Difference between revisions of "GChemPaint/C2/Editing-molecules/English"
Line 4: | Line 4: | ||
|- | |- | ||
||'''Slide Number 1''' | ||'''Slide Number 1''' | ||
+ | |||
+ | '''Title Slide''' | ||
||Hello everyone. | ||Hello everyone. | ||
Line 23: | Line 25: | ||
'''Learning Objectives''' | '''Learning Objectives''' | ||
||We will also learn to, | ||We will also learn to, | ||
+ | |||
* Add and modify a local charge on an atom | * Add and modify a local charge on an atom | ||
Line 58: | Line 61: | ||
||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. | Observe N in the tool box. | ||
|- | |- | ||
Line 83: | Line 87: | ||
||Click and drag the bonds thrice on the Nitrogen atom. | ||Click and drag the bonds thrice on the Nitrogen atom. | ||
||To draw threee bonds to Nitrogen atom | ||To draw threee bonds to Nitrogen atom | ||
+ | |||
Click and drag the bonds thrice on Nitrogen atom. | Click and drag the bonds thrice on Nitrogen atom. | ||
|- | |- | ||
Line 93: | Line 98: | ||
||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 102: | Line 108: | ||
This pair does not take part in bonding. | This pair does not take part in bonding. | ||
− | + | It is a '''lone pair''' of electrons. | |
|- | |- | ||
||'''Slide Number 6''' | ||'''Slide Number 6''' | ||
Line 114: | Line 120: | ||
|- | |- | ||
|| | || | ||
− | ||Let's now draw ''''Carbonic acid(H2CO3)''' and '''Sulphuric acid(H2SO4)''' | + | ||Let's now draw ''''Carbonic acid(H2CO3)''' and '''Sulphuric acid(H2SO4)'''. |
|- | |- | ||
||'''Slide Number 7''' | ||'''Slide Number 7''' | ||
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||Let's convert the opposite bonds as '''double 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 existiing one''' tool>> |
+ | |||
+ | click on the existing bonds. | ||
||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. | ||
Line 227: | Line 235: | ||
||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'''. | ||
+ | |||
Observe that '''Carbonate ion (CO32-)''' is formed. | Observe that '''Carbonate ion (CO32-)''' is formed. | ||
|- | |- | ||
Line 237: | Line 246: | ||
||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 ( | + | Observe that '''Sulphate ion (SO_4^2-)''' is formed. |
|- | |- | ||
||'''Slide Number 7''' | ||'''Slide Number 7''' | ||
Line 244: | Line 253: | ||
||* Draw '''Nitric acid (HNO3)''' structure | ||* Draw '''Nitric acid (HNO3)''' structure | ||
− | * Show the local charge on the '''Nitrate ion( | + | * Show the local charge on the '''Nitrate ion(NO^3-)''' |
Your output should look like this. | Your output should look like this. | ||
Line 261: | Line 270: | ||
||Click on '''Add or modify an atom''' tool and then click on the '''Display area'''. | ||Click on '''Add or modify an atom''' tool and 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 a atom''' tool>>Click on '''Na'''. | ||
Line 298: | Line 307: | ||
* '''Add a four membered cycle''' | * '''Add a four membered cycle''' | ||
− | *and some more '''cycle tools''' and then | + | * and some more '''cycle tools''' and then |
* '''Add a cycle'''. | * '''Add a cycle'''. | ||
Line 324: | Line 333: | ||
|- | |- | ||
||Show this part fast. | ||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'''. | ||
|- | |- | ||
|| | || | ||
Line 347: | Line 358: | ||
||'''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. | ||
||Enter the filename as '''Editing Molecules''' | ||Enter the filename as '''Editing Molecules''' | ||
Line 366: | Line 379: | ||
* Add and modify a local charge on a group of atoms | * Add and modify a local charge on a group of atoms | ||
|- | |- | ||
− | + | ||'''Slide Number 9''' | |
'''Summary''' | '''Summary''' | ||
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* Add cycloheptane ring to the Display area | * Add cycloheptane ring to the Display area | ||
+ | |||
* Change it to tricyclic compound. | * Change it to tricyclic compound. | ||
|- | |- |
Revision as of 13:06, 2 August 2013
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 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. It is a lone pair of electrons. |
Slide Number 6
Assignment |
Assignment
|
Let's now draw 'Carbonic acid(H2CO3) and Sulphuric acid(H2SO4). | |
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.
|
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 ion (SO_4^2-) is formed. |
Slide Number 7
Assignment |
* Draw Nitric acid (HNO3) structure
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.
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.
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 -
|
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,
|
Slide Number 9
Summary |
We have also learnt to,
|
Slide Number 10
Assignment |
As an assignment
|
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. |