Avogadro/C2/Hydrogen-Bonding/English-timed

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.
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Contributors and Content Editors

PoojaMoolya, Sandhya.np14