GChemPaint/C2/Editing-molecules/English-timed
From Script | Spoken-Tutorial
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 Submenu 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 Submenu 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(NO3-) |
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 Submenu 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 Submenu 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 summarises 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