Avogadro/C2/Create-Surfaces/English-timed

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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 Settings 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.
08:07 This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
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08:22 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India
08:29 This tutorial is contributed by Viswa Janani Vasudhevan and Snehalatha Kaliappan.

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Contributors and Content Editors

PoojaMoolya, Sandhya.np14