we have learnt 

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|10:16
|* '''NIST WebBook page for this molecule.'''

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|10:19
|* '''Pub-Chem page for the  molecule'''

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|10:22
|* Find molecular weight of the compound using '''Chemical calculator'''.

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|10:25
|* Obtain graph of '''mass spectrum''' of a molecule

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|10:29
|* Save the molecule in '''.mol''' format 

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|10:32
|* Add reaction conditions and reagents on the reaction arrow

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|10:36
|* Add and edit a reaction

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|10:39
|* Convert reaction molecules into 3D structures

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|10:42
|As an assignment 

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|10:44
|Draw chemical reaction of:
 1)'''Propene''' (C3H6)(C<sub>3</sub>H<sub>6</sub>) and '''Bromine'''(Br-Br) molecule with '''Carbon tetra chloride'''(CCl<sub>4</sub>) as a '''catalyst'''. 
 
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|10:51
|2)'''Benzene''' and '''Chlorine'''(Cl-Cl) molecule with '''Anhydrous Aluminum Chloride'''(AlCl<sub>3</sub>) as a '''catalyst'''.

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|10:57
|Your completed assignment should look like this.

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|11:01
|Watch the video available at this URL '''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''

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|11:05
|It summarizes the Spoken Tutorial project

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|11:08
|If you do not have good bandwidth, you can download and watch it 

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|11:12
|The Spoken Tutorial Project Team Conducts workshops using spoken tutorials

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|11:17
|Gives certificates to those who pass an on-line test 

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|11:20
|For more details, please write to '''contact@spoken-tutorial.org''' 

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|11:27
|Spoken Tutorial Project is a part of the Talk to a Teacher project 

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|11:31
|It is supported by the National Mission on Education through ICT, MHRD, Government of India

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|11:36
|More information on this Mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro'''

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|11:41
|This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining. s

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