Difference between revisions of "GChemPaint/C2/Editing-molecules/English-timed"

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Title of the tutorial: Editing molecules
 
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Author: Madhuri Ganapathi
 
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Key words: Video tutorial, GChemPaint tools- Add an electron pair to an atom, Add or modify an atom, Add a bond or change the multiplicity of the existing one, Add a six membered cycle, Increment the charge of an atom
 
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{|border =1
 
{|border =1
 
|'''Time'''
 
|'''Time'''
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|00:01
 
|00:01
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|Hello everyone.
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|Hello everyone.Welcome the tutorial on '''Editing Molecules''' in '''GChemPaint'''.
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|00:02
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|Welcome the tutorial on '''Editing Molecules''' in '''GChemPaint'''.
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|00:06
 
|00:06
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|In this tutorial, we will learn to
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|In this tutorial, we will learn to:
  
 
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|00:09
 
|00:09
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|* Add unbound electrons on an atom
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| Add unbound electrons on an atom
  
 
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|00:12
 
|00:12
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|* Draw Carbonic acid and Sulphuric acid structures.
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| Draw Carbonic acid and Sulphuric acid structures  
  
 
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|00:16
 
|00:16
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|* Add and modify a local charge on a group of atoms
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|Add and modify a local charge on a group of atoms.
  
 
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|00:23
 
|00:23
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|* Add and modify a local charge on an atom
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| Add and modify a local charge on an atom
  
 
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|00:26
 
|00:26
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|* Add cyclic molecules
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| Add cyclic molecules
  
 
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|00:29
 
|00:29
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|* Convert mono-cyclic molecules to bi-cyclic molecules.
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|Convert mono-cyclic molecules to bi-cyclic molecules.
  
 
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|00:34
 
|00:34
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|Here I am using
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|Here I am using'''Ubuntu Linux''' OS version. 12.04,
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|00:35
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|'''Ubuntu Linux''' OS version. 12.04
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|00:46
 
|00:46
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|To follow this tutorial you should be familiar with,
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|To follow this tutorial you should be familiar with
  
 
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|01:24
 
|01:24
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|Press capital '''H'''.  A '''Submenu''' with a list of elements starting with '''H''' appears.
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|Press capital '''H'''.  A '''Sub-menu''' with a list of elements starting with '''H''' appears.
  
 
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|01:38
 
|01:38
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|To draw three bonds to '''Nitrogen''' atom
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|To draw three bonds to '''Nitrogen''' atom,
  
 
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|01:41
 
|01:41
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|Click and drag the bonds thrice on '''Nitrogen''' atom.
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|click and drag the bonds thrice on '''Nitrogen''' atom.
  
 
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|01:46
 
|01:46
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|Orient the bonds to form a '''Pyramid''' like structure.
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|Orient the bonds to form a '''pyramid''' like structure.
  
 
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|02:20
 
|02:20
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|As an assignment,
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|As an assignment, Draw Phosphorus trichloride structure
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|02:21
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|* Draw Phosphorus trichloride structure
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|02:24
 
|02:24
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|* Add a pair of un-bound electrons on the Phosphorus atom.  
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|Add a pair of un-bound electrons on the Phosphorus atom.  
  
 
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|02:34
 
|02:34
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|Here is a slide for, '''Carbonic acid''' and '''Sulphuric acid''' structures.
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|Here is a slide for '''Carbonic acid''' and '''Sulphuric acid''' structures.
  
 
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|03:25
 
|03:25
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|Select '''O'''.
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|Select '''O'''.Click on  '''Add or modify an atom''' tool.
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|03:26
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|Click on  '''Add or modify an atom''' tool
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|03:47
 
|03:47
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|Select '''S'''
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|Select '''S'''.Click on  '''Add or modify an atom''' tool.
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|03:48
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|Click on  '''Add or modify an atom''' tool.
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|03:57
 
|03:57
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|Now anywhere on the '''Display area''' press  capital '''O'''  
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|Now anywhere on the '''Display area''' press  capital '''O'''.
  
 
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|04:01
 
|04:01
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|A '''Submenu''' with 2 options '''O''' and '''Os''' opens.
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|A '''sub-menu''' with 2 options '''O''' and '''Os''' opens.
  
 
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|05:49
 
|05:49
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|Observe that '''Sulphate ion '''SO<sub>4</sub><sup>2-</sup>''' is formed.
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|Observe that '''Sulphate ion '''SO<sub>4</sub><sup>2-</sup>''' is formed.As an assignment,
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|05:56
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|As an assignment,
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|05:57
 
|05:57
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|* Draw '''Nitric acid (HNO<sub>3</sub>)''' structure
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| Draw '''Nitric acid (HNO<sub>3</sub>)''' structure
  
 
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|05:59
 
|05:59
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|* Show the local charge on the '''Nitrate ion(NO<sup>3-</sup>)'''
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| Show the local charge on the '''Nitrate ion(NO<sup>-</sup><sub>3</sub>)'''.
  
 
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|06:16
 
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|A '''Submenu''' opens in which we will select '''Na'''.
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|A '''sub-menu''' opens in which we will select '''Na'''.
  
 
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|06:21
 
|06:21
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|Click on '''Add or modify an atom''' tool
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|Click on '''Add or modify an atom''' tool.
  
 
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|07:14
 
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|The Fourth toolbar in the tool box is the '''Cycle''' tool
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|The Fourth toolbar in the tool box is the '''Cycle''' tool.
  
 
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|07:24
 
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|* '''Add a three membered cycle'''
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|'''Add a three membered cycle'''
  
 
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|07:26
 
|07:26
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|* '''Add a four membered cycle'''
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|'''Add a four membered cycle'''
  
 
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|07:29
 
|07:29
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|* Add some more '''cycle''' tools  
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|And some more '''cycle''' tools  
  
 
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|07:52
 
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|A '''Submenu''' opens. Select '''Atom''' and then click on '''Display symbol'''.
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|A '''sub-menu''' opens. Select '''Atom''' and then click on '''Display symbol'''.
  
 
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|07:58
 
|07:58
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|Likewise let us add atoms on all the corners.  
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|Likewise, let us add atoms on all the corners.  
  
 
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|08:27
 
|08:27
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|To save the file, Click on '''Save the current file''' icon on the toolbar.
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|To save the file, click on '''Save the current file''' icon on the toolbar.
  
 
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|08:32
 
|08:32
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|'''Save as''' dialogue box opens.
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|'''Save as''' dialog box opens.
  
 
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|08:45
 
|08:45
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|*  Add unbound electrons on an atom
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| Add unbound electrons on an atom
  
 
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|08:48
 
|08:48
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|*  Draw  Carbonic acid and Sulphuric acid structures.  
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|Draw  Carbonic acid and Sulphuric acid structures.  
  
 
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|08:53
 
|08:53
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|*  Add and modify a local charge on a group of atoms
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|Add and modify a local charge on a group of atoms
  
 
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|09:00
 
|09:00
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|*  Add and modify a local charge on an atom
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|Add and modify a local charge on an atom
  
 
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|09:04
 
|09:04
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|*  Add cyclic molecules
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|Add cyclic molecules
  
 
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|09:06
 
|09:06
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|*  Convert mono-cyclic molecules to bi-cyclic molecules.
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|Convert mono-cyclic molecules to bi-cyclic molecules.
  
 
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|09:11
 
|09:11
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|As an assignment
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|As an assignment,
  
 
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|09:13
 
|09:13
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|* Add a seven membered cycle to the Display area  
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|Add a seven membered cycle to the Display area  
  
 
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|09:16
 
|09:16
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|* Change it to a tricyclic compound.  
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|Change it to a tricyclic compound.  
  
 
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|09:24
 
|09:24
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|It summarises the Spoken Tutorial project.
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|It summarizes the Spoken Tutorial project.
  
 
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|09:32
 
|09:32
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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
  
 
|-
 
|-
 
|09:36
 
|09:36
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|Gives certificates to those who pass an online test  
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|Gives certificates to those who pass an online test.
  
 
|-
 
|-
 
|09:40
 
|09:40
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|For more details, please write to '''contact@spoken-tutorial.org '''
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|For more details, please write to '''contact@spoken-tutorial.org '''.
  
 
|-
 
|-
 
|09:46
 
|09:46
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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.
  
 
|-
 
|-
 
|09:50
 
|09:50
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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.
  
 
|-
 
|-
 
|09:57
 
|09:57
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|More information on this Mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro '''
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|More information on this Mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro '''.
  
 
|-
 
|-

Latest revision as of 15:20, 28 October 2020

Time Narration
00:01 Hello everyone.Welcome the tutorial on Editing Molecules in GChemPaint.
00:06 In this tutorial, we will learn to:
00:09 Add unbound electrons on an atom
00:12 Draw Carbonic acid and Sulphuric acid structures
00:16 Add and modify a local charge on a group of atoms.
00:21 We will also learn to,
00:23 Add and modify a local charge on an atom
00:26 Add cyclic molecules
00:29 Convert mono-cyclic molecules to bi-cyclic molecules.
00:34 Here I am usingUbuntu Linux OS version. 12.04,
00:39 GChemPaint version 0.12.10
00:46 To follow this tutorial you should be familiar with
00:50 GChemPaint chemical structure editor.
00:53 If not, for relevant tutorials, please visit our website.
00:58 I have opened a new GChemPaint application.
01:02 Let's first draw Ammonia structure.
01:06 Click on Current element drop down arrow button.
01:09 Select N from the table.
01:11 Observe N in the tool box.
01:15 Click on Add or modify an atom tool.
01:18 Then click on Display area.
01:21 NH3 is seen on the Display area.
01:24 Press capital H. A Sub-menu with a list of elements starting with H appears.
01:30 Select H from the list.
01:33 Click on Add a bond or change the multiplicity of the existing one tool.
01:38 To draw three bonds to Nitrogen atom,
01:41 click and drag the bonds thrice on Nitrogen atom.
01:46 Orient the bonds to form a pyramid like structure.
01:51 Let us add a pair of un-bound electrons on Nitrogen atom.
01:56 Click on Add an electron pair to an atom tool.
02:01 Then click on Nitrogen atom of Ammonia.
02:05 Observe the changes.
02:07 Note that Nitrogen of Ammonia now has a pair of electrons.
02:12 This pair does not take part in bonding.
02:16 This pair of electrons is lone pair.
02:20 As an assignment, Draw Phosphorus trichloride structure
02:24 Add a pair of un-bound electrons on the Phosphorus atom.
02:29 Now let's draw 'Carbonic acid(H2CO3) and Sulphuric acid(H2SO4) structures.
02:34 Here is a slide for Carbonic acid and Sulphuric acid structures.
02:40 First let us move Ammoniastructure aside.
02:44 To do so, click on Select one or more objects tool.
02:48 Then click on Ammonia structure and drag it to one side.
02:53 Now let's draw Carbonic acid structure.
02:56 Click on the Current element drop-down arrow button.
03:00 Select C from the table.
03:02 Click on Add a bond or change the multiplicity of the existing one tool.
03:07 Click on the Display area.
03:09 Orient three bonds in such a way that they form an inverted Y.
03:15 Draw the fourth bond as a double bond to any one of the bonds.
03:21 Now click on Current element drop down arrow button.
03:25 Select O.Click on Add or modify an atom tool.
03:30 Place the cursor near the bonds.
03:33 Click on the three bond positions.
03:37 Carbonic acid(H2CO3) structure is drawn.
03:40 Now let's draw Sulphuric acid structure.
03:44 Click on Current element drop down arrow button.
03:47 Select S.Click on Add or modify an atom tool.
03:52 Then click on Display area.
03:55 Observe H2S.
03:57 Now anywhere on the Display area press capital O.
04:01 A sub-menu with 2 options O and Os opens.
04:06 Select O.
04:08 Click on Add or modify an atom tool.
04:11 Then click on Add a bond or change the multiplicity of the existing one tool.
04:17 In the Property menu, increase the Bond length value to 200 or above.
04:23 Click on H2S to draw three bonds of OH to S.
04:29 Observe a positive charge near S.
04:32 This appears because Sulphur has to satisfy valency of 6.
04:39 For the fourth bond, first click on S .
04:43 Now drag the bond to one side without releasing the mouse.
04:47 Now let us convert the opposite bonds into double bonds.
04:52 Click on Add a bond or change the multiplicity of the existing one tool.
04:58 Then click on the opposite existing bonds of the structure.
05:03 Note that the positive charge is no longer visible.
05:08 Sulphuric acid structure is complete.
05:12 Next let us add a local charge on the Carbonic acid and Sulphuric acid structures.
05:18 To show local charge, Click on Decrement the charge of an atom tool.
05:24 Click on the two O-H groups of the Carbonic acid structure.
05:30 Observe that Carbonate ion CO32- is formed.
05:36 To show the local charge on Sulphuric acid structure.
05:41 Click on Decrement the charge of an atom tool.
05:44 Click on the two opposite O-H groups of Sulphuric acid.
05:49 Observe that Sulphate ion SO42- is formed.As an assignment,
05:57 Draw Nitric acid (HNO3) structure
05:59 Show the local charge on the Nitrate ion(NO-3).
06:02 Your completed assignment should look like this.
06:07 Let me quickly demonstrate how to add a local charge on an atom.
06:12 Anywhere on the Display area, press capital N.
06:16 A sub-menu opens in which we will select Na.
06:21 Click on Add or modify an atom tool.
06:24 Then click on the Display area.
06:27 Sodium atom appears on the Display area.
06:30 Click on Increment the charge of an atom tool.
06:35 Then Click on Na.
06:37 Observe a positive charge on the Sodium atom.
06:41 In a similar way, we can add a negative charge to an atom.
06:46 This can be done by choosing Decrement the charge of an atom tool.
06:51 Now let us learn to draw Cyclic molecules.
06:54 For this, we will open a new GChemPaint window.
06:59 Click on Create a new file icon on the toolbar.
07:03 Ensure that C that is Carbon is selected as element.
07:09 Also, ensure that Bond length is 200 or above.
07:14 The Fourth toolbar in the tool box is the Cycle tool.
07:19 There are various tools here that we can use.
07:22 For eg -
07:24 Add a three membered cycle
07:26 Add a four membered cycle
07:29 And some more cycle tools
07:32 and then * Add a cycle tool.
07:35 We will use Add a four membered cycle.
07:40 So, click on it.
07:42 Then click on the Display area.
07:44 Let us add atoms to the cycle at the corners.
07:49 Right click on any one of the corners.
07:52 A sub-menu opens. Select Atom and then click on Display symbol.
07:58 Likewise, let us add atoms on all the corners.
08:03 Obtained structure is Cyclobutane.
08:07 Now let us convert a mono-cyclic compound to bi-cyclic compound.
08:12 Click on Add a six membered cycle tool.
08:16 Then click on Display area.
08:19 Place the cursor on the cycle's bond and click again.
08:24 Observe the Bi-cyclic compound.
08:27 To save the file, click on Save the current file icon on the toolbar.
08:32 Save as dialog box opens.
08:35 Enter the file name as Editing Molecules
08:38 Click on Save button.
08:41 Let's summarize.
08:43 In this tutorial, we have learnt to,
08:45 Add unbound electrons on an atom
08:48 Draw Carbonic acid and Sulphuric acid structures.
08:53 Add and modify a local charge on a group of atoms
08:58 We have also learnt to,
09:00 Add and modify a local charge on an atom
09:04 Add cyclic molecules
09:06 Convert mono-cyclic molecules to bi-cyclic molecules.
09:11 As an assignment,
09:13 Add a seven membered cycle to the Display area
09:16 Change it to a tricyclic compound.
09:20 Watch the video available at this URL. http://spoken-tutorial.org/ What_is_a_Spoken_Tutorial
09:24 It summarizes the Spoken Tutorial project.
09:27 If you do not have good bandwidth, you can download and watch it.
09:32 The Spoken Tutorial Project Team: Conducts workshops using spoken tutorials
09:36 Gives certificates to those who pass an online test.
09:40 For more details, please write to contact@spoken-tutorial.org .
09:46 Spoken Tutorial Project is a part of the Talk to a Teacher project.
09:50 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
09:57 More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro .
10:03 This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Gaurav, Madhurig, PoojaMoolya, Pratik kamble, Sandhya.np14, Shruti arya

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