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

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{| border=1
+
{|border=1
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| '''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:
  
 
|-
 
|-
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| 00:09
+
|00:09
−
|* Create models of '''carboxylic acid''' and '''nitroalkane'''.
+
|Create models of '''carboxylic acid''' and '''nitroalkane'''.
  
 
|-
 
|-
−
| 00:14
+
|00:14
−
|* Label atoms in a '''model''' with symbol and number.
+
|Label atoms in a '''model''' with symbol and number.
  
 
|-
 
|-
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| 00:19
+
|00:19
−
|* Measure '''bond lengths''', '''bond angles '''and '''dihedral angles'''.
+
|Measure '''bond lengths''', '''bond angles '''and '''dihedral angles'''.
  
 
|-
 
|-
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| 00:24
+
|00:24
−
| To follow this tutorial, you should know  
+
|To follow this tutorial, you should know  
  
 
|-
 
|-
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| 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
+
|'''Ubuntu '''OS version 12.04
  
 
|-
 
|-
−
| 00:44
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|00:44
−
|* '''Jmol''' version 12.2.2 and
+
|'''Jmol''' version 12.2.2 and
  
 
|-
 
|-
−
| 00:47
+
|00:47
−
|* '''Java''' version 7.
+
|'''Java''' version 7.
  
 
|-
 
|-
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| 00:50
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|00:50
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| 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'''.
  
 
|-
 
|-
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| 00:56
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|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'''.  
  
 
|-
 
|-
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| 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
+
|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
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| 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
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|02:25
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| 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
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|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'''.
  
 
|-
 
|-
−
| 03:45
+
|03:50
−
|* Create models of '''1-butanoic acid''' and '''ethylacetate'''.
+
|Optimize the structure by doing energy minimization and  
  
 
|-
 
|-
−
| 03:50
+
|03:53
−
|* Optimize the structure by doing energy minimization and
+
|'''Save''' the image.
  
 
|-
 
|-
−
| 03:53
+
|03:56
−
|* '''Save''' the image.
+
−
 
+
−
|-
+
−
| 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
+
|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'''.
+
|Create models of '''carboxylic acid''' and '''nitroalkane'''.
  
 
|-
 
|-
−
| 08:26
+
|08:26
−
|* Label atoms in a model with symbol of the element and number.
+
|Label atoms in a model with symbol of the element and number.
  
 
|-
 
|-
−
| 08:31
+
|08:31
−
|* Measure '''bond lengths, bond angles''' and '''dihedral angles.'''
+
|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.
+
|Create models of molecules with single, double and triple bonds.
  
 
|-
 
|-
−
| 08:43
+
|08:43
−
|* Measure bond lengths between the '''carbon''' atoms.
+
|Measure bond lengths between the '''carbon''' atoms.
  
 
|-
 
|-
−
| 08:45
+
|08:45
−
|* And compare them.  
+
|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.
+
|Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 09:04
+
|09:04
−
|* Gives certificates to those who pass an on-line test.  
+
|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  
  
 
|-
 
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| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
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|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
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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.

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

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