Difference between revisions of "Jmol-Application/C2/Create-and-edit-molecular-models/English"

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# Create the models of <br/> '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''<br/>
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Create the models of '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''  
  
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# '''Use the Pop-up '''menu to change the display of the model to wireframe.
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Use the '''Pop-up''' menu to change the display of the model to wireframe.
  
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# Do energy minimization and save the image in '''PDF '''format.
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Do energy minimization and save the image in '''PDF '''format.
  
 
Your completed assignment should look as follows
 
Your completed assignment should look as follows

Revision as of 16:56, 17 September 2019

Title of script: Create and Edit Molecular models

Author: Snehalatha Kaliappan

Keyword: 3D models of chemical structures, molecular visualization, video tutorial.

  • Outline:-
  • Substitute the hydrogen in molecular model with a functional group.
  • Add and delete bonds
  • Add and delete atoms
  • Pop-up-menu (Contextual menu)


Visual Cue
Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Create and Edit molecular models in Jmol Application.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to,


  • Substitute hydrogen atom in a molecular model with a functional group.
  • Add and delete bonds.
  • Add and delete atoms.
  • and learn how to use the Pop-up menu also known as contextual menu.


Slide Number 3

Pr-requisites

To follow this tutorial you should be familiar with,


  • Jmol Application window and
  • Modelkit function that is used to create molecular models

For relevant tutorials, please visit our website.

Slide Number 4

System Requirement

To record this tutorial, I am using
  • Ubuntu OS version. 12.04
  • Jmol version 12.2.2
  • And Java version 7.


Click on “Dash Home” To open the Jmol Application, click on Dash home.
Type “Jmol” in the search box. Type Jmol in the search box.
Cursor on Jmol icon. Jmol icon appears on the screen
Click on the Jmol icon. Click on the Jmol icon to open the Jmol application window.
Cursor on Jmol panel.


Let's begin with the model of Propane, which we had created earlier.
Cursor on Jmol panel

Click on “open a file” icon.

To open the file, click on “Open a file” icon on the tool bar.
Cursor on the dialog box A dialog box appears on the screen.
Cursor on the dialog box Click on the folder where the required file is located.
Click on the “desktop”.

Click on the “open” button

My file is located on the Desktop.


So, I will select Desktop and click on the Open button.

Click on the “propane” file Type the file name in the “File or URL” text box.


Then, click on the Open button.

Cursor on the propane molecule. The Model of Propane appears on screen.
Cursor on the propane molecule. We can substitute hydrogens in the Propane with functional groups like:

hydroxy, amino, halogens like fluro, chloro, bromo and others.

Click on the Modelkit menu


Click on the check box against oxygen atom.

I want to add a hydroxy group to the Propane molecule, to convert it to Propanol.


Open the model kit menu. A list of functional groups is available here.


Check the box against oxygen atom.

Cursor on hydrogen atom >> Click on the hydrogen atom. Click on the hydrogen atom attached to the first carbon atom.
Cursor on the Hydroxyl group


Cursor on the propanol molecule

Observe that the hydrogen atom is replaced by hydroxy group. Oxygen atom is seen in red color here.


Propane in now converted to 1-Propanol.

Cursor on the propanol molecule Let's now try to convert 1-Propanol to 2-chloro-1-propanol.
Click on the check box against chloro group. Select Chloro group from the model kit menu.



Click on hydrogen atom Click on the hydrogen atom attached to the second carbon atom.
Cursor on the panel We now have the model of 2-chloro-1-propanol. Chlorine is seen in green color.


You can do energy minimization and save the image as dot mol file.

Slide number 5

Assignment

Here is an assignment.
  • Create models of the following molecules.
    3-bromo-1-butanol and 2-amino-4-chloro-pentane
  • Do energy minimization and save the image in JPEG format.

To save the image in different file formats:

Use “Save current view as an image” icon in the Tool bar.


Your completed assignment should look as follows



Cursor on Jmol panel with 2-chloro-1-propanol molecule.


Now lets go back to the Jmol Application window.


Jmol Application also offers a Pop-up menu.


You can access the pop-up menu by two different methods.

Right click the mouse button. Exit the model kit menu, if it is open.


Scroll down the model kit menu and click “exit model kit mode”.


To open the Pop-up menu, right-click the mouse button on the panel.


Pop-up menu appears on the panel.



Scroll down the Pop-up menu Pop-up menu offers many functions to modify the display of atoms.


It has a variety of selection and rendering options.

Scroll down the Pop-up menu Most of the functions in this menu are duplicated in the menu bar.
Cursor on the Pop-up menu. The items in the Pop-up menu are self-explanatory.


They don't need a detailed description.

Click on the Jmol panel Click on the Jmol panel to exit the Pop-up menu.
Cursor on the “Jmol” logo.


The second way to access the Pop-up menu is to click on the Jmol logo.


It is located at the bottom right corner of the Jmol panel.

Cursor on the 2-chloro-1-propanol molecule Now let's see how to edit this molecule and convert it to Ethane molecule.
Cursor on hydroxyl group, chlorine group, carbon and hydrogen atoms. For this, we will delete the hydroxy group, the chlorine group, the carbon and two hydrogen atoms.
Click on the modelkit menu. Open the model kit menu.
Click on the box against “delete atom”.


Click on oxygen, chlorine and carbon.

Check the box against “delete atom”.


Click on the atoms you want to delete.

Oxygen, chlorine and the carbon atom.

Cursor on the panel We have to add hydrogens to this molecule to create an ethane molecule.
Click on “add hydrogens” option from the modelkit menu. Click on “add hydrogens” option from the model kit menu.
Cursor on the Jmol panel. Two hydrogen atoms are added to the molecule.


We now have the model of Ethane on the screen.

Cursor on ethane molecule Let's learn how to create alkenes and alkynes.
Click on the modelkit menu.


Click on the “double” option in the modelkit menu.

To introduce a double bond in the molecule, open the model kit menu.


Check against “double” option.

Cursor on the bond between two carbon atoms. Place the cursor on the bond between two carbon atoms in the Ethane molecule.
Click on the bond. Red colored rings appear around the carbon atoms.

Click on the bond.

Observe that the single bond is converted to a double bond.

We have a model of Ethene on the panel.

Cursor on jmol panel Now lets convert Ethene to Ethyne,
Click on the modelkit menu.

Click on “triple”


Place the cursor on the double bond.

Click on the bond.

Click on the modelkit menu and select “triple” option.


Place the cursor on the double bond in the Ethene molecule and click on it.

Cursor on the molecule The double bond is converted to a triple bond.
Point to the model. This is the model of Ethyne.
Cursor on jmol panel Do the energy minimization to get the most stable conformation and save.
Slide Number 6

Summary

Let's summarize.


In this tutorial we have learnt to


  • Substitute the hydrogen atom in alkanes with a functional group.
  • Add bonds to convert alkanes to alkenes and alkynes
  • Add and delete atoms and
  • Use the Pop-up-menu.


Slide Number 7

Assignment

For the Assignment


Create the models of 2-fluoro-1,3-butadiene and 2-pentyne.

Use the Pop-up menu to change the display of the model to wireframe.

Do energy minimization and save the image in PDF format.

Your completed assignment should look as follows

Slide Number 8

Acknowledgement

Watch the video available at this URL.

http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial

It summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it

Slide Number 9

Acknowledgement

The Spoken Tutorial Project Team:

Conducts workshops using spoken tutorials

Gives certificates to those who pass an on-line test

For more details, please write to

contact@spoken-tutorial.org

Slide number 10

Acknowledgement

Spoken Tutorial Project is a part of the Talk to a Teacher project

It is supported by the National Mission on Education through ICT, MHRD, Government of India

More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro ]

This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Snehalathak

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