Difference between revisions of "Jmol-Application/C2/Measurements-and-Labeling/English"

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(Created page with ''''Title of script''': '''Measurements and labeling''' '''Author: '''Snehalatha Kaliappan '''Keywords: '''Molecular models, 3D-Visualization, video tutorial, Jmol tutorial, 3D …')
 
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel.
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Lets go back to the '''Jmol panel'''.  
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let's go back to the '''Jmol panel'''.  
  
 
This is the model of '''1-butanoic acid''' on screen.
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to “Display” select “Label” Click on “Number”
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to “Display” select “Label” Click on “Number”
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| “'''Number'''” option will give only numbering of atoms.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| “'''Number'''” option will give only numbering of atoms.
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Distance between any two atoms in a molecule can be measured using “'''Tools'''” menu.
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Latest revision as of 12:07, 25 February 2014

Title of script: Measurements and labeling

Author: Snehalatha Kaliappan

Keywords: Molecular models, 3D-Visualization, video tutorial, Jmol tutorial, 3D models of Carboxylic acid, 3D models of Nitroalkane.

Outline:-

  • Create models of Carboxylic acids and Nitroalkanes.
  • Label atoms with symbol and number.
  • Measure bond length, bond angles and dihedral angles.


Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Measurements and Labeling in Jmol Application.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to
  • Create models of carboxylic acid and nitroalkane.
  • Label atoms in a model with symbol and number.
  • Measure bond lengths, bond angles and dihedral angles.


Slide Number 3

Pre-requisites

To follow this tutorial, you should know
  • how to create and edit molecular models
  • in Jmol Application.

If not, watch the relevant tutorials available on our website.

Slide Number 4

System Requirement

To record this tutorial, I am using:

Ubuntu OS version. 12.04

Jmol version 12.2.2

Java version 7

Animation Video 1 Let's go through the steps on how to build a carboxyl group using this animation.


As an example, we will create a model of Ethanoic acid, commonly known as Acetic acid.

Animation Video 1


We will begin with a model of Ethane.


We have to convert one of the methyl groups to a carboxyl group.


Substitute two hydrogens attached to the same carbon atom with hydroxy group.

Animation Video 2 Delete hydrogens attached to one of the oxygen and Carbon.

Convert Carbon-Oxygen bond to a double bond.


Methyl group is converted to a Carboxyl group.


Observe that Ethane is converted to Ethanoic acid.


We will follow the above steps and create the model of Ethanoic acid in Jmol application.

Cursor on the Jmol Panel.

Cursor on ethane.

This is a model of Ethane on Jmol panel.
Cursor on methyl group. Let us convert a methyl group to a carboxyl group.
Click on the modelkit menu .


Check against oxygen atom.

Click on the hydrogens.

Select oxygen from the Modelkit menu.


Click on the hydrogens attached to the same carbon atom.

Open modelkit menu and check against “delete atom”. Now, check against delete atom option in the modelkit menu.
Cursor on the hydroxy group>>click on the hydrogen attached to oxygen atom. Delete the hydrogen attached to the oxygen.
Click on the hydrogen attached to the carbon atom. Also, delete hydrogen attached to the carbon.
Cursor on the bond between carbon and oxygen.


Check the “double” option in the modelkit menu.


Click on the bond connecting carbon and oxygen.

Then, let us introduce a double bond between carbon and oxygen.


So, check double option in the modelkit menu.


And click on the bond connecting carbon and oxygen.

Cursor on the model. We have a model of Acetic acid on screen.
Open the modelkit menu and click on “minimization”. Do the energy minimization to optimize the structure.
Cursor on the panel. We will follow a similar strategy to create a nitro group.
Open Jmol window and open the existing file of ethane molecule.


Here is the Jmol panel with a model of ethane.
Cursor on the panel Now let us convert this molecule to nitro-ethane.
Click on the modelkit menu>>

Check against nitrogen.

Click on the modelkit menu and check against Nitrogen.
Click on the hydrogen atom in the ethane molecule. Click on the hydrogen atom in ethane molecule.


Nitrogen atom is represented as blue sphere.

Click on the modelkit menu .


Check against oxygen atom.

Click on the hydrogens.

Next, we will substitute two hydrogens attached to nitrogen with hydroxy group.


Click on the modelkit menu and check against oxygen.


Then click on the hydrogens attached to the nitrogen.

Open modelkit menu and check against “delete atom”.

Click on the hydrogen attached to oxygen atom.

Delete the hydrogens attached to the oxygen atoms.


Open modelkit menu and check against delete atom.

Click on the hydrogen attached to oxygen atoms.

Check the “double” option in the modelkit menu.


Click on the bond connecting nitrogen and oxygen atoms.

Now we will introduce a double bond between nitrogen and oxygen atom.


Check the “double” option in the modelkit menu.

Click on the bond connecting nitrogen and oxygen atom.

Cursor on the model. This is a model of nitroethane on the panel.
Slide 5

Assignment

As an assignment-
  • Create models of 1-butanoic acid and ethylacetate.
  • Optimize the structure by doing energy minimization and
  • Save the image.

Your completed assignment should look as follows.

Cursor on Jmol panel. Let's go back to the Jmol panel.

This is the model of 1-butanoic acid on screen.

Cursor on Jmol panel. Let us learn to label the atoms in the model.


We do this with symbols corresponding to the element and number.

Click on “Display”.

Select “Label”

Open the display menu, and select Label from the scroll down menu.
Go to “Display” menu select “Label” Click on “Symbol” Select “Symbol” option to label all the atoms with the symbol corresponding to the element.
Go to “Display” menu select “Label” Click on “Name” “Name” option will give both symbol and number.
Go to “Display” select “Label” Click on “Number” “Number” option will give only numbering of atoms.
Go to “Display” select “Label”

Point to “None” but don't click.

One can erase the labels from the model, using the “None” option.
Right click on the panel to open the Pop-up menu.


Scroll down to 'style' and click on 'label'

We can also use the Pop-up menu to do all the above modifications.


Right click on the panel to open the Pop-up menu and check the various options.

Cursor on the panel. Distance between any two atoms in a molecule, can be measured using “Tools” menu.
Cursor on the panel.


Open the modelkit menu and click on “minimize”.


Before we measure, open the modelkit menu and click on “minimize”.


Energy minimization is now done and the model is in the most stable conformation.

Click “Tools” menu in the menu bar.


select “Distance Units”.


Now, click on “Tools” menu, select “Distance Units”.


Select options from the sub-menu, according to the requirement.

Click on ““Angstrom” . For example, I will choose Angstrom.


So, the bond lengths I measure, will be in Angstrom units.

Cursor on the panel.


Double-click on atom 9.


Double-click on atom 4.

Click on rotate molecule icon.


And bring the cursor to the panel.


I will measure the distance between atoms 9 and 4.


First double-click on the starting atom, which is atom number 9.


To fix the measurement, double-click on the ending atom, which is atom number 4.

The bond length is now displayed on the screen.

Double-click on atom 5 and atom 7. Let's do some more measurements of bond lengths.


Let's measure the bond-length between carbon and oxygen double-bond.


So, double-click on atom 5 and bring the cursor to atom number 7 and double-click on it.



Double-click on atom 5 and atom 6. Similarly, let's measure the carbon and oxygen single bond distance.


So, double-click on atom 5 and bring the cursor to atom 6 and double-click on it.


We can see on the panel all the bond lengths are displayed.

Cursor on the panel. We can also measure bond-angles and dihedral angles in a model.
Double-click on atom 9.


Click on atom 4.


Double-click atom 1.


For example we will measure the bond angle between atoms 9, 4 and 1.


Double-click on atom number 9, and then click on atom 4.


To fix the angle measurement, double-click on atom number 1.

We can see the bond-angle displayed on the screen.

Follow the same steps as above.

Double-click on atom 1 >> Click on atom 5 >> Double-click atom 6.


Let's measure another bond-angle, say, between atoms 1, 5 and 6.


Double-click on atom 1, click on atom 5 and lastly double-click atom number 6.

Double-click on atom number 8


Click on atom number 4.


Click on atom 1


Double-click on atom 2.

Measurement of torsional or dihedral angle involves 4 atoms.


So, we will choose atoms 8, 4,1 and 2.


For measurement of dihedral angle, first double-click on atom number 8.


Click on the atom number 4, and then on atom number 1.


Lastly, to fix the dihedral angle measurement, double-click on atom number 2.


We can see the dihedral angle measurement displayed on the screen.

Cursor on Jmol Panel.


Click on the “Click atom to measure distances” icon in the tool bar.

Values of all measurements made, can be viewed in a tabular form.


Click on “Click atom to measure distances” icon in the tool bar.

Cursor on the “Measurements” dialog box. “Measurements” dialog box opens on the panel.


It has a list of all the measurements made so far.

Cursor on the panel. We can now save the image and exit the application.
Slide Number 6

Summary

Let's summarize:


In this tutorial we have learnt to-

  • Create models of carboxylic acid and nitroalkane.
  • Label atoms in a model with symbol of the element and number.
  • Measure bond lengths, bond angles and dihedral angles.


Slide Number 7

Assignment

For the assignment-


  • Create models of molecules with single, double and triple bonds.
  • Measure bond lengths between the carbon atoms.
  • And compare them.


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 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 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

Nancyvarkey, Snehalathak

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