Difference between revisions of "Jmol-Application/C2/Measurements-and-Labeling/English-timed"
From Script | Spoken-Tutorial
Sandhya.np14 (Talk | contribs) |
PoojaMoolya (Talk | contribs) |
||
Line 1: | Line 1: | ||
− | {| border=1 | + | {|border=1 |
− | | '''Time''' | + | |'''Time''' |
− | | '''Narration''' | + | |'''Narration''' |
|- | |- | ||
− | | 00:01 | + | |00:01 |
− | | Welcome to this tutorial on '''Measurements and Labeling '''in '''Jmol Application.''' | + | |Welcome to this tutorial on '''Measurements and Labeling '''in '''Jmol Application.''' |
|- | |- | ||
− | | 00:06 | + | |00:06 |
− | | In this tutorial, we will learn to: | + | |In this tutorial, we will learn to: |
|- | |- | ||
− | | 00:09 | + | |00:09 |
− | | | + | |Create models of '''carboxylic acid''' and '''nitroalkane'''. |
|- | |- | ||
− | | 00:14 | + | |00:14 |
− | | | + | |Label atoms in a '''model''' with symbol and number. |
|- | |- | ||
− | | 00:19 | + | |00:19 |
− | | | + | |Measure '''bond lengths''', '''bond angles '''and '''dihedral angles'''. |
|- | |- | ||
− | | 00:24 | + | |00:24 |
− | | To follow this tutorial, you should know | + | |To follow this tutorial, you should know |
|- | |- | ||
− | | 00:27 | + | |00:27 |
− | | how to create and '''edit''' molecular models in '''Jmol Application.''' | + | |how to create and '''edit''' molecular models in '''Jmol Application.''' |
|- | |- | ||
− | | 00:32 | + | |00:32 |
|If not, watch the relevant tutorials available on our website. | |If not, watch the relevant tutorials available on our website. | ||
|- | |- | ||
− | | 00:37 | + | |00:37 |
− | | To record this tutorial, I am using: | + | |To record this tutorial, I am using: |
|- | |- | ||
− | | 00:39 | + | |00:39 |
− | | | + | |'''Ubuntu '''OS version 12.04 |
|- | |- | ||
− | | 00:44 | + | |00:44 |
− | | | + | |'''Jmol''' version 12.2.2 and |
|- | |- | ||
− | | 00:47 | + | |00:47 |
− | | | + | |'''Java''' version 7. |
|- | |- | ||
− | | 00:50 | + | |00:50 |
− | | Let's go through the steps on how to build a '''carboxyl''' group using this '''animation'''. | + | |Let's go through the steps on how to build a '''carboxyl''' group using this '''animation'''. |
|- | |- | ||
− | | 00:56 | + | |00:56 |
|As an example, we will create a model of '''Ethanoic acid, '''commonly known as '''Acetic acid'''. | |As an example, we will create a model of '''Ethanoic acid, '''commonly known as '''Acetic acid'''. | ||
|- | |- | ||
− | | 01:03 | + | |01:03 |
− | | We will begin with a model of '''Ethane'''. | + | |We will begin with a model of '''Ethane'''. |
|- | |- | ||
− | | 01:06 | + | |01:06 |
|We have to convert one of the '''methyl '''groups to a '''carboxyl''' group. | |We have to convert one of the '''methyl '''groups to a '''carboxyl''' group. | ||
|- | |- | ||
− | | 01:11 | + | |01:11 |
|Substitute two '''hydrogen'''s attached to the same '''carbon''' atom with '''hydroxy''' group. | |Substitute two '''hydrogen'''s attached to the same '''carbon''' atom with '''hydroxy''' group. | ||
|- | |- | ||
− | | 01:18 | + | |01:18 |
− | | Delete '''hydrogens''' attached to one of the '''oxygen''' and '''Carbon'''. | + | |Delete '''hydrogens''' attached to one of the '''oxygen''' and '''Carbon'''. |
|- | |- | ||
− | | 01:23 | + | |01:23 |
|Convert '''Carbon-Oxygen''' bond to a double-bond. | |Convert '''Carbon-Oxygen''' bond to a double-bond. | ||
|- | |- | ||
− | | 01:26 | + | |01:26 |
|'''Methyl '''group is converted to a '''Carboxyl''' group. | |'''Methyl '''group is converted to a '''Carboxyl''' group. | ||
|- | |- | ||
− | | 01:31 | + | |01:31 |
|Observe that '''Ethane''' is converted to '''Ethanoic acid.''' | |Observe that '''Ethane''' is converted to '''Ethanoic acid.''' | ||
|- | |- | ||
− | | 01:35 | + | |01:35 |
|We will follow the above steps and create the model of '''Ethanoic acid''' in '''Jmol application.''' | |We will follow the above steps and create the model of '''Ethanoic acid''' in '''Jmol application.''' | ||
|- | |- | ||
− | | 01:42 | + | |01:42 |
− | | This is a model of '''Ethane''' on '''Jmol panel'''. | + | |This is a model of '''Ethane''' on '''Jmol panel'''. |
|- | |- | ||
− | | | + | |01:46 |
− | | Let us convert a '''methyl''' group to a '''carboxyl '''group. | + | |Let us convert a '''methyl''' group to a '''carboxyl '''group. |
|- | |- | ||
− | | 01:50 | + | |01:50 |
− | | Select '''oxygen''' from the '''Modelkit''' menu. | + | |Select '''oxygen''' from the '''Modelkit''' menu. |
|- | |- | ||
− | | 01:54 | + | |01:54 |
|Click on the '''hydrogens''' attached to the same '''carbon''' atom. | |Click on the '''hydrogens''' attached to the same '''carbon''' atom. | ||
|- | |- | ||
− | | 01:58 | + | |01:58 |
− | | Now, check against '''Delete atom''' option in the '''modelkit''' menu. | + | |Now, check against '''Delete atom''' option in the '''modelkit''' menu. |
|- | |- | ||
− | | 02:02 | + | |02:02 |
− | | Delete the '''hydrogen''' attached to the '''oxygen.''' | + | |Delete the '''hydrogen''' attached to the '''oxygen.''' |
|- | |- | ||
− | | 02:07 | + | |02:07 |
− | | And also, delete '''hydrogen '''attached to the '''carbon'''. | + | |And also, delete '''hydrogen '''attached to the '''carbon'''. |
|- | |- | ||
− | | 02:11 | + | |02:11 |
− | | Then, let us introduce a double-bond between '''carbon''' and '''oxygen.''' | + | |Then, let us introduce a double-bond between '''carbon''' and '''oxygen.''' |
|- | |- | ||
− | | 02:16 | + | |02:16 |
|So, check '''double''' option in the '''modelkit''' menu | |So, check '''double''' option in the '''modelkit''' menu | ||
|- | |- | ||
− | | 02:20 | + | |02:20 |
|and click on the '''bond''' connecting '''carbon '''and '''oxygen'''. | |and click on the '''bond''' connecting '''carbon '''and '''oxygen'''. | ||
|- | |- | ||
− | | 02:25 | + | |02:25 |
− | | We have a model of '''Acetic acid '''on '''screen'''. | + | |We have a model of '''Acetic acid '''on '''screen'''. |
|- | |- | ||
− | | 02:28 | + | |02:28 |
− | | Do the '''energy minimization''' to optimize the structure. | + | |Do the '''energy minimization''' to optimize the structure. |
|- | |- | ||
− | | 02:32 | + | |02:32 |
− | | We will follow a similar strategy to create a '''nitro''' group. | + | |We will follow a similar strategy to create a '''nitro''' group. |
|- | |- | ||
− | | 02:37 | + | |02:37 |
− | | Here is the '''Jmol''' panel with a model of '''ethane.''' | + | |Here is the '''Jmol''' panel with a model of '''ethane.''' |
|- | |- | ||
− | | 02:40 | + | |02:40 |
− | | Now, let us convert this molecule to '''nitro-ethane.''' | + | |Now, let us convert this molecule to '''nitro-ethane.''' |
|- | |- | ||
− | | 02:45 | + | |02:45 |
− | | Click on the '''modelkit''' menu and check against '''Nitrogen'''. | + | |Click on the '''modelkit''' menu and check against '''Nitrogen'''. |
|- | |- | ||
− | | 02:50 | + | |02:50 |
− | | Click on the hydrogen atom in the ethane molecule. | + | |Click on the hydrogen atom in the ethane molecule. |
|- | |- | ||
− | | 02:54 | + | |02:54 |
|'''Nitrogen '''atom is represented as blue sphere. | |'''Nitrogen '''atom is represented as blue sphere. | ||
|- | |- | ||
|02:58 | |02:58 | ||
− | | Next, we will substitute two '''hydrogens '''attached to the '''nitrogen''' with a '''hydroxy''' group. | + | |Next, we will substitute two '''hydrogens '''attached to the '''nitrogen''' with a '''hydroxy''' group. |
|- | |- | ||
− | | 03:04 | + | |03:04 |
|Click on the '''modelkit''' menu and check against '''Oxygen (O).''' | |Click on the '''modelkit''' menu and check against '''Oxygen (O).''' | ||
|- | |- | ||
− | | 03:10 | + | |03:10 |
|Then click on the '''hydrogen'''s attached to the '''nitrogen'''. | |Then click on the '''hydrogen'''s attached to the '''nitrogen'''. | ||
|- | |- | ||
− | | 03:14 | + | |03:14 |
− | | Delete the '''hydrogens '''attached to the '''oxygen '''atoms. | + | |Delete the '''hydrogens '''attached to the '''oxygen '''atoms. |
|- | |- | ||
− | | 03:18 | + | |03:18 |
|Open '''modelkit menu '''and check against '''delete atom'''. | |Open '''modelkit menu '''and check against '''delete atom'''. | ||
|- | |- | ||
− | | 03:23 | + | |03:23 |
|Click on the '''hydrogen '''attached to the '''oxygen '''atoms. | |Click on the '''hydrogen '''attached to the '''oxygen '''atoms. | ||
Line 192: | Line 192: | ||
|- | |- | ||
− | | 03:32 | + | |03:32 |
|Check the “'''double'''” option in the '''modelkit''' menu. | |Check the “'''double'''” option in the '''modelkit''' menu. | ||
|- | |- | ||
− | | 03:36 | + | |03:36 |
|Click on the bond connecting '''nitrogen''' and '''oxygen''' atoms. | |Click on the bond connecting '''nitrogen''' and '''oxygen''' atoms. | ||
|- | |- | ||
− | | 03:40 | + | |03:40 |
− | | This is a model of '''nitroethane''' on the panel. | + | |This is a model of '''nitroethane''' on the panel. |
|- | |- | ||
− | | 03:44 | + | |03:44 |
− | | As an assignment- | + | |As an assignment-,Create models of '''1-butanoic acid''' and '''ethylacetate'''. |
|- | |- | ||
− | | 03: | + | |03:50 |
− | | | + | |Optimize the structure by doing energy minimization and |
|- | |- | ||
− | | 03: | + | |03:53 |
− | | | + | |'''Save''' the image. |
|- | |- | ||
− | + | |03:56 | |
− | + | ||
− | + | ||
− | + | ||
− | | 03:56 | + | |
|Your completed assignment should look as follows. | |Your completed assignment should look as follows. | ||
|- | |- | ||
− | | 04:02 | + | |04:02 |
− | | Let's go back to the '''Jmol panel'''. | + | |Let's go back to the '''Jmol panel'''. |
|- | |- | ||
− | | 04:04 | + | |04:04 |
|This is the model of '''1-butanoic acid''' on screen. | |This is the model of '''1-butanoic acid''' on screen. | ||
|- | |- | ||
− | | 04:08 | + | |04:08 |
− | | Let us learn to label the atoms in the model. | + | |Let us learn to label the atoms in the model. |
|- | |- | ||
− | | 04:12 | + | |04:12 |
|We do this with symbols corresponding to the '''element''' and number. | |We do this with symbols corresponding to the '''element''' and number. | ||
|- | |- | ||
|04:17 | |04:17 | ||
− | | Open the '''Display''' menu and select '''Label''' from the scroll down menu. | + | |Open the '''Display''' menu and select '''Label''' from the scroll down menu. |
|- | |- | ||
− | | 04:22 | + | |04:22 |
− | | Select “'''Symbol'''” option to label all the atoms with the symbol corresponding to the element. | + | |Select “'''Symbol'''” option to label all the atoms with the symbol corresponding to the element. |
|- | |- | ||
− | | 04:29 | + | |04:29 |
− | | "'''Name'''” option will give both symbol and the number. | + | |"'''Name'''” option will give both symbol and the number. |
|- | |- | ||
Line 256: | Line 252: | ||
|- | |- | ||
− | | 04:37 | + | |04:37 |
− | | One can erase the labels from the model using the "'''None'''" option. | + | |One can erase the labels from the model using the "'''None'''" option. |
|- | |- | ||
|04:43 | |04:43 | ||
− | | We can also use the Pop-up menu to do all the above modifications. | + | |We can also use the Pop-up menu to do all the above modifications. |
|- | |- | ||
− | | 04:48 | + | |04:48 |
|Right-click on the '''panel''' to open the Pop-up menu and check the various options. | |Right-click on the '''panel''' to open the Pop-up menu and check the various options. | ||
|- | |- | ||
− | | 04:55 | + | |04:55 |
− | | Distance between any two atoms in a molecule can be measured using '''Tools''' menu. | + | |Distance between any two atoms in a molecule can be measured using '''Tools''' menu. |
|- | |- | ||
− | | 05:01 | + | |05:01 |
− | | Before we measure, open the '''modelkit''' menu and click on '''minimize'''. | + | |Before we measure, open the '''modelkit''' menu and click on '''minimize'''. |
|- | |- | ||
− | | 05:07 | + | |05:07 |
|Energy minimization is now done and the model is in the most stable conformation. | |Energy minimization is now done and the model is in the most stable conformation. | ||
|- | |- | ||
− | | 05:14 | + | |05:14 |
− | | Now, click on '''Tools''' menu, select '''Distance Units'''. | + | |Now, click on '''Tools''' menu, select '''Distance Units'''. |
|- | |- | ||
− | | 05:20 | + | |05:20 |
|Select options from the sub-menu according to the requirement. | |Select options from the sub-menu according to the requirement. | ||
|- | |- | ||
− | | | + | |05:25 |
− | | For example, I will choose '''Angstrom.''' | + | |For example, I will choose '''Angstrom.''' |
|- | |- | ||
− | | 05:28 | + | |05:28 |
|So, the bond lengths I measure, will be in '''Angstrom''' units. | |So, the bond lengths I measure, will be in '''Angstrom''' units. | ||
|- | |- | ||
− | | 05:34 | + | |05:34 |
− | | Click on '''Rotate molecule''' icon and bring the cursor to the '''panel'''. | + | |Click on '''Rotate molecule''' icon and bring the cursor to the '''panel'''. |
|- | |- | ||
− | | 05:42 | + | |05:42 |
|I will measure the distance between atoms 9 and 4. | |I will measure the distance between atoms 9 and 4. | ||
|- | |- | ||
− | | 05:46 | + | |05:46 |
|First, double-click on the starting atom which is atom number 9. | |First, double-click on the starting atom which is atom number 9. | ||
|- | |- | ||
− | | 05:52 | + | |05:52 |
|To fix the measurement, double-click on the ending atom which is atom number 4. | |To fix the measurement, double-click on the ending atom which is atom number 4. | ||
|- | |- | ||
− | | 05:58 | + | |05:58 |
|The bond length is now displayed on the '''screen'''. | |The bond length is now displayed on the '''screen'''. | ||
|- | |- | ||
− | | 06:02 | + | |06:02 |
|Let's do some more measurements of '''bond lengths'''. | |Let's do some more measurements of '''bond lengths'''. | ||
|- | |- | ||
− | | 06:05 | + | |06:05 |
|Let's measure the '''bond-length''' between '''carbon''' and '''oxygen''' double-bond. | |Let's measure the '''bond-length''' between '''carbon''' and '''oxygen''' double-bond. | ||
|- | |- | ||
− | | 06:10 | + | |06:10 |
|So, double-click on atom number 5 and bring the cursor to atom number 7 and double-click on it. | |So, double-click on atom number 5 and bring the cursor to atom number 7 and double-click on it. | ||
|- | |- | ||
|06:19 | |06:19 | ||
− | | Similarly, let's measure the '''carbon '''and '''oxygen '''single-bond distance. | + | |Similarly, let's measure the '''carbon '''and '''oxygen '''single-bond distance. |
|- | |- | ||
− | | 06:25 | + | |06:25 |
|So, double-click on atom number 5 and bring the cursor to atom number 6 and double-click on it. | |So, double-click on atom number 5 and bring the cursor to atom number 6 and double-click on it. | ||
|- | |- | ||
− | | 06:34 | + | |06:34 |
|We can see that on the panel all the bond lengths are displayed. | |We can see that on the panel all the bond lengths are displayed. | ||
|- | |- | ||
− | | 06:39 | + | |06:39 |
− | | We can also measure '''bond-angles '''and '''dihedral angles '''in a model. | + | |We can also measure '''bond-angles '''and '''dihedral angles '''in a model. |
|- | |- | ||
− | | 06:44 | + | |06:44 |
− | | For example- we will measure the '''bond angle''' between atoms 9, 4 and 1. | + | |For example- we will measure the '''bond angle''' between atoms 9, 4 and 1. |
|- | |- | ||
− | | 06:51 | + | |06:51 |
|Double-click on atom number 9 and then click on atom 4. | |Double-click on atom number 9 and then click on atom 4. | ||
|- | |- | ||
− | | 06:56 | + | |06:56 |
|To fix the angle measurement, double-click on atom number 1. | |To fix the angle measurement, double-click on atom number 1. | ||
|- | |- | ||
− | | 07:01 | + | |07:01 |
|We can see the '''bond-angle '''displayed on the screen. | |We can see the '''bond-angle '''displayed on the screen. | ||
|- | |- | ||
− | | 07:05 | + | |07:05 |
− | | Let's measure another '''bond-angle, '''say, between atoms 1, 5 and 6. | + | |Let's measure another '''bond-angle, '''say, between atoms 1, 5 and 6. |
|- | |- | ||
− | | 07:12 | + | |07:12 |
|Double-click on atom number 1, click on atom number 5 and lastly double-click on atom number 6. | |Double-click on atom number 1, click on atom number 5 and lastly double-click on atom number 6. | ||
|- | |- | ||
− | | 07:23 | + | |07:23 |
− | | Measurement of '''torsional''' or '''dihedral angle''' involves 4 atoms. | + | |Measurement of '''torsional''' or '''dihedral angle''' involves 4 atoms. |
|- | |- | ||
− | | 07:29 | + | |07:29 |
|So, we will choose atoms 8, 4, 1 and 2. | |So, we will choose atoms 8, 4, 1 and 2. | ||
|- | |- | ||
− | | 07:34 | + | |07:34 |
|For measurement of '''dihedral angle, '''first double-click on atom number 8. | |For measurement of '''dihedral angle, '''first double-click on atom number 8. | ||
|- | |- | ||
− | | 07:39 | + | |07:39 |
|Click on the atom number 4 and then on atom number 1. | |Click on the atom number 4 and then on atom number 1. | ||
|- | |- | ||
− | | 07:43 | + | |07:43 |
|And lastly, to fix the '''dihedral angle''' measurement, double-click on atom number 2. | |And lastly, to fix the '''dihedral angle''' measurement, double-click on atom number 2. | ||
|- | |- | ||
− | | 07:50 | + | |07:50 |
|We can see the '''dihedral angle''' measurement displayed on the screen. | |We can see the '''dihedral angle''' measurement displayed on the screen. | ||
|- | |- | ||
− | | 07:55 | + | |07:55 |
− | | Values of all measurements made, can be viewed in a tabular form. | + | |Values of all measurements made, can be viewed in a tabular form. |
|- | |- | ||
Line 400: | Line 396: | ||
|- | |- | ||
− | | 08:06 | + | |08:06 |
− | | '''Measurements''' dialog-box opens on the '''panel'''. | + | |'''Measurements''' dialog-box opens on the '''panel'''. |
|- | |- | ||
− | | 08:10 | + | |08:10 |
|It has a list of all the measurements made so far. | |It has a list of all the measurements made so far. | ||
|- | |- | ||
− | | 08:14 | + | |08:14 |
− | | We can now '''save''' the image and exit the '''application'''. | + | |We can now '''save''' the image and exit the '''application'''. |
|- | |- | ||
− | | 08:17 | + | |08:17 |
− | | Let's summarize: | + | |Let's summarize: |
|- | |- | ||
− | | 08:19 | + | |08:19 |
|In this tutorial, we have learnt to- | |In this tutorial, we have learnt to- | ||
|- | |- | ||
− | | 08:22 | + | |08:22 |
− | | | + | |Create models of '''carboxylic acid''' and '''nitroalkane'''. |
|- | |- | ||
− | | 08:26 | + | |08:26 |
− | | | + | |Label atoms in a model with symbol of the element and number. |
|- | |- | ||
− | | 08:31 | + | |08:31 |
− | | | + | |Measure '''bond lengths, bond angles''' and '''dihedral angles.''' |
|- | |- | ||
− | | 08:36 | + | |08:36 |
− | | For the assignment- | + | |For the assignment- |
|- | |- | ||
− | | 08:38 | + | |08:38 |
− | | | + | |Create models of molecules with single, double and triple bonds. |
|- | |- | ||
− | | 08:43 | + | |08:43 |
− | | | + | |Measure bond lengths between the '''carbon''' atoms. |
|- | |- | ||
− | | 08:45 | + | |08:45 |
− | | | + | |And compare them. |
|- | |- | ||
− | | 08:48 | + | |08:48 |
− | | Watch the video available at this URL. | + | |Watch the video available at this URL. |
http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial | http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial | ||
|- | |- | ||
− | | 08:51 | + | |08:51 |
|It summarizes the Spoken Tutorial project. | |It summarizes the Spoken Tutorial project. | ||
|- | |- | ||
− | | 08:54 | + | |08:54 |
|If you do not have good bandwidth, you can download and watch it. | |If you do not have good bandwidth, you can download and watch it. | ||
|- | |- | ||
− | | 08:59 | + | |08:59 |
− | | The '''Spoken Tutorial''' Project team: | + | |The '''Spoken Tutorial''' Project team: |
|- | |- | ||
− | | 09:01 | + | |09:01 |
− | | | + | |Conducts workshops using spoken tutorials. |
|- | |- | ||
− | | 09:04 | + | |09:04 |
− | | | + | |Gives certificates to those who pass an on-line test. |
|- | |- | ||
− | | 09:08 | + | |09:08 |
|For more details, please write to: | |For more details, please write to: | ||
'''contact@spoken-tutorial.org''' | '''contact@spoken-tutorial.org''' | ||
|- | |- | ||
− | | 09:15 | + | |09:15 |
− | | Spoken Tutorial project is a part of the '''Talk to a Teacher''' project. | + | |Spoken Tutorial project is a part of the '''Talk to a Teacher''' project. |
|- | |- | ||
− | | 09:19 | + | |09:19 |
|It is supported by the National Mission on Education through ICT, MHRD, Government of India. | |It is supported by the National Mission on Education through ICT, MHRD, Government of India. | ||
|- | |- | ||
− | | 09:26 | + | |09:26 |
|More information on this mission is available at this link. | |More information on this mission is available at this link. | ||
http://spoken-tutorial.org/NMEICT-Intro | http://spoken-tutorial.org/NMEICT-Intro | ||
|- | |- | ||
− | | 09:31 | + | |09:31 |
− | | This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. | + | |This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. |
− | + | ||
|} | |} |
Latest revision as of 16:50, 28 March 2017
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.
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. |
09:31 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |