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Time Narration
00:01 Welcome to this tutorial on Measurements and Labeling in Jmol Application.
00:06 In this tutorial, we will learn to:
00:09 Create models of carboxylic acid and nitroalkane.
00:14 Label atoms in a model with symbol and number.
00:19 Measure bond lengths, bond angles and dihedral angles.
00:24 To follow this tutorial, you should know
00:27 how to create and edit molecular models in Jmol Application.
00:32 If not, watch the relevant tutorials available on our website.
00:37 To record this tutorial, I am using:
00:39 Ubuntu OS version 12.04
00:44 Jmol version 12.2.2 and
00:47 Java version 7.
00:50 Let's go through the steps on how to build a carboxyl group using this animation.
00:56 As an example, we will create a model of Ethanoic acid, commonly known as Acetic acid.
01:03 We will begin with a model of Ethane.
01:06 We have to convert one of the methyl groups to a carboxyl group.
01:11 Substitute two hydrogens attached to the same carbon atom with hydroxy group.
01:18 Delete hydrogens attached to one of the oxygen and Carbon.
01:23 Convert Carbon-Oxygen bond to a double-bond.
01:26 Methyl group is converted to a Carboxyl group.
01:31 Observe that Ethane is converted to Ethanoic acid.
01:35 We will follow the above steps and create the model of Ethanoic acid in Jmol application.
01:42 This is a model of Ethane on Jmol panel.
01:46 Let us convert a methyl group to a carboxyl group.
01:50 Select oxygen from the Modelkit menu.
01:54 Click on the hydrogens attached to the same carbon atom.
01:58 Now, check against Delete atom option in the modelkit menu.
02:02 Delete the hydrogen attached to the oxygen.
02:07 And also, delete hydrogen attached to the carbon.
02:11 Then, let us introduce a double-bond between carbon and oxygen.
02:16 So, check double option in the modelkit menu
02:20 and click on the bond connecting carbon and oxygen.
02:25 We have a model of Acetic acid on screen.
02:28 Do the energy minimization to optimize the structure.
02:32 We will follow a similar strategy to create a nitro group.
02:37 Here is the Jmol panel with a model of ethane.
02:40 Now, let us convert this molecule to nitro-ethane.
02:45 Click on the modelkit menu and check against Nitrogen.
02:50 Click on the hydrogen atom in the ethane molecule.
02:54 Nitrogen atom is represented as blue sphere.
02:58 Next, we will substitute two hydrogens attached to the nitrogen with a hydroxy group.
03:04 Click on the modelkit menu and check against Oxygen (O).
03:10 Then click on the hydrogens attached to the nitrogen.
03:14 Delete the hydrogens attached to the oxygen atoms.
03:18 Open modelkit menu and check against delete atom.
03:23 Click on the hydrogen attached to the oxygen atoms.
03:26 Now, we will introduce a double-bond between nitrogen and oxygen atoms.
03:32 Check the “double” option in the modelkit menu.
03:36 Click on the bond connecting nitrogen and oxygen atoms.
03:40 This is a model of nitroethane on the panel.
03:44 As an assignment-,Create models of 1-butanoic acid and ethylacetate.
03:50 Optimize the structure by doing energy minimization and
03:53 Save the image.
03:56 Your completed assignment should look as follows.
04:02 Let's go back to the Jmol panel.
04:04 This is the model of 1-butanoic acid on screen.
04:08 Let us learn to label the atoms in the model.
04:12 We do this with symbols corresponding to the element and number.
04:17 Open the Display menu and select Label from the scroll down menu.
04:22 Select “Symbol” option to label all the atoms with the symbol corresponding to the element.
04:29 "Name” option will give both symbol and the number.
04:34 "Number" option will give only numbering of atoms.
04:37 One can erase the labels from the model using the "None" option.
04:43 We can also use the Pop-up menu to do all the above modifications.
04:48 Right-click on the panel to open the Pop-up menu and check the various options.
04:55 Distance between any two atoms in a molecule can be measured using Tools menu.
05:01 Before we measure, open the modelkit menu and click on minimize.
05:07 Energy minimization is now done and the model is in the most stable conformation.
05:14 Now, click on Tools menu, select Distance Units.
05:20 Select options from the sub-menu according to the requirement.
05:25 For example, I will choose Angstrom.
05:28 So, the bond lengths I measure, will be in Angstrom units.
05:34 Click on Rotate molecule icon and bring the cursor to the panel.
05:42 I will measure the distance between atoms 9 and 4.
05:46 First, double-click on the starting atom which is atom number 9.
05:52 To fix the measurement, double-click on the ending atom which is atom number 4.
05:58 The bond length is now displayed on the screen.
06:02 Let's do some more measurements of bond lengths.
06:05 Let's measure the bond-length between carbon and oxygen double-bond.
06:10 So, double-click on atom number 5 and bring the cursor to atom number 7 and double-click on it.
06:19 Similarly, let's measure the carbon and oxygen single-bond distance.
06:25 So, double-click on atom number 5 and bring the cursor to atom number 6 and double-click on it.
06:34 We can see that on the panel all the bond lengths are displayed.
06:39 We can also measure bond-angles and dihedral angles in a model.
06:44 For example- we will measure the bond angle between atoms 9, 4 and 1.
06:51 Double-click on atom number 9 and then click on atom 4.
06:56 To fix the angle measurement, double-click on atom number 1.
07:01 We can see the bond-angle displayed on the screen.
07:05 Let's measure another bond-angle, say, between atoms 1, 5 and 6.
07:12 Double-click on atom number 1, click on atom number 5 and lastly double-click on atom number 6.
07:23 Measurement of torsional or dihedral angle involves 4 atoms.
07:29 So, we will choose atoms 8, 4, 1 and 2.
07:34 For measurement of dihedral angle, first double-click on atom number 8.
07:39 Click on the atom number 4 and then on atom number 1.
07:43 And lastly, to fix the dihedral angle measurement, double-click on atom number 2.
07:50 We can see the dihedral angle measurement displayed on the screen.
07:55 Values of all measurements made, can be viewed in a tabular form.
08:00 Click on “Click atom to measure distances” icon in the tool bar.
08:06 Measurements dialog-box opens on the panel.
08:10 It has a list of all the measurements made so far.
08:14 We can now save the image and exit the application.
08:17 Let's summarize:
08:19 In this tutorial, we have learnt to-
08:22 Create models of carboxylic acid and nitroalkane.
08:26 Label atoms in a model with symbol of the element and number.
08:31 Measure bond lengths, bond angles and dihedral angles.
08:36 For the assignment-
08:38 Create models of molecules with single, double and triple bonds.
08:43 Measure bond lengths between the carbon atoms.
08:45 And compare them.
08:48 Watch the video available at this URL.]_is_a_Spoken_Tutorial

08:51 It summarizes the Spoken Tutorial project.
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09:31 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14