Avogadro/C2/Create-Surfaces/English-timed
From Script | Spoken-Tutorial
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| 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. |
| 08:15 | We conduct workshops using Spoken Tutorials and give certificates. Please contact us. |
| 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.
Thank you for joining. |
