Jmol-Application/C2/Measurements-and-Labeling/English-timed

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
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 nitrogen with hydroxy group.
03:04	Click on the modelkit menu and check against oxygen.
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 oxygen atoms.
03:26	Now we will introduce a double bond between nitrogen and oxygen atom.
03:32	Check the “double” option in the modelkit menu.
03:36	Click on the bond connecting nitrogen and oxygen atom.
03:40	This is a model of nitroethane on the panel.
03:44	As an assignment-
03:45	* 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 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 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 5 and bring the cursor to atom 6 and double-click on it.
06:34	We can see 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 1, click on atom 5 and lastly double-click 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	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. http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial
08:51	It summarizes the Spoken Tutorial project
08:54	If you do not have good bandwidth, you can download and watch it
08:59	The Spoken Tutorial Project Team:
09:01	Conducts workshops using spoken tutorials
09:04	Gives certificates to those who pass an on-line test
09:08	For more details, please write to contact@spoken-tutorial.org
09:15	Spoken Tutorial Project is a part of the Talk to a Teacher project
09:19	It is supported by the National Mission on Education through ICT, MHRD, Government of India
09:26	More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro ]
09:31	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14