Difference between revisions of "Jmol-Application/C2/Measurements-and-Labeling/English-timed"
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|* how to create and edit molecular models | |* how to create and edit molecular models | ||
| − | + | * in '''Jmol Application.''' | |
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Revision as of 16:18, 12 August 2014
| 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. |
| 04:54 | 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. |
| 05:48 | 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: |
| 08:20 | 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 |
| 09:09 | 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 |
| 09:20 | 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. |
