Difference between revisions of "GChemPaint/C3/Orbital-Overlap/English-timed"
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| + | Title of the tutorial: Orbital Overlap | ||
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| + | Author: Madhuri Ganapathi | ||
| + | |||
| + | Key words: Atomic orbital, Add or modify an atomic orbital tool, rotation and resize of orbitals, positive, negative overlaps and zero overlap, Video tutorial | ||
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|'''Time''' | |'''Time''' | ||
Revision as of 16:52, 12 August 2014
Title of the tutorial: Orbital Overlap
Author: Madhuri Ganapathi
Key words: Atomic orbital, Add or modify an atomic orbital tool, rotation and resize of orbitals, positive, negative overlaps and zero overlap, Video tutorial
| Time | Narration |
| 00:00 | Hello everyone. |
| 00:01 | Welcome to this tutorial on Orbital Overlap in GChemPaint. |
| 00:06 | In this tutorial, we will learn |
| 00:08 | * About different types of orbitals |
| 00:11 | * Rotation and resize of orbitals |
| 00:14 | * Types of orbital overlaps |
| 00:17 | Here I am using Ubuntu Linux OS version 12.04. |
| 00:21 | GChemPaint version 0.12.10. |
| 00:26 | To follow this tutorial, you should be familiar with |
| 00:31 | GChemPaint chemical structure editor. |
| 00:34 | If not, for relevant tutorials, please visit our website. |
| 00:38 | Let us first see what an atomic orbital is. |
| 00:42 | An atomic orbital is a mathematical function. |
| 00:46 | It describes the wave-like behavior of an electron in an atom. |
| 00:52 | An orbital is a region of space with maximum probability of finding an electron. |
| 00:58 | This is an 's' orbital. |
| 01:00 | It has spherical shape. |
| 01:03 | Here are 'p' orbitals in different axes. |
| 01:06 | 'p' orbitals are "dumb-bell" shaped. |
| 01:09 | Next, we have 'd' orbitals in different axes. |
| 01:13 | 'd' orbitals are double "dumb-bell" shaped. |
| 01:17 | I have opened a new GChemPaint application. |
| 01:20 | Let us first learn about orbitals. |
| 01:24 | Click on Add or modify an atomic orbital tool. |
| 01:28 | Orbital property window opens. |
| 01:30 | This window contains fields like- Coefficient, Rotation and Type. |
| 01:36 | First, I will begin with Type. |
| 01:40 | By default, 's' orbital is selected. |
| 01:42 | Let us click on p, d xy and d z square orbital radio buttons. |
| 01:50 | Notice the different orbital shapes displayed alongside. |
| 01:54 | Next let us check the Coefficient and Rotation properties. |
| 01:59 | Coefficient property has values from -1.00 to 1.00. |
| 02:04 | Using Coefficient field values, we can vary the size of the orbital. |
| 02:10 | Notice that the size of the orbital alongside, has changed. |
| 02:15 | Rotation property has values from -180(minus) to 180. |
| 02:20 | We can rotate the orbitals clockwise or anticlockwise. |
| 02:25 | Values can be changed by using the up or down arrows. |
| 02:30 | Let us see how to use orbitals to show different types of Positive overlaps. |
| 02:36 | Here is a slide for Positive overlap of different orbitals. |
| 02:40 | 's-s'overlap, 's-p'overlap, 'p-p'overlap and 'p-p' side-wise overlap. |
| 02:51 | Let us draw Hydrogen molecule on the Display area. |
| 02:55 | Press H on the keyboard. |
| 02:58 | Set the Co-efficient value to one. |
| 03:01 | Click on Add or modify an atom tool. |
| 03:04 | Click Add a bond tool. |
| 03:07 | Ensure that bond length is around 130. |
| 03:11 | Click on the Display area. |
| 03:14 | Hydrogen molecule is formed. |
| 03:17 | Let's start with 's-s' end-on overlap. |
| 03:20 | Click on Add or modify an atomic orbital tool. |
| 03:24 | Click on 's' orbital, |
| 03:28 | Then click on Hydrogen atoms of Hydrogen molecule. |
| 03:33 | Observe 's-s' end-on overlap. |
| 03:35 | Now to 'p-p' end-on overlap. |
| 03:38 | Press F on the keyboard. |
| 03:42 | Click on Add or modify an atom tool. |
| 03:45 | Click Add a bond tool. |
| 03:49 | Ensure that bond length is around 200. |
| 03:53 | Click on the Display area. |
| 03:56 | Fluorine molecule is formed. |
| 03:59 | Click on Add or modify an atomic orbital tool. |
| 04:02 | Click on the 'p' orbital. |
| 04:05 | To form 'p-p' end-on overlap, we need 'p' orbitals in horizontal direction. |
| 04:11 | Let us increase the Rotation value to 90. |
| 04:15 | Click on the 'p' orbital. |
| 04:18 | Click on one Fluorine atom. |
| 04:21 | Likewise, repeat the process and rotate the 'p' orbital to '-90'(minus90). |
| 04:27 | Click on the other Fluorine atom. |
| 04:30 | In case you are not able to view the orbital clearly, you can resize the orbital. |
| 04:36 | To do so, we have to change the Coefficient value. |
| 04:40 | Right click on the orbital, select Orbital then click on Properties. |
| 04:46 | Orbital properties dialog box opens. |
| 04:50 | Reduce the Coefficient value till you see a proper overlap. |
| 04:54 | Click on Close button |
| 04:57 | I will repeat the process for the other orbital |
| 05:01 | Observe 'p-p' end-on overlap. |
| 05:04 | Now to 'd-d' end-on overlap using 'dz^2' orbital. |
| 05:09 | Come to the Display Area and press capital F on the keyboard. |
| 05:14 | Select Fe from the list. |
| 05:17 | Click on Add or modify an atom tool. |
| 05:20 | Click on the Display area. |
| 05:23 | Click on Add a bond tool. |
| 05:26 | Click on iron atom(Fe) to draw a bond. |
| 05:29 | Click on Add or modify an atomic orbital tool. |
| 05:32 | Select 'dz^2' orbital radio button. |
| 05:37 | For proper overlap, decrease the Coefficient value to 0.8. |
| 05:42 | Click on the bonded Iron atoms to overlap "dz^2" orbitals. |
| 05:49 | Observe 'd-d' end-on overlap. |
| 05:52 | Now let's learn about side-wise overlap of 'p' orbitals. |
| 05:57 | Ensure that current element is Carbon. |
| 06:02 | Click on Add a bond tool. |
| 06:05 | Ensure Bond length is around 90. |
| 06:08 | Click on the Display area. |
| 06:12 | Click on Add or modify an atomic orbital tool. |
| 06:16 | Increase the Coefficient value to one |
| 06:20 | Click on 'p' orbital radio button. |
| 06:23 | Rotate the 'p' orbital to vertical position if it is in horizontal position. |
| 06:29 | Click on the edges of the bonds. |
| 06:32 | Observe the 'p-p' side-wise overlap. |
| 06:37 | In this type of overlap, lobes of orbitals are of same sign. |
| 06:43 | Next, we will move to negative and zero overlaps. |
| 06:46 | Here is a slide for negative overlaps. |
| 06:51 | I have opened a new GChempaint application. |
| 06:55 | Now, I will demonstrate how to draw a negative overlap. |
| 06:59 | Click on Add a bond tool. |
| 07:02 | Ensure that Bond length is around 90. |
| 07:05 | Click on the Display area. |
| 07:08 | Click on Add or modify an atomic orbital tool. |
| 07:12 | Click on 'p' orbital radio button then click on one edge of the bond. |
| 07:17 | Rotate the 'p' orbital to 180 degree to flip it upside down. |
| 07:23 | Then click other edge of the bond. |
| 07:27 | Observe negative overlap. |
| 07:29 | In this type of overlap, lobes of orbitals are of opposite sign. |
| 07:34 | Now, let's learn how to create a zero overlap. |
| 07:38 | Here is a slide for zero overlap. |
| 07:42 | Click on Add a bond tool. |
| 07:45 | Click on the Display area. |
| 07:48 | Click on Add or modify an atomic orbital tool. |
| 07:52 | Click on the 'p' orbital. |
| 07:54 | Rotate the 'p' orbital to original position. |
| 07:59 | Click on one edge of the bond. |
| 08:02 | Click on 's' orbital |
| 08:05 | and then click on other edge of the bond. |
| 08:09 | Observe zero overlap. |
| 08:12 | In this type of overlap, orientation of the orbitals is not same. |
| 08:17 | Let us summarize what we have learnt. |
| 08:20 | In this tutorial we have learnt, * About different types of orbitals |
| 08:24 | * End-on and side-wise overlaps |
| 08:27 | * Rotation and resize of orbitals |
| 08:30 | * Positive, negative and zero overlap. |
| 08:34 | Here is an assignment. |
| 08:36 | * Draw 's-p' end-on overlap with Hydrogen chloride(H-Cl) molecule |
| 08:40 | * Draw side-wise overlap of 'dxy-dxy' orbitals |
| 08:44 | * Draw other negative and zero overlaps. |
| 08:48 | * Hint: Rotate and resize the orbitals for proper overlap. |
| 08:56 | Your completed assignment should look like this. |
| 09:00 | Watch the video available at this URL http://spoken-tutorial.org/What_is_a_Spoken_Tutorial |
| 09:04 | It summarizes the Spoken Tutorial project |
| 09:07 | If you do not have good bandwidth, you can download and watch it |
| 09:12 | The Spoken Tutorial Project Team Conducts workshops using spoken tutorials |
| 09:16 | Gives certificates to those who pass an on-line test |
| 09:20 | For more details, please write to contact@spoken-tutorial.org |
| 09:27 | Spoken Tutorial Project is a part of the Talk to a Teacher project |
| 09:31 | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
| 09:37 | More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro |
| 09:43 | Drawings are contributed by Arathi |
| 09:45 | This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining. |
