Difference between revisions of "GChemPaint/C3/Analysis-of-compounds/English-timed"

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Title of the tutorial: '''Analysis Of Compounds '''
 
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Author: '''Madhuri Ganapathi'''
 
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Key words:''' Molecular contextual menu,Chemical calculator, Composition, Isotropic pattern, video tutorial'''
 
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{|border=1
 
{|border=1
 
|'''Time'''
 
|'''Time'''
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|00:07
 
|00:07
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|In this tutorial, we will learn about,
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|In this tutorial, we will learn about:
  
 
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|-
 
|00:10
 
|00:10
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|* Molecular contextual menu
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| Molecular contextual menu
  
 
|-
 
|-
 
|00:12
 
|00:12
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|* Save the molecule in '''.mol''' format  
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| Save the molecule in '''.mol''' format  
  
 
|-
 
|-
 
|00:15
 
|00:15
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|* Add and edit a reaction
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| Add and edit a reaction
  
 
|-
 
|-
 
|00:18
 
|00:18
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|* Add reaction conditions and reagents on the reaction arrow
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| Add reaction conditions and reagents on the reaction arrow
  
 
|-
 
|-
 
|00:22
 
|00:22
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|* Convert reaction molecules into 3D  
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| Convert reaction molecules into 3D.
  
 
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|-
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|00:28
 
|00:28
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|'''Ubuntu Linux''' OS version 12.04.
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|'''Ubuntu Linux''' OS version 12.04,
  
 
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|00:37
 
|00:37
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|You will also require '''Internet connectivity'''.
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|You will also require '''internet connectivity'''.
  
 
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|01:43
 
|01:43
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|* '''NIST WebBook page for this molecule'''
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| '''NIST WebBook page for this molecule'''
  
 
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|-
 
|01:46
 
|01:46
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|*''' PubChem page for this molecule'''  
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|''' PubChem page for this molecule'''  
  
 
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|01:48
 
|01:48
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|* '''Open in Calculator'''
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| '''Open in Calculator'''
  
 
|-
 
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|01:51
 
|01:51
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|Click on '''NIST Web page for this molecule'''
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|Click on '''NIST Web page for this molecule'''.
  
 
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|03:19
 
|03:19
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|* '''Formula'''  
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| '''Formula'''  
  
 
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|03:21
 
|03:21
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|* '''Raw formula'''
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| '''Raw formula'''
  
 
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|03:23
 
|03:23
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|* '''Molecular weight in g.mol-1''' ( gram.mole-inverse)
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| '''Molecular weight in g.mol-1''' ( gram.mole-inverse)
  
 
|-
 
|-
 
|03:26
 
|03:26
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|* '''Compound's elemental mass percentage(%) analysis'''.
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| '''Compound's elemental mass percentage(%) analysis'''.
  
 
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|-
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|03:35
 
|03:35
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|It shows a graph of '''mass spectrum''' with a peak at '''Molecular weight''' of the compound.
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|It shows a graph of '''mass spectrum''' with a peak at '''Molecular weight''' of the compound.As an assignment-
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|03:42
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|As an assignment
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|04:17
 
|04:17
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|Click on '''Atom''' then click on '''Display symbol'''.  
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|Click on '''Atom''' and then click on '''Display symbol'''.  
  
 
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|04:39
 
|04:39
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|Type the filename as '''1,3-butadiene'''.  
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|Type the file name as '''1,3-butadiene'''.  
  
 
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|-
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|04:56
 
|04:56
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|For example, type the filename as '''1,3butadiene.mol''' or '''.mdl'''
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|For example, type the filename as '''1,3butadiene.mol''' or '''.mdl'''.
  
 
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|-
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|05:31
 
|05:31
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|As an assignment,  
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|As an assignment,  Convert '''Benzene''' structure from 2D to 3D.
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  Convert '''Benzene''' structure from 2D to 3D.
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|-
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|05:41
 
|05:41
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|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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|This is a chemical reaction of '''Ethyl chloride'''  with '''Alcoholic Potassium hydroxide''' and '''Aqueous Potassium hydroxide''' to yield '''Ethene''' and '''Ethanol''' respectively.  
  
 
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|07:22
 
|07:22
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|Right click on the arrow.
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|Right click on the arrow.A sub-menu opens.
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|-
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|07:23
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|A sub-menu opens.
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|-
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|07:58
 
|07:58
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|Drag to see the attachement as a '''catalyst'''.
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|Drag to see the attachment as a '''catalyst'''.
  
 
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|08:06
 
|08:06
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|Press '''CTRL + C''' to copy and '''CTRL+V''' twice to paste the structures.
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|Press '''Ctrl + C''' to copy and '''Ctrl+V''' twice to paste the structures.
  
 
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|09:20
 
|09:20
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|Type the file name as '''Ethyl Chloride.mol'''  
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|Type the file name as '''Ethyl Chloride.mol'''.
  
 
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|09:54
 
|09:54
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|To view the compound in 3D, right click on the file, choose '''Open with Molecules viewer'''.
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|To view the compound in 3D, right click on the file, choose the option '''Open with Molecules viewer'''.
  
 
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|-
 
|10:02
 
|10:02
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|Likewise, I will open all the files with '''Molecules viewer'''
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|Likewise, I will open all the files with '''Molecules viewer'''.
  
 
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|10:07
 
|10:07
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|Observe the compounds in 3D.  <Pause>
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|Observe the compounds in 3D.   
  
 
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|10:14
 
|10:14
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|In this tutorial we have learnt  
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|In this tutorial we have learnt:
  
 
|-
 
|-
 
|10:16
 
|10:16
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|* '''NIST WebBook page for this molecule.'''
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|'''NIST WebBook page for this molecule.'''
  
 
|-
 
|-
 
|10:19
 
|10:19
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|* '''Pub-Chem page for the  molecule'''
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|'''Pub-Chem page for the  molecule'''
  
 
|-
 
|-
 
|10:22
 
|10:22
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|* Find molecular weight of the compound using '''Chemical calculator'''.
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| Find molecular weight of the compound using '''Chemical calculator'''.
  
 
|-
 
|-
 
|10:25
 
|10:25
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|* Obtain graph of '''mass spectrum''' of a molecule
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|Obtain graph of '''mass spectrum''' of a molecule
  
 
|-
 
|-
 
|10:29
 
|10:29
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|* Save the molecule in '''.mol''' format  
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| Save the molecule in '''.mol''' format  
  
 
|-
 
|-
 
|10:32
 
|10:32
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|* Add reaction conditions and reagents on the reaction arrow
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| Add reaction conditions and reagents on the reaction arrow
  
 
|-
 
|-
 
|10:36
 
|10:36
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|* Add and edit a reaction
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| Add and edit a reaction
  
 
|-
 
|-
 
|10:39
 
|10:39
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|* Convert reaction molecules into 3D structures
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| Convert reaction molecules into 3D structures.
  
 
|-
 
|-
 
|10:42
 
|10:42
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|As an assignment  
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|As an assignment-
  
 
|-
 
|-
 
|10:44
 
|10:44
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|Draw chemical reaction of: '''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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|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
 
|10:51
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|'''Benzene''' and '''Chlorine'''(Cl-Cl) molecule with '''Anhydrous Aluminum Chloride'''(AlCl<sub>3</sub>) as a '''catalyst'''.
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| 2) '''Benzene''' and '''Chlorine'''(Cl-Cl) molecule with '''Anhydrous Aluminum Chloride'''(AlCl<sub>3</sub>) as a '''catalyst'''.
  
 
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|11:01
 
|11:01
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|Watch the video available at this URL '''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''
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|Watch the video available at this URL '''http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial'''.
  
 
|-
 
|-
 
|11:05
 
|11:05
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|It summarizes the Spoken Tutorial project
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|It summarizes the Spoken Tutorial project.
  
 
|-
 
|-
 
|11:08
 
|11:08
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|If you do not have good bandwidth, you can download and watch it  
+
|If you do not have good bandwidth, you can download and watch it.
  
 
|-
 
|-
 
|11:12
 
|11:12
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|The Spoken Tutorial Project Team Conducts workshops using spoken tutorials
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|The Spoken Tutorial Project Team: Conducts workshops using spoken tutorials.
  
 
|-
 
|-
 
|11:17
 
|11:17
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|Gives certificates to those who pass an on-line test  
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|Gives certificates to those who pass an on-line test.
  
 
|-
 
|-
 
|11:20
 
|11:20
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|For more details, please write to '''contact@spoken-tutorial.org'''  
+
|For more details, please write to '''contact@spoken-tutorial.org'''.
  
 
|-
 
|-
 
|11:27
 
|11:27
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|Spoken Tutorial Project is a part of the Talk to a Teacher project  
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|Spoken Tutorial Project is a part of the Talk to a Teacher project.
  
 
|-
 
|-
 
|11:31
 
|11:31
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|It is supported by the National Mission on Education through ICT, MHRD, Government of India
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|It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
 
|11:36
 
|11:36
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|More information on this Mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro'''
+
|More information on this Mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro'''.
  
 
|-
 
|-
 
|11:41
 
|11:41
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|This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining. s
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|This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
  
 
|-
 
|-

Latest revision as of 17:59, 27 March 2017

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.
11:01 Watch the video available at this URL http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial.
11:05 It summarizes the Spoken Tutorial project.
11:08 If you do not have good bandwidth, you can download and watch it.
11:12 The Spoken Tutorial Project Team: Conducts workshops using spoken tutorials.
11:17 Gives certificates to those who pass an on-line test.
11:20 For more details, please write to contact@spoken-tutorial.org.
11:27 Spoken Tutorial Project is a part of the Talk to a Teacher project.
11:31 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
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.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Sandhya.np14

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