GChemPaint/C2/Editing-molecules/English-timed

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

Time	Narration
00:01	Hello everyone.
00:02	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 using
00:35	Ubuntu 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,
02:21	* 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.
03:26	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.
03:48	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.
05:56	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 dialogue 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