Jmol Application/C2/Create-and-edit-molecular-models/English-timed
From Script | Spoken-Tutorial
Title of script: Create and Edit Molecular models
Author: Snehalatha Kaliappan
Keyword: 3D models of chemical structures, molecular visualization, video tutorial.
| Time | Narration |
| 00:01 | Hello everyone.
Welcome to this tutorial on Create and Edit molecular models in Jmol Application. |
| 00:09 | In this tutorial, we will learn to, |
| 00:12 | * Substitute hydrogen atom in a molecular model with a functional group. |
| 00:17 | * Add and delete bonds. |
| 00:20 | * Add and delete atoms. |
| 00:23 | * and learn how to use the Pop-up menu also known as contextual menu. |
| 00:29 | To follow this tutorial you should be familiar with, |
| 00:32 | * Jmol Application window and |
| 00:36 | * Modelkit function that is used to create molecular models |
| 00:41 | For relevant tutorials, please visit our website. |
| 00:46 | To record this tutorial, I am using |
| 00:49 | * Ubuntu OS version. 12.04 |
| 00:53 | * Jmol version 12.2.2 |
| 00:57 | * And Java version 7. |
| 01:00 | To open the Jmol Application, click on Dash home. |
| 01:05 | Type Jmol in the search box. |
| 01:08 | Jmol icon appears on the screen |
| 01:11 | Click on the Jmol icon to open the Jmol application window. |
| 01:17 | Let's begin with the model of Propane, which we had created earlier. |
| 01:22 | To open the file, click on “Open file” icon on the tool bar. |
| 01:27 | A dialog box appears on the screen. |
| 01:30 | Click on the folder where the required file is located. |
| 01:34 | My file is located on the Desktop. |
| 01:37 | So, I will select Desktop and click on the Open button. |
| 01:43 | Type the file name in the “File or URL” text box. |
| 01:48 | Then, click on the Open button. |
| 01:51 | The Model of Propane appears on screen. |
| 01:55 | We can substitute hydrogens in the Propane with functional groups like: |
| 01:59 | hydroxy, amino, halogens like fluro, chloro, bromo and others. |
| 02:07 | I want to add a hydroxy group to the Propane molecule, to convert it to Propanol. |
| 02:13 | Open the model kit menu. A list of functional groups is available here. |
| 02:20 | Check the box against oxygen atom. |
| 02:23 | Click on the hydrogen atom attached to the first carbon atom. |
| 02:28 | Observe that the hydrogen atom is replaced by hydroxy group. Oxygen atom is seen in red color here. |
| 02:37 | Propane is now converted to 1-Propanol. |
| 02:41 | Let's now try to convert 1-Propanol to 2-chloro-1-propanol. |
| 02:47 | Select Chloro group from the model kit menu. |
| 02:51 | Click on the hydrogen atom attached to the second carbon atom. |
| 02:57 | We now have the model of 2-chloro-1-propanol. Chlorine is seen in green color here. |
| 03:04 | You can do energy minimization and save the image as dot mol file. |
| 03:10 | Here is an assignment. |
| 03:11 | * Create models of the following molecules.3-bromo-1-butanol and 2-amino-4-chloro-pentane |
| 03:20 | * Do energy minimization and save the image in JPEG format. |
| 03:25 | To save the image in different file formats: |
| 03:28 | Use “Save current view as an image” icon in the Tool bar. |
| 03:33 | Your completed assignment should look as follows |
| 03:40 | Now lets go back to the Jmol Application window. |
| 03:45 | Jmol Application also offers a Pop-up menu. |
| 03:50 | You can access the pop-up menu by two different methods. |
| 03:55 | Exit the model kit menu, if it is open. |
| 03:59 | Scroll down the model kit menu and click “exit model kit mode”. |
| 04:04 | To open the Pop-up menu, right-click the mouse button on the panel. |
| 04:09 | Pop-up menu appears on the panel. |
| 04:12 | Pop-up menu offers many functions to modify the display of atoms. |
| 04:18 | It has a variety of selection and rendering options. |
| 04:22 | Most of the functions in this menu are duplicated in the menu bar. |
| 04:28 | The items in the Pop-up menu are self-explanatory. |
| 04:32 | They don't need a detailed description. |
| 04:35 | Click on the Jmol panel to exit the Pop-up menu. |
| 04:39 | The second way to access the Pop-up menu is to click on the Jmol logo. |
| 04:44 | It is located at the bottom right corner of the Jmol panel. |
| 04:49 | Now let's see how to edit this molecule and convert it to Ethane molecule. |
| 04:55 | For this, we will delete the hydroxy group, the chlorine group, the carbon and two hydrogen atoms. |
| 05:05 | Open the model kit menu. |
| 05:08 | Check the box against “delete atom”. |
| 05:12 | Click on the atoms you want to delete. |
| 05:15 | Oxygen, chlorine and the carbon atom. |
| 05:21 | We have to add hydrogens to this molecule to create an ethane molecule. |
| 05:26 | Click on “add hydrogens” option from the model kit menu. |
| 05:32 | Two hydrogen atoms are added to the molecule. |
| 05:36 | We now have the model of Ethane on the screen. |
| 05:40 | Let's learn how to create alkenes and alkynes. |
| 05:45 | To introduce a double bond in the molecule, open the model kit menu. |
| 05:50 | Check against “double” option. |
| 05:53 | Place the cursor on the bond between two carbon atoms in the Ethane molecule. |
| 05:58 | Red colored rings appear around the carbon atoms. |
| 06:01 | Click on the bond. |
| 06:05 | Observe that the single bond is converted to a double bond. |
| 06:09 | We have a model of Ethene on the panel. |
| 06:13 | Now lets convert Ethene to Ethyne, |
| 06:16 | Click on the modelkit menu and check against “triple” option. |
| 06:21 | Place the cursor on the double bond in the Ethene molecule and click on it. |
| 06:28 | The double bond is converted to a triple bond. |
| 06:31 | This is the model of Ethyne. |
| 06:34 | Do the energy minimization to get the most stable conformation and save. |
| 06:40 | Let's summarize. |
| 06:41 | In this tutorial we have learnt to |
| 06:43 | * Substitute the hydrogen atom in alkanes with a functional group. |
| 06:48 | * Add bonds to convert alkanes to alkenes and alkynes |
| 06:52 | * Add and delete atoms and |
| 06:54 | * Use the Pop-up-menu. |
| 06:58 | For the Assignment |
| 06:59 | # Create the models of 2-fluoro-1,3-butadiene and 2-pentyne. |
| 07:06 | # Use the Pop-up menu to change the display of the model to wireframe. |
| 07:10 | # Do energy minimization and save the image in PDF format. |
| 07:16 | Your completed assignment should look as follows |
| 07:24 | Watch the video available at this URL.
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial |
| 07:27 | It summarizes the Spoken Tutorial project |
| 07:31 | If you do not have good bandwidth, you can download and watch it |
| 07:36 | The Spoken Tutorial Project Team: |
| 07:38 | Conducts workshops using spoken tutorials |
| 07:41 | Gives certificates to those who pass an on-line test |
| 07:45 | For more details, please write to contact@spoken-tutorial.org |
| 07:52 | Spoken Tutorial Project is a part of the Talk to a Teacher project |
| 07:57 | It is supported by the National Mission on Education through ICT, MHRD, Government of India |
| 08:04 | More information on this Mission is available at the following link http://spoken-tutorial.org/NMEICT-Intro ] |
| 08:08 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |
