Difference between revisions of "GChemPaint/C2/Editing-molecules/English"
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* Draw '''Nitric acid (HNO<sub>3</sub>)''' structure | * Draw '''Nitric acid (HNO<sub>3</sub>)''' structure | ||
− | * Show the local charge on the '''Nitrate ion(NO<sup> | + | * Show the local charge on the '''Nitrate ion(NO<sup>-</sup><sub>3</sub>)''' |
Your completed assignment should look like this. | Your completed assignment should look like this. |
Revision as of 11:57, 8 September 2014
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
|
Slide Number 3
Learning Objectives |
We will also learn to,
|
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,
|
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,
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 -
|
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 dialogue box opens. | Save as dialogue 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,
|
Slide Number 10
Summary |
We have also learnt to,
|
Slide Number 11
Assignment |
As an assignment
|
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. |