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

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(Created page with '{|border =1 !Visual Cue !Narration |- ||'''Slide Number 1''' ||Hello everyone. Welcome the tutorial on '''Editing Molecules''' in '''GChemPaint'''. |- ||'''Slide Number 2''' ''…')
 
 
(23 intermediate revisions by one other user not shown)
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 +
Title of the tutorial: Editing molecules
 +
 +
Author: Madhuri Ganapathi
 +
 +
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
 +
 +
 
{|border =1
 
{|border =1
 
!Visual Cue
 
!Visual Cue
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|-
 
|-
 
||'''Slide Number 1'''
 
||'''Slide Number 1'''
 +
 +
'''Title Slide'''
 
||Hello everyone.
 
||Hello everyone.
  
Line 15: Line 24:
 
* Add unbound electrons on an atom
 
* Add unbound electrons on an atom
  
−
* Draw Carbonic acid and Sulphuric acid structures.  
+
* Draw Carbonic acid and Sulphuric acid structures.  
  
 
* Add and modify a local charge on a group of atoms
 
* 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 and modify a local charge on an atom
Line 23: Line 37:
 
* Add cyclic molecules
 
* Add cyclic molecules
  
−
* Convert monocyclic molecules to bicyclic molecules.
+
* Convert mono-cyclic molecules to bi-cyclic molecules.
 
|-
 
|-
−
||'''Slide Number 3'''
+
||'''Slide Number 4'''
  
 
'''System Requirement'''
 
'''System Requirement'''
Line 34: Line 48:
 
'''GChemPaint''' version 0.12.10
 
'''GChemPaint''' version 0.12.10
 
|-
 
|-
−
||'''Slide Number 4'''
+
||'''Slide Number 5'''
  
 
'''Pre-requisites'''
 
'''Pre-requisites'''
Line 47: Line 61:
 
|-
 
|-
 
||
 
||
−
||Let's first draw an '''Ammonia''' structure.
+
||Let's first draw '''Ammonia''' structure.
−
|-
+
−
||Point to '''Periodic table combo''' button.
+
−
||For this I will use the '''Periodic table combo''' button.
+
 
|-
 
|-
 
||Click on  '''Current element''' drop down arrow button.
 
||Click on  '''Current element''' drop down arrow button.
 
||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.
 
||Select '''N''' from the table.
 
||Select '''N''' from the table.
 +
 +
Observe '''N''' in the tool box.
 
|-
 
|-
−
||Point to '''N'''
+
||Click on  '''Add or modify an atom''' tool
−
||Observe '''N''' in the tool box.
+
 
−
|-
+
>> click on '''Display area'''.
−
||Click on  '''Add or modify an atom''' tool>> click on '''Display area'''.
+
 
||Click on  '''Add or modify an atom''' tool.
 
||Click on  '''Add or modify an atom''' tool.
  
 
Then click on '''Display area'''.
 
Then click on '''Display area'''.
 
|-
 
|-
−
||Point to '''NH3'''
+
||Point to '''NH<sub>3</sub>'''
−
||Observe '''NH3''' on the '''Display area'''.
+
|| '''NH<sub>3</sub>''' is seen on the '''Display area'''.
 
|-
 
|-
 
||Press capital '''H'''.
 
||Press capital '''H'''.
Line 79: Line 91:
 
||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  thrice on the '''Nitrogen''' atom.
+
||Click on
−
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
+
 
 +
'''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 '''Nitrogen''' atom.
 +
||To draw three bonds to '''Nitrogen''' atom
  
−
Click and drag the bond thrice on '''Nitrogen''' atom.  
+
Click and drag the bonds thrice on '''Nitrogen''' atom.
 
|-
 
|-
 
||Point to the bonds
 
||Point to the bonds
−
||Orient the three bonds to form a '''Pyramid''' like structure.
+
||Orient the bonds to form a '''Pyramid''' like structure.
 
|-
 
|-
 
||
 
||
−
||Let's add a pair of  unbound electrons on  '''Nitrogen''' atom.
+
||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
 +
 
 +
>> click on the '''Nitrogen''' atom.
 
||Click on '''Add an electron pair to an atom''' tool.
 
||Click on '''Add an electron pair to an atom''' tool.
 +
 
Then click on '''Nitrogen''' atom of  '''Ammonia'''.
 
Then click on '''Nitrogen''' atom of  '''Ammonia'''.
  
Line 97: Line 119:
 
|-
 
|-
 
||Point to the unbound electrons.
 
||Point to the unbound electrons.
−
||Note that '''Nitrogen''' of '''Ammonia''' has a pair of  electrons that do not take part in bonding.
+
||Note that '''Nitrogen''' of '''Ammonia''' now has a pair of  electrons.
  
−
This pair of electrons is '''lone pair'''.
+
This pair does not take part in bonding.
 +
 
 +
This pair of electrons is '''lone pair'''.
 +
|-
 +
||'''Slide Number 6'''
 +
 
 +
'''Assignment'''
 +
||As an assignment,
 +
 
 +
* Draw Phosphorus trichloride structure
 +
 
 +
* Add a pair of un-bound electrons on the Phosphorus atom.  
 
|-
 
|-
 
||
 
||
−
||Let's now draw ''''Carbonic acid(H2CO3)''' and '''Sulphuric acid(H2SO4)''' structures on the same window.
+
||Now let's draw ''''Carbonic acid(H<sub>2</sub>CO<sub>3</sub>)''' and '''Sulphuric acid(H<sub>2</sub>SO<sub>4</sub>)''' structures.  
 
|-
 
|-
−
||Slide  Number
+
||'''Slide  Number 7'''
  
 
Structures of '''Carbonic acid''' and '''Sulphuric acid'''.
 
Structures of '''Carbonic acid''' and '''Sulphuric acid'''.
−
||Here is a slide for the structures of  '''Carbonic acid''' and '''Sulphuric acid'''.
+
||Here is a slide for,
 +
 
 +
'''Carbonic acid''' and '''Sulphuric acid''' structures.
 
|-
 
|-
 
||
 
||
−
||Let's move '''Ammonia(NH3)''' structure to aside.
+
||First let's move '''Ammonia'''structure aside.
−
|-
+
−
||Click on '''Select one or more objects''' tool>>Click on the structure and drag to aside
+
−
||Click on '''Select one or more objects'''  tool.
+
  
−
Click on the structure and drag to aside
+
To do so, click on '''Select one or more objects''' tool.
 +
 
 +
Then click on '''Ammonia''' structure and drag it to one side.
 
|-
 
|-
 
||
 
||
−
||Let's first draw '''Carbonic acid''' structure.
+
||Now let's 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 the '''Current element''' arrow button.
 
||Click on the '''Current element''' arrow button.
  
 
Select '''C''' from the table.
 
Select '''C''' from the table.
 
|-
 
|-
−
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
+
||Click on
−
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
+
 
 +
'''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'''.
 
||Click on the '''Display area'''.
Line 133: Line 173:
 
||Click on the '''Display area'''.
 
||Click on the '''Display area'''.
  
−
Orient three bonds in such a way that they form an inverted Y.
+
'''Orient''' three bonds in such a way that they form an inverted Y.
 
|-
 
|-
 
||Point to the fourth bond.
 
||Point to the fourth bond.
−
||Let's draw fourth bond as a double bond to any one of the bonds.
+
||Draw the fourth bond as a '''double bond''' to any one of the bonds.
 
|-
 
|-
−
||Click on '''Periodic table Combo''' button
+
||Click on '''Current element''' drop down  button.
−
||Now click on '''Periodic table Combo''' button
+
||Now click on '''Current element''' drop down button.
 
|-
 
|-
 
||Select '''O'''.
 
||Select '''O'''.
Line 148: Line 188:
 
|-
 
|-
 
||Point to the cursor.
 
||Point to the cursor.
−
||Place the cursor near the bonds.
+
||Place the cursor near the bonds.
 
|-
 
|-
 
||Click on the bond positions.
 
||Click on the bond positions.
 
||Click on the three bond positions.
 
||Click on the three bond positions.
  
−
'''Carbonic acid(H2CO3)''' structure is drawn.
+
'''Carbonic acid(H<sub>2</sub>CO<sub>3</sub>)''' structure is drawn.
 
|-
 
|-
 
||
 
||
−
||Let's draw the '''Sulphuric acid''' structure.  
+
||Now let's draw '''Sulphuric acid''' structure.  
 
|-
 
|-
−
||Click on '''Periodic table Combo''' button.
+
||Click on '''Current element''' drop down button.
−
||Click on '''Periodic table Combo''' button.
+
||Click on '''Current element''' drop down button.
 
|-
 
|-
 
||Select '''S'''
 
||Select '''S'''
 
||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
−
Point to H2S.
+
 
 +
>>Click on the '''Display area'''.
 
||Click on  '''Add or modify an atom''' tool.
 
||Click on  '''Add or modify an atom''' tool.
−
Click on the '''Display area'''.
+
 
−
Observe '''H2S'''.
+
Then click on '''Display area'''.
 +
 
 +
Observe '''H<sub>2</sub>S'''.
 
|-
 
|-
−
||Press  capital '''O'''  
+
||Click on the Display area>> Press  capital '''O'''  
  
 
A '''Submenu''' with '''O''' and '''Os''' opens.
 
A '''Submenu''' with '''O''' and '''Os''' opens.
−
||Press capital '''O'''  
+
||Now anywhere on the '''Display area''' press capital '''O'''  
−
A '''Submenu''' with '''O''' and '''Os''' opens.
+
 
 +
A '''Submenu''' with 2 options '''O''' and '''Os''' opens.
 
|-
 
|-
 
||Select '''O'''.
 
||Select '''O'''.
 
||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
 +
 
 +
>> click on '''Add a bond or change the multiplicity of the existing one''' tool.  
 
||Click on  '''Add or modify an atom''' tool.
 
||Click on  '''Add or modify an atom''' tool.
  
−
Then click on '''Add a bond or change the multiplicity of the existing one''' tool.  
+
Then click on  
 +
 
 +
'''Add a bond or change the multiplicity of the existing one''' tool.  
 
|-
 
|-
−
||Click on '''H2S''' to draw the three bonds of '''OH''' to '''S'''.
+
||In the '''Property''' menu
−
||Click on '''H2S''' to draw the three bonds of OH to '''S'''.
+
 
 +
>>make the '''Bond length value''' to 200 or above.
 +
||In the '''Property''' menu,
 +
 
 +
increase the '''Bond length''' value to 200 or above.
 +
|-
 +
||Click on '''H<sub>2</sub>S''' to draw  three bonds.
 +
||Click on '''H<sub>2</sub>S''' to draw three bonds of '''OH''' to '''S'''.
 +
|-
 +
 
 +
||Point to positive charge near S.
 +
|| Observe a  positive charge near S. 
 +
 
 +
This appears because '''Sulphur''' has to satisfy '''valency''' of 6.
 
|-
 
|-
 
||Click on '''S''' and drag the bond to a side without releasing the mouse.  
 
||Click on '''S''' and drag the bond to a side without releasing the mouse.  
−
||To draw the fourth '''OH''' bond,
+
||For the fourth bond, first click on '''S''' .
  
−
click on '''S''' and drag the bond to a side without releasing the mouse.
+
Now drag the bond to one side without releasing the mouse.
 
|-
 
|-
−
||  
+
||Point to any 2 opposite bonds.
−
||Let's convert the opposite '''OH''' bonds as double bonds as shown in the slide.
+
||Now let's convert the opposite bonds  into '''double bonds'''.
 
|-
 
|-
−
||Click on '''Add a bond or change the multiplicity of the existiing one''' tool>>click on the existing bonds.
+
||Click on
−
||Click on '''Add a bond or change the multiplicity of the existing one''' tool.
+
  
 +
'''Add a bond or change the multiplicity of the existing 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.  
 
Then click on the opposite existing bonds of the structure.  
 +
|-
 +
||Point to the structure
 +
||Note that the positive charge is no longer visible.
  
−
'''Sulphuric acid''' structure is drawn.
+
'''Sulphuric acid''' structure is complete.
 
|-
 
|-
 
||
 
||
Line 207: Line 276:
 
|-
 
|-
 
||Click on '''Decrement the charge of an atom''' tool.
 
||Click on '''Decrement the charge of an atom''' tool.
−
||To show local charge on '''Carbonic acid'''.
+
||To show local charge, Click on '''Decrement the charge of an atom''' tool.
−
 
+
−
Click on '''Decrement the charge of an atom''' tool.
+
 
|-
 
|-
 
||Click on two  '''O-H''' groups.
 
||Click on two  '''O-H''' groups.
−
||Click on the two '''O-H''' groups of the '''Carbonic acid'''.   
+
||Click on the two '''O-H''' groups of the '''Carbonic acid''' structure.   
−
Observe that '''Carbonate ion''' is formed.
+
 
 +
Observe that '''Carbonate ion (CO<sub>3</sub><sup>2-</sup>)''' is formed.
 
|-
 
|-
 
||Click on '''Decrement the charge of an atom''' tool.
 
||Click on '''Decrement the charge of an atom''' tool.
Line 223: Line 291:
 
||Click on the two opposite  '''O-H''' groups of '''Sulphuric acid'''.
 
||Click on the two opposite  '''O-H''' groups of '''Sulphuric acid'''.
  
−
Observe that '''Sulphate''' is formed.
+
Observe that '''Sulphate ion (SO<sub>4</sub><sup>2-</sup>)''' is formed.
 
|-
 
|-
−
||'''Slide Number 5'''
+
||'''Slide Number 8'''
  
 
'''Assignment'''
 
'''Assignment'''
−
||* Draw '''Nitric acid''' structure(HNO3)
+
||As an assignment,
  
−
* Show the local charge on the '''Nitrate ion'''(NO3-)
+
* Draw '''Nitric acid (HNO<sub>3</sub>)''' structure
  
−
Your output should look like this.
+
* Show the local charge on the '''Nitrate ion(NO<sup>-</sup><sub>3</sub>)'''
 +
 
 +
Your completed assignment should look like this.
 
|-
 
|-
 
||
 
||
−
||Let's now show the charges on '''Sodium''' and '''Chlorine''' atoms.
+
||Let me quickly demonstrate how to add a local charge on an atom.
 
|-
 
|-
−
||Press capital ''N'''.
+
||Press capital '''N'''.
  
 
Point to the '''Submenu'''
 
Point to the '''Submenu'''
−
||Press capital ''N'''.
+
||Anywhere on the '''Display area''', press capital '''N'''.
  
−
A '''Submenu''' opens in which let's select '''Na'''.
+
A '''Submenu''' opens in which we will select '''Na'''.
 
|-
 
|-
−
||Click on '''Add or modify an atom''' tool>>Click on the '''Display area'''.
+
||Click on '''Add or modify an atom''' tool
−
||Click on '''Add or modify an atom''' tool.
+
  
−
Click on the '''Display area'''.
+
>>Click on the '''Display area'''.
 +
||Click on '''Add or modify an atom''' tool
  
−
Na atom is displayed on the '''Display area'''.
+
Then click on the '''Display area'''.
 +
 
 +
Sodium 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
 +
 
 +
>>Click on '''Na'''.
 
||Click on '''Increment the charge of an atom''' tool.
 
||Click on '''Increment the charge of an atom''' tool.
  
Line 258: Line 332:
 
Observe a positive charge on the '''Sodium''' atom.
 
Observe a positive charge on the '''Sodium''' atom.
 
|-
 
|-
−
||Point to the list
+
||Point to Decrement the charge of an atom tool.
−
||Likewise press capital '''C'''.
+
||In a similar way, we can add a '''negative''' charge to an atom.
  
−
A '''Submenu''' opens in which let's select '''Cl'''.
+
This can be done by choosing '''Decrement the charge of an atom''' tool.
 
|-
 
|-
−
||Click on the ''''Display area'''.
+
||
−
||Click on the '''Display area'''.
+
||Now let's learn to draw '''Cyclic''' molecules.
  
−
Observe '''HCl''' on the '''Display area'''.
+
For this, we will open a new GChemPaint window.
 
|-
 
|-
−
||Click '''Decrement the charge of a atom''' tool>>Click on '''HCl'''.
+
||Click on '''Create a new file''' icon on the toolbar.
−
||Click  '''Decrement the charge of an atom''' tool.
+
||Click on '''Create a new file''' icon on the toolbar.
−
 
+
−
Click on '''HCl'''.
+
−
 
+
−
Observe a negative charge on the '''Chlorine''' atom.
+
−
|-
+
−
||Click on '''Periodic table combo''' button.
+
−
||Let's change the current element to '''Carbon'''.
+
−
 
+
−
Click on '''Periodic table combo''' button.
+
 
|-
 
|-
 
||
 
||
−
||Now let's learn to draw '''Cyclic''' molecules.
+
||Ensure that '''C''' that is '''Carbon''' is selected as element.
−
|-
+
−
||Click on '''Create a new file''' icon on the toolbar.
+
−
||Let's open a new window.
+
  
−
Click on '''Create a new file''' icon on the toolbar.
+
Also, ensure that  '''Bond length''' is 200 or above.
 
|-
 
|-
−
||Point to the tool box
+
||Point to the cycle tools bar in the  tool box
 +
||The Fourth toolbar in the tool box is '''Cycle''' tool
 +
 
 +
There are various  tools here that we can use.
 +
 
 +
For eg -
  
−
Point to differenet tools
 
−
||Observe different cycle tools on tool box.
 
 
* '''Add a three membered cycle'''
 
* '''Add a three membered cycle'''
  
 
* '''Add a four membered cycle'''
 
* '''Add a four membered cycle'''
  
−
* '''Add a five membered cycle'''
+
* and some more '''cycle''' tools and then
−
 
+
−
* '''Add a six membered cycle'''
+
−
 
+
−
* '''Add a seven membered cycle'''
+
−
 
+
−
* '''Add a eight membered cycle'''
+
  
 
* '''Add a cycle'''.
 
* '''Add a cycle'''.
 
|-
 
|-
−
||
+
||Point to  '''Add a four membered cycle''' tool
−
||Let's now add a  four membered cycle to the '''Display area'''.
+
||We will use '''Add a  four membered cycle'''.
 
|-
 
|-
−
||Click on '''Add a four membered cycle''' tool>>Click on the '''Display area'''.
+
||Click on '''Add a four membered cycle''' tool
−
||Click on '''Add a four membered cycle''' tool.
+
  
−
Click on the '''Display area'''.
+
>>Click on the '''Display area'''.
 +
||So, click on it.
 +
 
 +
Then click on the '''Display area'''.
 
|-
 
|-
 
||
 
||
−
||Let's now add atoms to the cycle at the corners.
+
||Let's add atoms to the cycle at the corners.
 
|-
 
|-
−
||Right click on any one of the corners>>A '''Submenu''' opens.
+
||Right click on any one of the corners
 +
 
 +
>>A '''Submenu''' opens.
 
||Right click any one of the corners.
 
||Right click any one of the corners.
  
 
A '''Submenu''' opens.
 
A '''Submenu''' opens.
 
|-
 
|-
−
||Select '''Atom'''>>Then click on '''Display symbol'''.
+
||Select '''Atom'''
 +
 
 +
>>Then click on '''Display symbol'''.
 
||Select '''Atom'''.
 
||Select '''Atom'''.
  
 
Then click on '''Display symbol'''.
 
Then click on '''Display symbol'''.
 
|-
 
|-
−
||Point to the corners.
+
||Show this part fast.
−
||Likewise let's add atoms on all the corners. Obtained structure is '''Cyclobutane'''.
+
||Likewise let's add atoms on all the corners.  
 +
 
 +
Obtained structure is '''Cyclobutane'''.
 
|-
 
|-
 
||
 
||
−
||Let's now convert a monocyclic compoud to bicyclic compoud.
+
||Let's now convert a mono-cyclic compound to bi-cyclic compound.
 
|-
 
|-
−
||Click on '''Add a six membered cycle''' tool>> click on the '''Display area'''.
+
||Click on '''Add a six membered cycle''' tool
 +
 
 +
>> click on the '''Display area'''.
 
||Click on '''Add a six membered cycle''' tool.
 
||Click on '''Add a six membered cycle''' tool.
  
−
Then click on the '''Display area'''.
+
Then click on '''Display area'''.
 
|-
 
|-
 
||Click on the cycle bond
 
||Click on the cycle bond
 
||Place the cursor on the cycle's bond and click again.
 
||Place the cursor on the cycle's bond and click again.
  
−
Observe the '''Bicyclic compound'''.
+
Observe the '''Bi-cyclic compound'''.
 
|-
 
|-
 
||Click on '''Save the current file''' icon on the toolbar.
 
||Click on '''Save the current file''' icon on the toolbar.
Line 351: Line 420:
 
||'''Save as''' dialog box opens.
 
||'''Save as''' dialog box opens.
 
|-
 
|-
−
||Enter the filename as '''Editing Molecules'''>>Click on '''Save''' button.
+
||Enter the file name as '''Editing Molecules'''
−
||Enter the filename as '''Editing Molecules'''
+
 
 +
>>Click on '''Save''' button.
 +
||Enter the file name as '''Editing Molecules'''
  
 
Click on '''Save''' button.
 
Click on '''Save''' button.
 
|-
 
|-
 
||
 
||
−
||Let's summarize what we have learnt.
+
||Let's summarize.
 
|-
 
|-
−
||'''Slide Number 6'''
+
||'''Slide Number 9'''
  
 
'''Summary'''
 
'''Summary'''
 
||In this tutorial, we have learnt to,
 
||In this tutorial, we have learnt to,
  
−
*  Add ubound electrons on an atom
+
*  Add unbound electrons on an atom
  
 
*  Draw  Carbonic acid and Sulphuric acid structures.  
 
*  Draw  Carbonic acid and Sulphuric acid structures.  
  
 
*  Add and modify a local charge on a group of atoms
 
*  Add and modify a local charge on a group of atoms
 +
|-
 +
||'''Slide Number 10'''
 +
 +
'''Summary'''
 +
||We have also learnt to,
  
 
*  Add and modify a local charge on an atom
 
*  Add and modify a local charge on an atom
Line 374: Line 450:
 
*  Add cyclic molecules
 
*  Add cyclic molecules
  
−
*  Convert monocyclic molecules to bicyclic molecules.
+
*  Convert mono-cyclic molecules to bi-cyclic molecules.
 
|-
 
|-
−
||'''Slide Number 7'''
+
||'''Slide Number 11'''
  
 
'''Assignment'''
 
'''Assignment'''
 
||As an assignment
 
||As an assignment
  
−
* Add cycloheptane ring to the Display area  
+
* Add a seven membered cycle to the Display area  
−
* Change it to tricyclic compound.  
+
 
−
Your completed assignment's output should look like this. 
+
* Change it to a tricyclic compound.  
 
|-
 
|-
−
||'''Slide Number 8'''
+
||'''Slide Number 12'''
  
 
'''Acknowledgement'''  
 
'''Acknowledgement'''  
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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.
 
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||The Spoken Tutorial Project Team:  
 
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It is supported by the National Mission on Education through ICT, MHRD, Government of India
 
It is supported by the National Mission on Education through ICT, MHRD, Government of India
  
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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  
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'''http://spoken-tutorial.org/NMEICT-Intro '''
  
 
This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
 
This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining.  
 
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Latest revision as of 15:11, 28 October 2020

Title of the tutorial: Editing molecules

Author: Madhuri Ganapathi

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


Visual Cue Narration
Slide Number 1

Title Slide

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 mono-cyclic molecules to bi-cyclic 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 Nitrogen atom. To draw three bonds to Nitrogen atom

Click and drag the bonds thrice on Nitrogen atom.

Point to the bonds Orient the 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 now has a pair of electrons.

This pair does not take part in bonding.

This pair of electrons is lone pair.

Slide Number 6

Assignment

As an assignment,
  • Draw Phosphorus trichloride structure
  • Add a pair of un-bound electrons on the Phosphorus atom.
Now let's draw 'Carbonic acid(H2CO3) and Sulphuric acid(H2SO4) structures.
Slide Number 7

Structures of Carbonic acid and Sulphuric acid.

Here is a slide for,

Carbonic acid and Sulphuric acid structures.

First let's move Ammoniastructure aside.

To do so, click on Select one or more objects tool.

Then click on Ammonia structure and drag it to one side.

Now let's 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 the 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.

Now let's draw 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 Display area.

Observe H2S.

Click on the Display area>> Press capital O

A Submenu with O and Os opens.

Now anywhere on the Display area 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 existing 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 three bonds. Click on H2S to draw three bonds of OH to S.
Point to positive charge near S. Observe a positive charge near S.

This appears because Sulphur has to satisfy valency of 6.

Click on S and drag the bond to a side without releasing the mouse. For the fourth bond, first click on S .

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

Point to any 2 opposite bonds. Now let's convert the opposite bonds into double bonds.
Click on

Add a bond or change the multiplicity of the existing 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 positive 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 structure.

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 ion (SO42-) is formed.

Slide Number 8

Assignment

As an assignment,
  • Draw Nitric acid (HNO3) structure
  • Show the local charge on the Nitrate ion(NO-3)

Your completed assignment should look like this.

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

Point to the Submenu

Anywhere on the Display area, press capital N.

A Submenu opens in which we will select Na.

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.

Sodium atom appears on the Display area.

Click on Increment the charge of an 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.
Ensure that C that is Carbon is selected as element.

Also, ensure that Bond length is 200 or above.

Point to the cycle tools bar in the tool box The Fourth toolbar in the tool box is Cycle tool

There are various 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.
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 mono-cyclic compound to bi-cyclic compound.
Click on Add a six membered cycle tool

>> click on the Display area.

Click on Add a six membered cycle tool.

Then click on Display area.

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

Observe the Bi-cyclic 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 file name as Editing Molecules

>>Click on Save button.

Enter the file name as Editing Molecules

Click on Save button.

Let's summarize.
Slide Number 9

Summary

In this tutorial, we have learnt 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 10

Summary

We have also learnt to,
  • Add and modify a local charge on an atom
  • Add cyclic molecules
  • Convert mono-cyclic molecules to bi-cyclic molecules.
Slide Number 11

Assignment

As an assignment
  • Add a seven membered cycle to the Display area
  • Change it to a tricyclic compound.
Slide Number 12

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 13 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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