Avogadro/C2/Create-Surfaces/English-timed

Time	Narration
00:01	Warm greetings everyone. Welcome to this tutorial on Create surfaces.
00:07	In this tutorial, we will learn to: View properties of the molecule
00:13	Label the atoms with partial charge
00:17	Create Van der waals surface
00:20	Color the surface according to the electrostatic potential energies.
00:25	Here I am using Ubuntu Linux OS version. 14.04 Avogadro version 1.1.1.
00:35	To follow this tutorial, you should be familiar with: Avogadro interface.
00:41	If not, for relevant tutorials, please visit our website.
00:47	Here I have opened the Avogadro window.
00:51	Insert a molecule of butane from Insert Fragment Library.
00:57	Click on Build menu then click on Insert ->fragment
01:04	Double click on alkanes folder to open. Select butane.cml.
01:11	Click on Insert button.
01:14	Close the dialog box.
01:17	A model of n-butane is displayed on the panel.
01:21	Clear the selection using Select none option from the Select menu.
01:26	Let us display molecular properties of the molecule.
01:30	Click on View menu, select Properties option.
01:35	From the sub-menu, click on Molecule Properties.
01:39	Molecule Properties window opens with information such as, IUPAC Molecule Name, Molecular weight, Chemical Formula, Dipole moment etc.
01:54	Click on OK to close the window.
01:57	Similarly to view the Atom Properties: Click on Atom properties option from the properties menu.
02:04	A table opens with values of properties such as: Element, Type, Valence, Formal charge etc for each atom in the molecule.
02:17	Close the dialog box.
02:20	Explore other properties like Angle, Torsion and Conformer from the list.
02:27	Let us now learn to label the atoms in the molecule with partial charge.
02:33	Click on Display settings: From the Display Types list, check the box against Label.
02:43	Click on the Spanner symbol on the right side of Label check box.
02:48	Label Settings window opens.
02:51	Click on Partial charge option from atom labels text drop down. Now all the atoms in the molecule are labeled with partial charge.
03:01	The partial charge distribution helps to predict the reactivity of the carbon atoms.
03:07	Inductive effect can be explained by labeling the atoms with partial charge.
03:14	Replace a hydrogen with chlorine. Notice the change in the value of partial charge along the carbon chain.
03:22	Because of the inductive effect carbons close to chlorine become more positive.
03:28	We have also an option to label the bonds. Click on the bond labels text box.
03:35	The drop-down menu has options to label the bonds.
03:39	Click on bond length. The bond lengths for all the bonds are displayed on the panel.
03:46	To change the color of the labels, click on the box filled with color.
03:51	Select the color from the Select atoms label color window. Click on OK button.
03:59	We can shift the labels in X, Y and Z direction.
04:04	Click on the increment or decrement buttons in the label shift menu. Close the dialog box.
04:12	Another very useful feature of Avogadro, is the ability to create surfaces.
04:18	The option for creating surfaces is available in the extensions menu.
04:24	Click on extensions menu, then click on create surfaces option.
04:30	A create surface dialog box opens on the screen.
04:34	Surface type drop-down has two options: Van der waals and electro-static potential.
04:42	Electrostatic potential surfaces are not yet supported in Avogadro.
04:48	Choose Van der waals option. In the Color By drop down select Nothing.
04:55	Set Resolution to Medium
04:58	Iso value to zero. Click on Calculate button.
05:04	Close the dialog box.
05:07	The van der waals surface is displayed on the Panel.
05:11	Van der waals surface is a representation of surface through which a molecule interacts with other molecules.
05:19	To change the surface settings: Click on the spanner symbol corresponding to surfaces.
05:26	A surface setting dialog box opens. Drag the slider to adjust the opacity.
05:34	In the Render drop-down there are different display options to choose such as: Fill, lines and points.
05:42	The default option is fill.
05:45	To change the color of the surface: Click on the box filled with color next to positive option.
05:52	Select the color from the basic color chart by clicking on the color. Click on OK button.
06:00	Next from the Create surface window: Choose Electrostatic potential from the Color by drop-down.
06:07	Set the resolution to medium. Set the Iso value to 0.02.
06:14	Setting low Iso value gives a finer surface.
06:18	Click on Calculate button.
06:21	On the panel we see the surface of 1-chloro butane Colored according to the electro-static potential values of atoms.
06:31	Electrostatic potential surface illustrates charge distributions of the molecule.
06:37	They are also used in predicting the behavior of molecules
06:42	By default, areas of high electronegativity are colored in red and least in blue.
06:49	Here are a few more examples of molecules with electro-static potential surfaces.
06:56	Aniline and cyclohexylamine.
07:00	The electron density on the Nitrogen of cyclohexylamine is more localized than it is in aniline.
07:08	Hence cyclohexylamine is a stronger base.
07:12	Let's summarize. In this tutorial we have learnt to: View properties of the molecule.
07:20	Label the atoms with partial charge.
07:24	Create Van der waals surface
07:27	Color the surface according to the electrostatic potential energies.
07:33	As an assignment : Compare the reactivity of acetaldehyde and formamide using electro-static potential surface.
07:43	Label the atoms with partial charge.
07:47	Your completed assignment should look as follows.
07:51	Negative charge indicated in red is more localized on the oxygen atom of acetaldehyde.
07:58	The Negative charge is more delocalized in formamide.
08:02	Hence Acetaldehyde is more reactive than Formamide.
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08:29	This tutorial is contributed by Viswa Janani Vasudhevan and Snehalatha Kaliappan. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14