Avogadro/C2/Hydrogen-Bonding/English-timed

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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.

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Contributors and Content Editors

PoojaMoolya, Sandhya.np14