Jmol-Application/C2/Create-and-edit-molecular-models/English-timed

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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 the 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, let's 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, let's 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.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14