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

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 +
{|border =1
 +
!Visual Cue
 +
!Narration
 +
|-
 +
||'''Slide Number 1'''
 +
||Hello everyone.
  
 +
Welcome the tutorial on '''Editing Molecules''' in '''GChemPaint'''.
 +
|-
 +
||'''Slide Number 2'''
 +
 +
'''Learning Objectives'''
 +
||In this tutorial, we will learn to
 +
 +
* Add unbound electrons on an atom
 +
 +
* Draw  Carbonic acid and Sulphuric acid structures.
 +
 +
* Add and modify a local charge on a group of atoms
 +
|-
 +
||'''Slide Number 3'''
 +
 +
'''Learning Objectives'''
 +
||We will also learn to,
 +
* Add and modify a local charge on an atom
 +
 +
* Add cyclic molecules
 +
 +
* Convert monocyclic molecules to bicyclic molecules.
 +
|-
 +
||'''Slide Number 4'''
 +
 +
'''System Requirement'''
 +
||Here I am using
 +
 +
'''Ubuntu Linux''' OS version. 12.04
 +
 +
'''GChemPaint''' version 0.12.10
 +
|-
 +
||'''Slide Number 5'''
 +
 +
'''Pre-requisites'''
 +
||To follow this tutorial you should be familiar with,
 +
 +
'''GChemPaint''' chemical structure editor.
 +
 +
If not, for relevant tutorials,  please visit our website.
 +
|-
 +
|| Switch to '''GChemPaint''' application.
 +
||I have opened a new '''GChemPaint''' application. 
 +
|-
 +
||
 +
||Let's first draw  '''Ammonia''' structure.
 +
|-
 +
||Click on  '''Current element''' drop down arrow button.
 +
||Click on  '''Current element''' drop down arrow button.
 +
|-
 +
||Select '''N'' from the table.
 +
||Select '''N''' from the table.
 +
Observe N in the tool box.
 +
|-
 +
||Click on  '''Add or modify an atom''' tool>> click on '''Display area'''.
 +
||Click on  '''Add or modify an atom''' tool.
 +
 +
Then click on '''Display area'''.
 +
|-
 +
||Point to '''NH3'''
 +
|| '''NH3'''  is seen on the '''Display area'''.
 +
|-
 +
||Press capital '''H'''.
 +
 +
Point to the '''Submenu'''.
 +
||Press capital '''H'''.
 +
 +
A '''Submenu''' with a list of elements starting with '''H''' appears.
 +
|-
 +
||Select '''H''' from the list.
 +
||Select '''H''' from the list.
 +
|-
 +
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
 +
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
 +
|-
 +
||Click and drag the bonds thrice on the Nitrogen atom.
 +
||To draw threee bonds to Nitrogen atom
 +
Click and drag the bonds thrice on Nitrogen atom.
 +
|-
 +
||Point to the bonds
 +
||Orient the three bonds to form a '''Pyramid''' like structure.
 +
|-
 +
||
 +
||Let's add a pair of  un-bound electrons on  '''Nitrogen''' atom.
 +
|-
 +
||Click on '''Add an electron pair to an atom''' tool>> click on the '''Nitrogen''' atom.
 +
||Click on '''Add an electron pair to an atom''' tool.
 +
Then click on '''Nitrogen''' atom of  '''Ammonia'''.
 +
 +
Observe the changes.
 +
|-
 +
||Point to the unbound electrons.
 +
||Note that '''Nitrogen''' of '''Ammonia''' has a pair of  electrons.
 +
 +
This pair does not take part in bonding.
 +
 +
This pair of electrons is '''lone pair'''.
 +
|-
 +
||'''Slide Number 6'''
 +
 +
'''Assignment'''
 +
||'''Assignment'''
 +
 +
* Draw Phosphorus trichloride structure
 +
 +
* Add a pair of un-bound electrons to the Phosphorus atom.
 +
|-
 +
||
 +
||Let's now draw ''''Carbonic acid(H2CO3)''' and '''Sulphuric acid(H2SO4)''' structures on the same window.
 +
|-
 +
||'''Slide  Number 7'''
 +
 +
Structures of '''Carbonic acid''' and '''Sulphuric acid'''.
 +
||Here is a slide for the structures of  '''Carbonic acid''' and '''Sulphuric acid'''.
 +
|-
 +
||
 +
||Let's first draw '''Carbonic acid''' structure.
 +
|-
 +
||Click on the '''Current element''' arrow button>>Select '''C''' from the table.
 +
||Click on the '''Current element''' arrow button.
 +
 +
Select '''C''' from the table.
 +
|-
 +
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
 +
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
 +
|-
 +
||Click on the '''Display area'''.
 +
 +
Point to the orientation
 +
||Click on the '''Display area'''.
 +
 +
'''Orient''' three bonds  in such a way that they form an inverted Y.
 +
|-
 +
||Point to the fourth bond.
 +
||Draw fourth bond as a '''double bond''' to any one of the bonds.
 +
|-
 +
||Click on '''Current element''' drop down  button.
 +
||Now click on '''Current element''' drop down button.
 +
|-
 +
||Select '''O'''.
 +
||Select '''O'''.
 +
|-
 +
||Click on  '''Add or modify an atom''' tool
 +
||Click on  '''Add or modify an atom''' tool
 +
|-
 +
||Point to the cursor.
 +
||Place the cursor  near the bonds.
 +
|-
 +
||Click on the bond positions.
 +
||Click on the three bond positions.
 +
 +
'''Carbonic acid(H2CO3)''' structure is drawn.
 +
|-
 +
||
 +
||Let's draw the '''Sulphuric acid''' structure.
 +
|-
 +
||Click on  '''Current element''' drop down button.
 +
||Click on  '''Current element''' drop down button.
 +
|-
 +
||Select '''S'''
 +
||Select '''S'''
 +
|-
 +
||Click on  '''Add or modify an atom''' tool>>Click on the '''Display area'''.
 +
||Click on  '''Add or modify an atom''' tool.
 +
 +
Then click on the '''Display area'''.
 +
 +
Observe '''H2S'''.
 +
|-
 +
||Click on the Display area>> Press  capital '''O'''
 +
 +
A '''Submenu''' with '''O''' and '''Os''' opens.
 +
||Press  capital '''O'''
 +
A '''Submenu''' with 2 options '''O''' and '''Os''' opens.
 +
|-
 +
||Select '''O'''.
 +
||Select '''O'''.
 +
|-
 +
||Click on  '''Add or modify an atom''' tool>> click on '''Add a bond or change the multiplicity of the existiing one''' tool.
 +
||Click on  '''Add or modify an atom''' tool.
 +
 +
Then click on '''Add a bond or change the multiplicity of the existing one''' tool.
 +
|-
 +
||In the '''Property''' menu>>make the '''Bond length value''' to 200 or above.
 +
||In the '''Property''' menu, increase the '''Bond length value''' to 200 or above.
 +
|-
 +
||Click on '''H2S''' to draw the three bonds.
 +
||Click on '''H2S''' to draw the three bonds of '''OH''' to '''S'''.
 +
|-
 +
||Click on '''S''' and drag the bond to a side without releasing the mouse.
 +
||For the fourth '''OH''' bond, first click on '''S'''.
 +
 +
Now drag the bond to one side without releasing the mouse button.
 +
|-
 +
||Point to plus 2 charge near S.
 +
|| Observe a plus 2 charge near S. 
 +
 +
This appears because Sulphur has to satisfy valency of 6.
 +
|-
 +
||Point to any 2 opposite bonds.
 +
||Let's convert the opposite bonds as '''double bonds'''.
 +
|-
 +
||Click on '''Add a bond or change the multiplicity of the existiing one''' tool>>click on the existing bonds.
 +
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
 +
 +
 +
Then click on the opposite existing bonds of the structure.
 +
|-
 +
||Point to the structure
 +
||Note that the plus 2 charge is no longer visible.
 +
 +
'''Sulphuric acid''' structure is complete.
 +
|-
 +
||
 +
||Next let's add a local charge on the '''Carbonic acid''' and '''Sulphuric acid''' structures.
 +
|-
 +
||Click on '''Decrement the charge of an atom''' tool.
 +
||To show local charge, Click on '''Decrement the charge of an atom''' tool.
 +
|-
 +
||Click on two  '''O-H''' groups.
 +
||Click on the two '''O-H''' groups of the '''Carbonic acid'''. 
 +
Observe that '''Carbonate ion (CO32-)''' is formed.
 +
|-
 +
||Click on '''Decrement the charge of an atom''' tool.
 +
||To show local charge on  '''Sulphuric acid''' structure.
 +
 +
Click on '''Decrement the charge of an atom''' tool.
 +
|-
 +
||Click on the two opposite  '''O-H''' groups.
 +
||Click on the two opposite  '''O-H''' groups of '''Sulphuric acid'''.
 +
 +
Observe that '''Sulphate (SO42-)''' is formed.
 +
|-
 +
||'''Slide Number 7'''
 +
 +
'''Assignment'''
 +
||* Draw '''Nitric acid (HNO3)''' structure
 +
 +
* Show the local charge on the '''Nitrate ion(NO3-)'''
 +
 +
Your output should look like this.
 +
|-
 +
||
 +
||Let me quickly demonstrate how to add a charge to an atom.
 +
|-
 +
||Press capital ''N'''.
 +
 +
Point to the '''Submenu'''
 +
||Anywhere on the '''Display area''', press capital ''N'''.
 +
 +
A '''Submenu''' opens in which let's select '''Na'''.
 +
|-
 +
||Click on '''Add or modify an atom''' tool>>Click on the '''Display area'''.
 +
||Click on '''Add or modify an atom''' tool and then click on the '''Display area'''.
 +
 +
Na atom appears on the '''Display area'''.
 +
|-
 +
||Click on '''Increment the charge of a atom''' tool>>Click on '''Na'''.
 +
||Click on '''Increment the charge of an atom''' tool.
 +
 +
Then Click on '''Na'''.
 +
 +
Observe a positive charge on the '''Sodium''' atom.
 +
|-
 +
||Point to Decrement the charge of an atom tool.
 +
||In a similar way, we can add a '''negative''' charge to an atom. 
 +
 +
This can be done by choosing '''Decrement the charge of an atom''' tool.
 +
|-
 +
||
 +
||Now let's learn to draw '''Cyclic''' molecules.
 +
 +
For this, we will open a new GChemPaint window.
 +
|-
 +
||Click on '''Create a new file''' icon on the toolbar.
 +
||Click on '''Create a new file''' icon on the toolbar.
 +
|-
 +
||Place the window within the recording area.
 +
||Let me adjust the window position.
 +
|-
 +
||
 +
||Ensure that C i.e. Carbon is selected as the current element.
 +
 +
Also, ensure that the Bond length is 200 or above.
 +
|-
 +
||Point to the cycle tools bar in the  tool box
 +
||There are various cycle tools here that we can use.
 +
For eg -
 +
* '''Add a three membered cycle'''
 +
 +
* '''Add a four membered cycle'''
 +
 +
*and some more '''cycle tools''' and then
 +
 +
* '''Add a cycle'''.
 +
|-
 +
||Point to  '''Add a four membered cycle''' tool
 +
||We will use ''Add a  four membered cycle''' to the '''Display area'''.
 +
|-
 +
||Click on '''Add a four membered cycle''' tool>>Click on the '''Display area'''.
 +
||So, click on it.
 +
 +
Then click on the '''Display area'''.
 +
|-
 +
||
 +
||Let's add atoms to the cycle at the corners.
 +
|-
 +
||Right click on any one of the corners>>A '''Submenu''' opens.
 +
||Right click any one of the corners.
 +
 +
A '''Submenu''' opens.
 +
|-
 +
||Select '''Atom'''>>Then click on '''Display symbol'''.
 +
||Select '''Atom'''.
 +
 +
Then click on '''Display symbol'''.
 +
|-
 +
||Show this part fast.
 +
||Likewise let's add atoms on all the corners. Obtained structure is '''Cyclobutane'''.
 +
|-
 +
||
 +
||Let's now convert a monocyclic compoud to bicyclic compoud.
 +
|-
 +
||Click on '''Add a six membered cycle''' tool>> click on the '''Display area'''.
 +
||Click on '''Add a six membered cycle''' tool.
 +
 +
Then click on the '''Display area'''.
 +
|-
 +
||Click on the cycle bond
 +
||Place the cursor on the cycle's bond and click again.
 +
 +
Observe the '''Bicyclic compound'''.
 +
|-
 +
||Click on '''Save the current file''' icon on the toolbar.
 +
||To save the file,
 +
 +
Click on '''Save the current file''' icon on the toolbar.
 +
|-
 +
||'''Save as''' dialog box opens.
 +
||'''Save as''' dialog box opens.
 +
|-
 +
||Enter the filename as '''Editing Molecules'''>>Click on '''Save''' button.
 +
||Enter the filename as '''Editing Molecules'''
 +
 +
Click on '''Save''' button.
 +
|-
 +
||
 +
||Let's summarize.
 +
|-
 +
||'''Slide Number 8'''
 +
 +
'''Summary'''
 +
||In this tutorial, we have learnt to,
 +
 +
*  Add ubound electrons on an atom
 +
 +
*  Draw  Carbonic acid and Sulphuric acid structures.
 +
 +
*  Add and modify a local charge on a group of atoms
 +
|-
 +
||||'''Slide Number 9'''
 +
 +
'''Summary'''
 +
||We have also learnt to,
 +
 +
*  Add and modify a local charge on an atom
 +
 +
*  Add cyclic molecules
 +
 +
*  Convert monocyclic molecules to bicyclic molecules.
 +
|-
 +
||'''Slide Number 10'''
 +
 +
'''Assignment'''
 +
||As an assignment
 +
 +
* Add cycloheptane ring to the Display area
 +
* Change it to tricyclic compound.
 +
|-
 +
||'''Slide Number 8'''
 +
 +
'''Acknowledgement'''
 +
||Watch the video available at this URL.
 +
 +
http://spoken-tutorial.org/ What_is_a_Spoken_Tutorial
 +
 +
It summarises the Spoken Tutorial project.
 +
 +
If you do not have good bandwidth, you can download and watch it.
 +
|-
 +
||''' Slide Number 9'''
 +
||The Spoken Tutorial Project Team:
 +
 +
Conducts workshops using spoken tutorials
 +
 +
Gives certificates to those who pass an online test
 +
 +
For more details, please write to
 +
 +
'''contact@spoken-tutorial.org '''
 +
|-
 +
||'''Slide number 10'''
 +
||Spoken Tutorial Project is a part of the Talk to a Teacher project
 +
 +
It is supported by the National Mission on Education through ICT, MHRD, Government of India
 +
 +
More information on this Mission is available at this link  '''http://spoken-tutorial.org/NMEICT-Intro '''
 +
 +
This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.
 +
|-

Revision as of 12:58, 2 August 2013

Visual Cue Narration
Slide Number 1 Hello everyone.

Welcome the tutorial on Editing Molecules in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to
  • Add unbound electrons on an atom
  • Draw Carbonic acid and Sulphuric acid structures.
  • Add and modify a local charge on a group of atoms
Slide Number 3

Learning Objectives

We will also learn to,
  • Add and modify a local charge on an atom
  • Add cyclic molecules
  • Convert monocyclic molecules to bicyclic molecules.
Slide Number 4

System Requirement

Here I am using

Ubuntu Linux OS version. 12.04

GChemPaint version 0.12.10

Slide Number 5

Pre-requisites

To follow this tutorial you should be familiar with,

GChemPaint chemical structure editor.

If not, for relevant tutorials, please visit our website.

Switch to GChemPaint application. I have opened a new GChemPaint application.
Let's first draw Ammonia structure.
Click on Current element drop down arrow button. Click on Current element drop down arrow button.
Select 'N from the table. Select N from the table.

Observe N in the tool box.

Click on Add or modify an atom tool>> click on Display area. Click on Add or modify an atom tool.

Then click on Display area.

Point to NH3 NH3 is seen on the Display area.
Press capital H.

Point to the Submenu.

Press capital H.

A Submenu with a list of elements starting with H appears.

Select H from the list. Select H from the list.
Click on Add a bond or change the multiplicity of the existing one tool. Click on Add a bond or change the multiplicity of the existing one tool.
Click and drag the bonds thrice on the Nitrogen atom. To draw threee bonds to Nitrogen atom

Click and drag the bonds thrice on Nitrogen atom.

Point to the bonds Orient the three bonds to form a Pyramid like structure.
Let's add a pair of un-bound electrons on Nitrogen atom.
Click on Add an electron pair to an atom tool>> click on the Nitrogen atom. Click on Add an electron pair to an atom tool.

Then click on Nitrogen atom of Ammonia.

Observe the changes.

Point to the unbound electrons. Note that Nitrogen of Ammonia has a pair of electrons.

This pair does not take part in bonding.

This pair of electrons is lone pair.

Slide Number 6

Assignment

Assignment
  • Draw Phosphorus trichloride structure
  • Add a pair of un-bound electrons to the Phosphorus atom.
Let's now draw 'Carbonic acid(H2CO3) and Sulphuric acid(H2SO4) structures on the same window.
Slide Number 7

Structures of Carbonic acid and Sulphuric acid.

Here is a slide for the structures of Carbonic acid and Sulphuric acid.
Let's first draw Carbonic acid structure.
Click on the Current element arrow button>>Select C from the table. Click on the Current element arrow button.

Select C from the table.

Click on Add a bond or change the multiplicity of the existing one tool. Click on Add a bond or change the multiplicity of the existing one tool.
Click on the Display area.

Point to the orientation

Click on the Display area.

Orient three bonds in such a way that they form an inverted Y.

Point to the fourth bond. Draw fourth bond as a double bond to any one of the bonds.
Click on Current element drop down button. Now click on Current element drop down button.
Select O. Select O.
Click on Add or modify an atom tool Click on Add or modify an atom tool
Point to the cursor. Place the cursor near the bonds.
Click on the bond positions. Click on the three bond positions.

Carbonic acid(H2CO3) structure is drawn.

Let's draw the Sulphuric acid structure.
Click on Current element drop down button. Click on Current element drop down button.
Select S Select S
Click on Add or modify an atom tool>>Click on the Display area. Click on Add or modify an atom tool.

Then click on the Display area.

Observe H2S.

Click on the Display area>> Press capital O

A Submenu with O and Os opens.

Press capital O

A Submenu with 2 options O and Os opens.

Select O. Select O.
Click on Add or modify an atom tool>> click on Add a bond or change the multiplicity of the existiing one tool. Click on Add or modify an atom tool.

Then click on Add a bond or change the multiplicity of the existing one tool.

In the Property menu>>make the Bond length value to 200 or above. In the Property menu, increase the Bond length value to 200 or above.
Click on H2S to draw the three bonds. Click on H2S to draw the three bonds of OH to S.
Click on S and drag the bond to a side without releasing the mouse. For the fourth OH bond, first click on S.

Now drag the bond to one side without releasing the mouse button.

Point to plus 2 charge near S. Observe a plus 2 charge near S.

This appears because Sulphur has to satisfy valency of 6.

Point to any 2 opposite bonds. Let's convert the opposite bonds as double bonds.
Click on Add a bond or change the multiplicity of the existiing one tool>>click on the existing bonds. Click on Add a bond or change the multiplicity of the existing one tool.


Then click on the opposite existing bonds of the structure.

Point to the structure Note that the plus 2 charge is no longer visible.

Sulphuric acid structure is complete.

Next let's add a local charge on the Carbonic acid and Sulphuric acid structures.
Click on Decrement the charge of an atom tool. To show local charge, Click on Decrement the charge of an atom tool.
Click on two O-H groups. Click on the two O-H groups of the Carbonic acid.

Observe that Carbonate ion (CO32-) is formed.

Click on Decrement the charge of an atom tool. To show local charge on Sulphuric acid structure.

Click on Decrement the charge of an atom tool.

Click on the two opposite O-H groups. Click on the two opposite O-H groups of Sulphuric acid.

Observe that Sulphate (SO42-) is formed.

Slide Number 7

Assignment

* Draw Nitric acid (HNO3) structure
  • Show the local charge on the Nitrate ion(NO3-)

Your output should look like this.

Let me quickly demonstrate how to add a charge to an atom.
Press capital N'.

Point to the Submenu

Anywhere on the Display area', press capital N.

A Submenu opens in which let's select Na.

Click on Add or modify an atom tool>>Click on the Display area. Click on Add or modify an atom tool and then click on the Display area.

Na atom appears on the Display area.

Click on Increment the charge of a atom tool>>Click on Na. Click on Increment the charge of an atom tool.

Then Click on Na.

Observe a positive charge on the Sodium atom.

Point to Decrement the charge of an atom tool. In a similar way, we can add a negative charge to an atom.

This can be done by choosing Decrement the charge of an atom tool.

Now let's learn to draw Cyclic molecules.

For this, we will open a new GChemPaint window.

Click on Create a new file icon on the toolbar. Click on Create a new file icon on the toolbar.
Place the window within the recording area. Let me adjust the window position.
Ensure that C i.e. Carbon is selected as the current element.

Also, ensure that the Bond length is 200 or above.

Point to the cycle tools bar in the tool box There are various cycle tools here that we can use. 
For eg -
  • Add a three membered cycle
  • Add a four membered cycle
  • and some more cycle tools and then
  • Add a cycle.
Point to Add a four membered cycle tool We will use Add a four membered cycle' to the Display area.
Click on Add a four membered cycle tool>>Click on the Display area. So, click on it.

Then click on the Display area.

Let's add atoms to the cycle at the corners.
Right click on any one of the corners>>A Submenu opens. Right click any one of the corners.

A Submenu opens.

Select Atom>>Then click on Display symbol. Select Atom.

Then click on Display symbol.

Show this part fast. Likewise let's add atoms on all the corners. Obtained structure is Cyclobutane.
Let's now convert a monocyclic compoud to bicyclic compoud.
Click on Add a six membered cycle tool>> click on the Display area. Click on Add a six membered cycle tool.

Then click on the Display area.

Click on the cycle bond Place the cursor on the cycle's bond and click again.

Observe the Bicyclic compound.

Click on Save the current file icon on the toolbar. To save the file,

Click on Save the current file icon on the toolbar.

Save as dialog box opens. Save as dialog box opens.
Enter the filename as Editing Molecules>>Click on Save button. Enter the filename as Editing Molecules

Click on Save button.

Let's summarize.
Slide Number 8

Summary

In this tutorial, we have learnt to,
  • Add ubound electrons on an atom
  • Draw Carbonic acid and Sulphuric acid structures.
  • Add and modify a local charge on a group of atoms
Slide Number 9

Summary

We have also learnt to,
  • Add and modify a local charge on an atom
  • Add cyclic molecules
  • Convert monocyclic molecules to bicyclic molecules.
Slide Number 10

Assignment

As an assignment
  • Add cycloheptane ring to the Display area
  • Change it to tricyclic compound.
Slide Number 8

Acknowledgement

Watch the video available at this URL.

http://spoken-tutorial.org/ What_is_a_Spoken_Tutorial

It summarises the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.

Slide Number 9 The Spoken Tutorial Project Team:

Conducts workshops using spoken tutorials

Gives certificates to those who pass an online test

For more details, please write to

contact@spoken-tutorial.org

Slide number 10 Spoken Tutorial Project is a part of the Talk to a Teacher project

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

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

This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, PoojaMoolya

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