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

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.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14