Difference between revisions of "Avogadro/C2/Hydrogen-Bonding/English-timed"
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|00:07 | |00:07 | ||
| − | |In this tutorial, we will learn to | + | |In this tutorial, we will learn to: configure Avogadro, |
|- | |- | ||
|00:11 | |00:11 | ||
| − | | | + | |show hydrogen bonding in molecules, |
|- | |- | ||
|00:14 | |00:14 | ||
| − | | | + | |measure length of hydrogen '''bond'''s, |
|- | |- | ||
|00:16 | |00:16 | ||
| − | | | + | |show '''Force display''' type and show '''dipole moment'''s in molecules. |
|- | |- | ||
|00:22 | |00:22 | ||
| − | |Here I am using | + | |Here I am using: '''Ubuntu Linux OS''' version '''14.04''', |
|- | |- | ||
|00:27 | |00:27 | ||
| − | |Avogadro version 1.1.1 | + | |'''Avogadro''' version '''1.1.1''' and working internet connection. |
|- | |- | ||
|00:34 | |00:34 | ||
| − | |To follow this tutorial, you should be familiar with | + | |To follow this tutorial, you should be familiar with ''''Avogadro' interface'''. |
|- | |- | ||
|00:40 | |00:40 | ||
| − | |If not, for relevant tutorials, please visit our website. | + | |If not, for relevant tutorials, please visit our '''website'''. |
|- | |- | ||
|00:45 | |00:45 | ||
| − | |Structures used in this tutorial are provided as code | + | |Structures used in this tutorial are provided as '''code file'''s for your reference. |
|- | |- | ||
| Line 49: | Line 49: | ||
|- | |- | ||
|00:56 | |00:56 | ||
| − | |Click on '''Draw Tool''' | + | |Click on '''Draw Tool''' icon and click on the '''panel'''. |
|- | |- | ||
|01:01 | |01:01 | ||
| − | |'''methane''' is drawn on the ''' | + | |'''methane''' is drawn on the '''panel'''. |
|- | |- | ||
|01:04 | |01:04 | ||
| − | |Now we will learn to configure '''Avogadro'''. | + | |Now, we will learn to configure '''Avogadro'''. |
|- | |- | ||
| Line 79: | Line 79: | ||
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|01:24 | |01:24 | ||
| − | |By default '''General''' menu is selected. | + | |By default, '''General''' menu is selected. |
|- | |- | ||
|01:28 | |01:28 | ||
| − | |'''General''' menu has two | + | |'''General''' menu has two '''slider'''s: '''Quality''' and '''Fog'''. |
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| Line 107: | Line 107: | ||
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|02:02 | |02:02 | ||
| − | |High quality rendering | + | |High quality rendering is set for printing and publishing images. |
|- | |- | ||
| Line 139: | Line 139: | ||
|- | |- | ||
|02:40 | |02:40 | ||
| − | |Next to '''Plugins''' menu. | + | |Next, to '''Plugins''' menu. |
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| Line 151: | Line 151: | ||
|- | |- | ||
|02:51 | |02:51 | ||
| − | |Click on '''Axes'''. Details about '''Axes Display Type''' are displayed in '''Details''' text box. | + | |Click on '''Axes'''. Details about '''Axes Display Type''' are displayed in the '''Details''' text box. |
|- | |- | ||
|02:59 | |02:59 | ||
| − | |Similarly you can see the details of other '''Display Types'''. | + | |Similarly, you can see the details of other '''Display Types'''. |
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| Line 199: | Line 199: | ||
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|03:50 | |03:50 | ||
| − | |If any of the '''Display Types''' is not activated in the '''Display Types''' menu | + | |If any of the '''Display Types''' is not activated in the '''Display Types''' menu, click on '''Add''' button. |
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| Line 215: | Line 215: | ||
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|04:11 | |04:11 | ||
| − | |'''Hydrogen Bond Display Type''' appears in the '''Display Types''' menu. | + | |'''"Hydrogen Bond" Display Type''' appears in the '''Display Types''' menu. |
|- | |- | ||
|04:16 | |04:16 | ||
| − | |Now I will demonstrate hydrogen bonding in '''polar methanol''' molecules. | + | |Now, I will demonstrate hydrogen bonding in '''polar methanol''' molecules. |
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|04:26 | |04:26 | ||
| − | |For demonstration I need a group of '''methane''' molecules. | + | |For demonstration, I need a group of '''methane''' molecules. |
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| Line 235: | Line 235: | ||
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|04:36 | |04:36 | ||
| − | |By default '''Draw Settings''' menu has | + | |By default, '''Draw Settings''' menu has '''Element''' as '''Carbon''' and '''Bond Order''' as '''Single'''. |
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| Line 295: | Line 295: | ||
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|05:48 | |05:48 | ||
| − | |For this I will fetch the molecule from '''Chemical structure database'''. | + | |For this, I will fetch the molecule from '''Chemical structure database'''. |
|- | |- | ||
|05:54 | |05:54 | ||
| − | |Close all the previously opened windows and open a new window. | + | |Close all the previously opened windows and open a new '''window'''. |
|- | |- | ||
|05:59 | |05:59 | ||
| − | |Click on '''File''' menu navigate to '''Import'''.Click on '''Fetch by Chemical name'''. | + | |Click on '''File''' menu, navigate to '''Import'''. Click on '''Fetch by Chemical name'''. |
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| Line 311: | Line 311: | ||
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|06:09 | |06:09 | ||
| − | |Type '''ortho-nitrophenol''' in lower case and click on OK button. | + | |Type '''ortho-nitrophenol''' in lower case and click on '''OK''' button. |
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| Line 343: | Line 343: | ||
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|06:46 | |06:46 | ||
| − | |During optimization process, Intra molecular Hydrogen bond is formed within the molecules. | + | |During optimization process, '''Intra molecular Hydrogen bond''' is formed within the molecules. |
|- | |- | ||
|06:54 | |06:54 | ||
| − | |Hydrogen bond is formed between | + | |Hydrogen bond is formed between Oxygen of '''nitro''' group and Hydrogen of '''Hydroxy''' group in the molecule. |
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| Line 363: | Line 363: | ||
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|07:14 | |07:14 | ||
| − | |Hydrogen bond length is displayed at the bottom of the Panel. | + | |'''Hydrogen bond''' length is displayed at the bottom of the Panel. |
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|07:23 | |07:23 | ||
| − | |Hydrogen bonds | + | |Hydrogen bonds: determine unique solvent capabilities of water and stabilize crystal structure of ice, |
|- | |- | ||
|07:32 | |07:32 | ||
| − | | | + | |hold complementary strands of DNA together, |
|- | |- | ||
|07:36 | |07:36 | ||
| − | | | + | |determine and stabilize structures of proteins and nucleic acids, |
|- | |- | ||
|07:41 | |07:41 | ||
| − | | | + | |involve in the mechanism of enzyme catalysis. |
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| Line 399: | Line 399: | ||
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|08:00 | |08:00 | ||
| − | |Observe inter molecular hydrogen bonding in '''Para-hydroxybenzoic acid''' molecules | + | |Observe inter molecular hydrogen bonding in '''Para-hydroxybenzoic acid''' molecules |
| − | + | and '''adenine''' and '''uracil''' molecules. | |
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| Line 413: | Line 413: | ||
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|08:19 | |08:19 | ||
| − | |In the '''Display Types''' click on '''Force''' check box. | + | |In the '''Display Types''', click on '''Force''' check box. |
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| Line 429: | Line 429: | ||
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|08:36 | |08:36 | ||
| − | |During optimization process | + | |During optimization process, '''Force''' display type shows forces acting on each atom with green arrows. |
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| Line 441: | Line 441: | ||
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|08:55 | |08:55 | ||
| − | |Now to '''dipole moment''' in a molecule. | + | |Now, to '''dipole moment''' in a molecule. |
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| Line 453: | Line 453: | ||
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|09:09 | |09:09 | ||
| − | |Dipole moment is expressed in Debye units. | + | |Dipole moment is expressed in '''Debye''' units. |
|- | |- | ||
|09:13 | |09:13 | ||
| − | |Now I will show dipole moment in hydrogen cyanide(HCN) and water molecules. | + | |Now, I will show dipole moment in hydrogen cyanide(HCN) and water molecules. |
|- | |- | ||
| Line 463: | Line 463: | ||
|Open a new window. | |Open a new window. | ||
| − | Using Draw tool, draw hydrogen cyanide(HCN) molecule on the Panel. | + | Using '''Draw''' tool, draw hydrogen cyanide(HCN) molecule on the Panel. |
|- | |- | ||
| Line 471: | Line 471: | ||
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|09:31 | |09:31 | ||
| − | |Select Nitrogen, Select | + | |Select '''Nitrogen''', Select '''Bond Order''' as '''triple''' and draw a bond as shown. |
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| Line 479: | Line 479: | ||
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|09:44 | |09:44 | ||
| − | |To show '''dipole moment''' click on '''Dipole''' check box in '''Display Types'''. | + | |To show '''dipole moment''', click on '''Dipole''' check box in '''Display Types'''. |
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| Line 493: | Line 493: | ||
|Navigate to '''Properties''' and select '''Molecule Properties'''. | |Navigate to '''Properties''' and select '''Molecule Properties'''. | ||
| − | Molecule Properties window opens. | + | '''Molecule Properties''' window opens. |
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| Line 501: | Line 501: | ||
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|10:13 | |10:13 | ||
| − | |Similarly the estimated dipole moment of water is '''0.245D'''. | + | |Similarly, the estimated dipole moment of water is '''0.245D'''. |
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| Line 509: | Line 509: | ||
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|10:23 | |10:23 | ||
| − | |In this tutorial we have learnt to- | + | |In this tutorial, we have learnt to- |
| − | + | configure Avogadro, | |
|- | |- | ||
|10:27 | |10:27 | ||
| − | | | + | |show intermolecular hydrogen bonding in Methanol, |
|- | |- | ||
|10:31 | |10:31 | ||
| − | | | + | |show intramolecular hydrogen bonding in ortho-nitrophenol, |
|- | |- | ||
|10:35 | |10:35 | ||
| − | | | + | |measure length of hydrogen bonds, |
|- | |- | ||
|10:38 | |10:38 | ||
| − | | | + | |show Force display type in water molecules, |
|- | |- | ||
|10:42 | |10:42 | ||
| − | | | + | |show dipole moments in HCN and water molecules. |
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| Line 542: | Line 542: | ||
|- | |- | ||
|10:59 | |10:59 | ||
| − | |This video summarises the Spoken Tutorial project. | + | |This video summarises the '''Spoken Tutorial''' project. |
| − | 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. |
|- | |- | ||
Latest revision as of 18:08, 8 July 2018
| Time | Narration |
| 00:01 | Warm greetings! Welcome to this tutorial on Hydrogen bonding in molecules. |
| 00:07 | In this tutorial, we will learn to: configure Avogadro, |
| 00:11 | show hydrogen bonding in molecules, |
| 00:14 | measure length of hydrogen bonds, |
| 00:16 | show Force display type and show dipole moments in molecules. |
| 00:22 | Here I am using: Ubuntu Linux OS version 14.04, |
| 00:27 | Avogadro version 1.1.1 and working internet connection. |
| 00:34 | To follow this tutorial, you should be familiar with 'Avogadro' interface. |
| 00:40 | If not, for relevant tutorials, please visit our website. |
| 00:45 | Structures used in this tutorial are provided as code files for your reference. |
| 00:52 | I have opened a new Avogadro window. |
| 00:56 | Click on Draw Tool icon and click on the panel. |
| 01:01 | methane is drawn on the panel. |
| 01:04 | Now, we will learn to configure Avogadro. |
| 01:08 | Go to Settings menu and click on Configure Avogadro. |
| 01:13 | Settings dialog box appears. |
| 01:16 | Dialog box has a side menu with three menu items-
General Plugins Project tree. |
| 01:24 | By default, General menu is selected. |
| 01:28 | General menu has two sliders: Quality and Fog. |
| 01:34 | Quality of rendering increases as you drag the slider from Low to High. |
| 01:41 | Drag the Quality slider to Low and click on Apply button. |
| 01:47 | Notice that structure is not properly rendered. |
| 01:51 | Drag the Quality slider to High, and click on Apply button. |
| 01:56 | Notice that molecule appears bright with high quality rendering. |
| 02:02 | High quality rendering is set for printing and publishing images. |
| 02:07 | It uses more CPU power. |
| 02:11 | Drag the Quality slider to Medium and click on Apply. |
| 02:16 | Medium quality setting works fine for general viewing purpose. |
| 02:21 | Now to Fog slider. |
| 02:24 | Drag the Fog slider to Lots and click on Apply button. |
| 02:28 | Notice that structure is fogged. |
| 02:32 | Drag the Fog slider to Some and click on Apply. Structure appears clearly. |
| 02:40 | Next, to Plugins menu. |
| 02:43 | Display Types drop downs appear. |
| 02:46 | Notice that all the Display Types check boxes are enabled. |
| 02:51 | Click on Axes. Details about Axes Display Type are displayed in the Details text box. |
| 02:59 | Similarly, you can see the details of other Display Types. |
| 03:04 | I will un-check all the check boxes and click on Apply button. |
| 03:11 | Ball and Stick check box alone is seen in the Display Types menu. |
| 03:16 | Uncheck Ball and Stick Display Type checkbox. |
| 03:20 | If Ball and Stick is also disabled, molecule disappears from the Panel. |
| 03:26 | Click on Ball and Stick check box to enable the display. |
| 03:30 | To enable all the Display Types go to Plugins. |
| 03:33 | Click on all check boxes in Display Types drop down. |
| 03:39 | Click on Apply button. |
| 03:41 | All Display Types are displayed in the Display Types drop down. |
| 03:46 | Click on OK to close the Settings dialog box. |
| 03:50 | If any of the Display Types is not activated in the Display Types menu, click on Add button. |
| 03:58 | Add Display Type dialog box appears. |
| 04:02 | Click on Types drop down and choose the Display Type you need. |
| 04:07 | I will choose Hydrogen Bond and click OK. |
| 04:11 | "Hydrogen Bond" Display Type appears in the Display Types menu. |
| 04:16 | Now, I will demonstrate hydrogen bonding in polar methanol molecules. |
| 04:22 | We already have a methane' molecule on the Panel. |
| 04:26 | For demonstration, I need a group of methane molecules. |
| 04:31 | Easy method to draw methane molecules is, using Draw tool. |
| 04:36 | By default, Draw Settings menu has Element as Carbon and Bond Order as Single. |
| 04:43 | Click on the Panel. |
| 04:46 | Click on Element drop down. Select Oxygen. |
| 04:50 | Then click on any one of the Hydrogens of the methane molecules. |
| 04:56 | We now have a group of Methanol molecules on the Panel. |
| 05:00 | Click on Hydrogen Bond check box in the Display Types. |
| 05:04 | Let's optimize the molecules for proper orientation. |
| 05:08 | Click on Auto Optimization Tool on the tool bar. |
| 05:12 | Auto Optimization Settings menu appears on the left. |
| 05:17 | In the Force Field drop down, select MMFF94. |
| 05:22 | Click on Start button to optimize. |
| 05:26 | You can see hydrogen bond formation as yellow dashed lines. |
| 05:31 | These lines are formed between hydrogen of one molecule and oxygen of other molecule. |
| 05:38 | Click on Stop to stop the Auto optimization. |
| 05:42 | I will now demonstrate intramolecular hydrogen bonding in ortho-nitrophenol. |
| 05:48 | For this, I will fetch the molecule from Chemical structure database. |
| 05:54 | Close all the previously opened windows and open a new window. |
| 05:59 | Click on File menu, navigate to Import. Click on Fetch by Chemical name. |
| 06:06 | Chemical Name text box appears. |
| 06:09 | Type ortho-nitrophenol in lower case and click on OK button. |
| 06:15 | Ortho-nitrophenol molecule appears on the Panel. |
| 06:19 | To show hydrogen bonding, you need a group of Ortho-nitrophenol molecules on the Panel. |
| 06:26 | I have copied and pasted molecules on the Panel. |
| 06:30 | Select the molecule using selection tool. |
| 06:34 | Press CTRL + C to copy and CTRL + V to paste. |
| 06:39 | Click on Hydrogen Bond check box. |
| 06:42 | Optimize the molecules for proper orientation if required. |
| 06:46 | During optimization process, Intra molecular Hydrogen bond is formed within the molecules. |
| 06:54 | Hydrogen bond is formed between Oxygen of nitro group and Hydrogen of Hydroxy group in the molecule. |
| 07:02 | Now let's measure the length of hydrogen bond. |
| 07:06 | Click on Click to Measure icon on the tool bar. |
| 07:10 | Click on hydrogen atom and Oxygen atom . |
| 07:14 | Hydrogen bond length is displayed at the bottom of the Panel. |
| 07:19 | This slide shows the importance of hydrogen bonding. |
| 07:23 | Hydrogen bonds: determine unique solvent capabilities of water and stabilize crystal structure of ice, |
| 07:32 | hold complementary strands of DNA together, |
| 07:36 | determine and stabilize structures of proteins and nucleic acids, |
| 07:41 | involve in the mechanism of enzyme catalysis. |
| 07:46 | As an assignment, show Hydrogen bonding in,
1. Para-hydroxybenzoic acid. 2. Nucleobases- adenine and uracil. |
| 07:56 | Your assignments should look as follows. |
| 08:00 | Observe inter molecular hydrogen bonding in Para-hydroxybenzoic acid molecules
and adenine and uracil molecules. |
| 08:10 | We have an option in the Display Types to show force for the molecules. |
| 08:15 | I will open a new window with a few water molecules. |
| 08:19 | In the Display Types, click on Force check box. |
| 08:23 | Click on Hydrogen Bond check box. |
| 08:26 | Click on Auto Optimization Tool icon on the tool bar. |
| 08:30 | Select MMFF94 Force Field. Click on Start button. |
| 08:36 | During optimization process, Force display type shows forces acting on each atom with green arrows. |
| 08:45 | Arrows illustrate direction and amount of force. |
| 08:49 | When a molecule is close to its optimization, arrows become small and vanish. |
| 08:55 | Now, to dipole moment in a molecule. |
| 08:59 | Dipole moment is due to charge separation in polar molecules. |
| 09:04 | Dipole moment(μ) = charge(Q) times distance of separation(r) |
| 09:09 | Dipole moment is expressed in Debye units. |
| 09:13 | Now, I will show dipole moment in hydrogen cyanide(HCN) and water molecules. |
| 09:20 | Open a new window.
Using Draw tool, draw hydrogen cyanide(HCN) molecule on the Panel. |
| 09:27 | Select Hydrogen and draw a bond to carbon. |
| 09:31 | Select Nitrogen, Select Bond Order as triple and draw a bond as shown. |
| 09:38 | Optimize the structure using MMFF94 Force Field. |
| 09:44 | To show dipole moment, click on Dipole check box in Display Types. |
| 09:50 | Dipole is shown using a red colored arrow. |
| 09:54 | To view the estimated dipole moment, go to View menu. |
| 09:57 | Navigate to Properties and select Molecule Properties.
Molecule Properties window opens. |
| 10:05 | Window shows estimated dipole moment of hydrogen cyanide as 0.396D. |
| 10:13 | Similarly, the estimated dipole moment of water is 0.245D. |
| 10:21 | Let's summarize. |
| 10:23 | In this tutorial, we have learnt to-
configure Avogadro, |
| 10:27 | show intermolecular hydrogen bonding in Methanol, |
| 10:31 | show intramolecular hydrogen bonding in ortho-nitrophenol, |
| 10:35 | measure length of hydrogen bonds, |
| 10:38 | show Force display type in water molecules, |
| 10:42 | show dipole moments in HCN and water molecules. |
| 10:48 | As an assignment,
1. Show dipole moments for carbon dioxide and methyl chloride molecules. 2. Show Force Display Type for ammonia molecules. |
| 10:59 | This video summarises the Spoken Tutorial project.
If you do not have good bandwidth, you can download and watch it. |
| 11:06 | We conduct workshops using Spoken Tutorials and give certificates.
Please contact us. |
| 11:12 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| 11:18 | This is Madhuri Ganapathi singing off. Thank you for joining. |
