Avogadro/C2/Hydrogen-Bonding/English

Visual Cue	Narration
Slide Number 1 Title Slide	Warm greetings! Welcome to this tutorial on Hydrogen bonding in molecules.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to, Configure Avogadro Show hydrogen bonding in molecules Measure length of hydrogen bonds Show Force display type and Show dipole moments in molecules.
Slide Number 3 System Requirement	Here I am using, Ubuntu Linux OS version 14.04 Avogadro version 1.1.1. and Working Internet connection.
Slide Number 4 Pre-requisties You should be familiar with: Avogadro interface. For relevant tutorials, visit our website. www.spoken-tutorial.org.	To follow this tutorial, you should be familiar with: Avogadro interface. If not, for relevant tutorials, please visit our website. Structures used in this tutorial are provided as code files for your reference.
Cursor on the Panel.	I have opened a new Avogadro window.
Click on Draw tool, icon>> Click on the Panel. Point to methane molecule.	Click on Draw Tool, icon and click on the Panel. Methane is drawn on the Panel.
Cursor on the Panel.	Now we will learn to configure Avogadro.
Go to Settings menu, click on Configure Avogadro.	Go to Settings menu and click on Configure Avogadro.
Settings dialog box appears.	Settings dialog box appears.
Cursor on dialog box. Point to the side menu item.	Dialog box has a side menu with three menu items- General Plugins Project tree.
Point to General menu.	By default General menu is selected.
Point to Quality and Fog.	General menu has two sliders: Quality and Fog.
Drag the slider from Low to High.	Quality of rendering increases as you drag the slider from Low to High.
Drag the Quality slider to Low, click on Apply button.	Drag the Quality slider to Low and click on Apply button. Notice that structure is not properly rendered.
Drag the Quality slider to high. Point to the molecule.	Drag the Quality slider to High, and click on Apply button. Notice that molecule appears bright with high quality rendering.
Slide Number 5 Quality High quality rendering: is set for printing and publishing images uses more CPU power.	High quality rendering- is set for printing and publishing images It uses more CPU power.
Drag the Quality slider to Medium. Point to the molecule.	Drag the Quality slider to Medium and click on Apply. Medium quality setting works fine for general viewing purpose.
Point to Fog slider.	Now to Fog slider.
Drag the Fog slider to Lots, click on Apply button. Point to the structure.	Drag the Fog slider to Lots and click on Apply button. Notice that structure is fogged.
Drag the Fog slider to Some, click on Apply. Point to the structure.	Drag the Fog slider to Some and click on Apply. Structure appears clearly.
Click on Plugins menu.	Next to Plugins menu.
Display Types drop down appears.	Display Types drop downs appear.
Point to Display Types check boxes.	Notice that all the Display Types check boxes are enabled.
Click on Axes. Point to Details text box.	Click on Axes. Details about Axes Display Type are displayed in Details text box.
Point to all Display Types. (click on some display types and show the details)	Similarly you can see the details of other Display Types.
un-check all the check boxes, click on Apply button.	I will un-check all the check boxes and click on Apply button.
Point to Ball and Stick check box in Display Types.	Ball and Stick check box alone is seen in the Display Types menu.
Uncheck the check box for Ball and Stick display. Point to the structure on the Panel.	Uncheck Ball and Stick Display Type checkbox. If Ball and Stick is also disabled, molecule disappears from the Panel.
Click the check box.	Click on Ball and Stick check box to enable the display.
Go to Plugins menu.	To enable all the Display Types go to Plugins.
Click on all check boxes Display Types drop down.	Click on all check boxes in Display Types drop down.
Click on Apply button.	Click on Apply button.
Cursor on Panel.	All Display Types are displayed in the Display Types drop down.
Click OK.	Click on OK to close the Settings dialog box.
Cursor on Display Types. Click on Add button.	If any of the Display Types is not activated in the Display Types menu: click on Add button.
Point to Add Display Types dialog box.	Add Display Type dialog box appears.
Click on Types drop down, choose the Display Types you need. Choose Hydrogen Bond, click OK.	Click on Types drop down and choose the Display Type you need. I will choose Hydrogen Bond and click OK.
Point to Hydrogen Bond Display Type in the Display Types menu.	Hydrogen Bond Display Type appears in the Display Types menu.
Cursor on the Panel.	Now I will demonstrate hydrogen bonding in polar methanol molecules.
Point to methane molecule on the Panel.	We already have a methane molecule on the 'Panel. For demonstration I need a group of methane molecules.
Point to Draw tool.	Easy method to draw methane molecules is, using Draw tool.
Point to Draw Settings menu.	By default Draw Settings menu has, Element as Carbon and Bond Order as Single. Click on the Panel.
Click on Element drop down>> select Oxygen.	Click on Element drop down. Select Oxygen.
Click on one of the Hydrogens of the methane molecules. Point to Methanol molecules on the Panel.	Then click on any one of the Hydrogens of the methane molecules. We now have a group of Methanol molecules on the Panel.
Click on Hydrogen Bond check box in the Display types.	Click on Hydrogen Bond check box in the Display Types.
Cursor on the Panel.	Let's optimize the molecules for proper orientation.
Click on Auto Optimization Tool icon on the tool bar.	Click on Auto Optimization Tool on the tool bar.
Point to the menu.	Auto Optimization Settings menu appears on the left.
Click on Force Field drop down list, select MMFF94.	In the Force Field drop down, select MMFF94.
Click on Start button.	Click on Start button to optimize.
Point to the yellow dashed lines. Click on Stop to close AutoOptimization Settings.	You can see hydrogen bond formation as yellow dashed lines. These lines are formed between hydrogen of one molecule and oxygen of other molecule. Click on Stop to stop the Auto optimization.
Cursor on the Panel.	I will now demonstrate intramolecular hydrogen bonding in ortho-nitrophenol.
Cursor on the Panel.	For this I will fetch the molecule from Chemical structure database.
Cursor on the Panel	Close all the previously opened windows and open a new window.
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.
Point to the box.	Chemical Name text box appears.
Type o-nitrophenol and click on OK.	Type o-nitrophenol in lower case and click on OK button. Ortho-nitrophenol molecule appears on the Panel.
Cursor on the Panel.	To show hydrogen bonding, you need a group of Ortho-nitrophenol molecules on the Panel.
Cursor on the Panel.	I have copied and pasted molecules on the Panel.
Point to selection tool on the tool bar. Press CTRL + C to copy, CTRL+ V to paste.	Select the molecule using selection tool. Press CTRL + C to copy and CTRL + V to paste.
Click on Hydrogen bond check box.	Click on Hydrogen Bond check box.
Click on Start in Auto Optimization menu.	Optimize the molecules for proper orientation if required.
Point to optimization process. Point to Hydrogen bond.	During optimization process, Intra molecular Hydrogen bond is formed within the molecules. Hydrogen bond is formed between, Oxygen of nitro group and Hydrogen of Hydroxy group in the molecule.
Cursor on the Panel.	Now let's measure the length of hydrogen bond.
Click on Click to Measure icon on the tool bar. Click on Oxygen atom and hydrogen atom.	Click on Click to Measure icon on the tool bar. Click on hydrogen atom and Oxygen atom . Hydrogen bond length is displayed at the bottom of the Panel.
Slide	This slide shows the importance of hydrogen bonding.
Slide Number 6 Significance of Hydrogen Bonding.	Hydrogen bonds- determine unique solvent capabilities of water and stabilize crystal structure of ice. hold complementary strands of DNA together. determine and stabilize structures of proteins and nucleic acids. involve in the mechanism of enzyme catalysis.
Slide Number 7 Assignment	As an assignment, show Hydrogen bonding in, 1. Para-hydroxybenzoic acid. 2. Nucleobases- adenine and uracil. Your assignments should look as follows. Observe inter molecular hydrogen bonding in Para-hydroxybenzoic acid molecules. And adenine and uracil molecules.
Point to Display Types menu.	We have an option in the Display Types to show force for the molecules.
Point to water molecules.	I will open a new window with a few water molecules.
In the Display Types click on Force check box.	In the Display Types click on Force check box.
Click on Hydrogen Bond check box.	Click on Hydrogen Bond check box.
Click on Auto Optimization Tool icon.	Click on Auto Optimization Tool icon on the tool bar.
Select MMFF94 Force Field.	Select MMFF94 Force Field.
Click on Start button.	Click on Start button.
Point to green arrows.	During optimization process: Force display type shows, forces acting on each atom with green arrows. Arrows illustrate direction and amount of force. When a molecule is close to its optimization, arrows become small and then vanish.
	Now to dipole moment in a molecule.
Slide Number 8 Dipole Moment	Dipole moment is due to charge separation in polar molecules. Dipole moment(μ) = charge(Q) * distance of separation(r) Dipole moment is expressed in Debye units.
Cursor on the Panel.	Now I will show dipole moment in hydrogen cyanide(HCN) and water molecules.
Point to Draw tool,	Open a new window. Using Draw tool, draw hydrogen cyanide(HCN) molecule on the Panel. Select Hydrogen and draw bond to carbon. Select Nitrogen, Select bond order as triple and draw a bond as shown.
Point to MMFF94 Force Field.	Optimize the structure using MMFF94 Force Field.
Click on Dipole check box in Display Types.	To show dipole moment click on Dipole check box in Display Types.
Point to red colored arrow	Dipole is shown using a red colored arrow.
Go View menu. Navigate to Properties >> select Molecule Properties. Point to the window.	To view the estimated dipole moment, go to View menu. Navigate to Properties and select Molecule Properties. Molecule Properties window opens.
Point to the estimated dipole moment of hydrogen cynaide.	Window shows estimated dipole moment of hydrogen cyanide as 0.396D.
Point to estimated dipole moment of water.	Similarly the estimated dipole moment of water is 0.245D.
	Let's summarize.
Slide Number Summary	In this tutorial we have learnt to- Configure Avogadro Show intermolecular hydrogen bonding in Methanol Show intramolecular hydrogen bonding in o-nitrophenol Measure length of hydrogen bonds Show Force display type in water molecules Show dipole moments in HCN and H2O molecules.
Slide Number 9 Assignment	As an assignment, 1. Show dipole moments for carbon dioxide and methyl chloride molecules. 2. Show Force Display Type for ammonia molecules.
Slide Number 10 Acknowledgement Watch the video available at http://spoken-tutorial.org /What is a Spoken Tutorial It summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.	This video summarises the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
Slide Number 11 The Spoken Tutorial Project Team Conducts workshops using spoken tutorials Gives certificates to those who pass an online test For more details, please write to contact@spoken-tutorial.org	We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
Slide number 12 Spoken Tutorial Project is a part of the Talk to a Teacher project It is supported by the National Mission on Education through ICT, MHRD, Government of India More information on this Mission is available at: http://spoken-tutorial.org/NMEICT-Intro	The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
	This is Madhuri Ganapathi singing off. Thank you for joining.

Contributors and Content Editors

Madhurig