Avogadro/C3/General-Features-in-Avogadro/English-timed
From Script | Spoken-Tutorial
| Time | Narration |
| 00:01 | Warm greetings! Welcome to this tutorial on General Features in Avogadro. |
| 00:08 | In this tutorial, we will learn about: Proton transfer in compounds by changing pH values, |
| 00:16 | load crystal structures, |
| 00:19 | show various Miller planes, |
| 00:22 | build super cells, |
| 00:24 | show geometries in coordination compounds and Build nanotubes. |
| 00:31 | Here I am using Ubuntu Linux OS version 14.04, |
| 00:37 | Avogadro version 1.1.1. |
| 00:41 | To follow this tutorial, you should be familiar with Avogadro interface. |
| 00:47 | If not, for relevant tutorials, please visit our website. |
| 00:52 | Example files used in this tutorial are provided as code files. |
| 00:58 | I have opened a new Avogadro window. |
| 01:01 | I will demonstrate proton transfer in compounds by changing pH values. |
| 01:07 | For this, I will load amino acids from Fragment library. |
| 01:12 | Using Build menu, go to Fragment library. |
| 01:16 | In the Fragment library, double click on Amino acids folder. |
| 01:21 | Select D-alanine.cml and click on Insert. |
| 01:26 | Close Insert Fragment dialog box. |
| 01:30 | Press CTRL, SHIFT and A to deselect the structure. |
| 01:34 | Using Navigation tool, rotate the structure for proper orientation. |
| 01:39 | I will demonstrate proton transfer in amino acids by changing pH. |
| 01:46 | Go to Build menu and select Add Hydrogens for pH. |
| 01:51 | Add Hydrogens for pH text box opens with default value 7.4. |
| 01:57 | In the text box, change pH value to 7.0.Click OK. |
| 02:04 | Notice the structure. Carboxylic group(COOH) has been converted to Carboxylate ion. |
| 02:11 | Amino group(NH2) gets protonated(NH3+). |
| 02:15 | Go to Build menu and select Add Hydrogens for pH. |
| 02:20 | In the text box, change pH to 2.0 and click Ok. |
| 02:26 | Carboxylate ion has been converted to Carboxylic group. |
| 02:31 | Go to Build menu and select Add Hydrogens for pH. |
| 02:35 | In the text box, change pH to 10.0 and click Ok. |
| 02:41 | Carboxylic group has been converted to Carboxylate ion. |
| 02:46 | Amino group(NH2) is deprotonated. |
| 02:49 | Press Delete key to delete the structure. |
| 02:52 | Now, I will demonstrate proton transfer in amines by changing pH. |
| 02:58 | For this, I will load ethylamine structure from Fragment library. |
| 03:05 | Close Insert Fragment dialog box. |
| 03:09 | Press CTRL, SHIFT and A to deselect the structure. |
| 03:13 | Using Navigation tool, rotate the structure for proper orientation. |
| 03:18 | Go to Build menu, click on Add Hydrogens for pH. |
| 03:23 | Add Hydrogens for pH text box opens. |
| 03:27 | In the text box, change pH value to 7.0. Click on OK. |
| 03:34 | Observe the structure. Amino group is protonated. |
| 03:39 | Go to Build menu, click on Add Hydrogens for pH. |
| 03:43 | In the text box, change pH to 2.0 and click OK. |
| 03:49 | Here we see no change in the structure. |
| 03:53 | As ethylamine shows proton transfer in basic medium only. |
| 03:59 | Go to Build menu, click on Add Hydrogens for pH. |
| 04:03 | In the text box, change pH to 10.0 and click OK. |
| 04:09 | Amino group gets deprotonated. |
| 04:12 | Now I will demonstrate how to load Crystal structures from Crystal Library and some Crystal properties. |
| 04:20 | Click on New icon on the tool bar to open a new window. |
| 04:25 | Go to File menu, navigate to Import and select Crystal. |
| 04:30 | Insert Crystal dialog box opens. |
| 04:34 | Here we can see different folders. |
| 04:37 | Double-click on halides folder. |
| 04:40 | Select NaCl-Halite.cif file and click on Insert. |
| 04:47 | Close Insert Crystal dialog box. |
| 04:51 | Here, I will close Tool Settings and Display Settings for proper view. |
| 04:58 | Crystal structure of sodium chloride is displayed on the Panel. |
| 05:02 | Along with the structure, its Cell Parameters are displayed. |
| 05:07 | On the top-left side of the Panel you can see:
Lattice Type Spacegroup and Unit cell volume of sodium chloride crystal. |
| 05:18 | Now I will show Miller planes for this crystal. |
| 05:22 | Before that, I will give a brief introduction about Miller indices. |
| 05:28 | Miller Indices are a set of three numbers (hkl). |
| 05:34 | They are used to specify directions and internal planes in crystal systems. |
| 05:41 | Now to Miller planes in sodium chloride crystal. |
| 05:45 | Go to View menu and click on Crystal View Options. |
| 05:51 | Crystal View Options menu gets loaded on the right. |
| 05:56 | Click on Miller Indices radio button. |
| 06:00 | I will change the values of 'h', 'k', 'l' to 2, 3, 2. |
| 06:07 | Notice the change in planes and position of atoms in the crystal. |
| 06:13 | Now I will explain how to build a super cell. |
| 06:17 | Go to Build menu and select Super Cell Builder. |
| 06:22 | Super Cell Parameters dialog box opens. |
| 06:26 | Under Super Cell Options, we can change unit cell parameters 'A', 'B' and 'C'. |
| 06:34 | I will change the field values of 'A', 'B' and 'C' to '2', '2', '2'. |
| 06:43 | Then click on Generate cell. Click on Close to close the dialog box. |
| 06:50 | Zoom the structure as required for proper view. |
| 06:55 | Crystal lattice is displayed on the Panel. |
| 06:59 | Now I will change Miller Indices to 3, 2, 3. |
| 07:05 | Rotate the cell using Navigation tool. |
| 07:09 | Here, dotted figure shows the plane. |
| 07:13 | You can see various planes by changing 'h', 'k', 'l' values. |
| 07:20 | Now, I will build octahedral geometry for Hexamminecobalt(III). |
| 07:26 | Click on New icon on the tool bar to open a new window. |
| 07:31 | To draw Hexammine cobalt(III), click on Draw tool icon. |
| 07:37 | In the Element drop down, select Other. |
| 07:41 | Periodic table window opens. |
| 07:44 | Select Cobalt from the table. |
| 07:47 | Close Periodic table window. |
| 07:50 | Click on the Panel. Select Nitrogen from Element drop down. |
| 07:56 | Click and drag to draw six bonds on cobalt atom. |
| 08:03 | Notice that each Nitrogen has two attached hydrogens. |
| 08:08 | In hexamminecobalt(III) structure, each nitrogen has three attached hydrogens. |
| 08:15 | Select Hydrogen from Element drop down. |
| 08:19 | Click and drag on all Nitrogen atoms. |
| 08:25 | Hexamminecobalt(III) structure is drawn on the Panel. |
| 08:29 | Click on Display Settings button to open Display Settings menu. |
| 08:36 | Now, I will show octahedral geometry of Hexamminecobalt(III) structure. |
| 08:42 | For this, I will use Polygon Display Type. |
| 08:46 | If Polygon Display Type is not activated, use Add button to activate. |
| 08:52 | Click on Polygon Display Type checkbox. |
| 08:56 | To optimize, click on Auto Optimization Tool on the tool bar. |
| 09:01 | In the Force Field drop down, select UFF. |
| 09:06 | Click on Start button to optimize. |
| 09:11 | Click on Stop to stop the Auto optimization process. |
| 09:16 | Using Navigation tool, rotate the structure to see octahedral geometry. |
| 09:22 | Similarly, this is pentagonal bipyramidal geometry of iodine heptafluoride. |
| 09:29 | Now we will see another feature in Build menu called Nanotube builder. |
| 09:35 | A nanotube is a nanometer-scale tube-like structure. |
| 09:40 | Examples of different types of nanotubes are: Boron carbon nitrogen, Boron carbon and Carbon. |
| 09:50 | A carbon nanotube is a miniature cylindrical carbon structure that has hexagonal graphite molecules attached at the edges. |
| 10:01 | Click on New icon on the tool bar to open a new window. |
| 10:06 | For a better view of the nanotube, I will change background color to blue. |
| 10:12 | Go to View and navigate to Set Background Color. |
| 10:17 | Select Color dialog box opens. |
| 10:21 | In the box, select blue colour and click Ok. |
| 10:26 | Go to Build menu and select Nanotube Builder. |
| 10:30 | Nanotube Builder menu opens below the Panel. |
| 10:35 | I will re-size Avogadro window to view Nanotube Builder menu. |
| 10:40 | You can set chirality indexes n, m to determine the type of nanotube. |
| 10:47 | I will set index values n and m to 4 and 4. |
| 10:53 | Change Length to 4.00 (four point zero and zero). |
| 10:57 | Set Unit field to Periodic units. |
| 11:01 | Click on Find double bonds checkbox to show double bonds in the nanotube. |
| 11:08 | Then click on Build. |
| 11:10 | Press CTRL + SHIFT + A to deselect the structure. |
| 11:15 | Using Navigation tool, rotate and zoom the nanotube for proper view. |
| 11:21 | Next I will build a nanotube with 6,6 index values. |
| 11:27 | Go to Build menu and select Nanotube Builder. |
| 11:31 | Change n and m values to 6 and 6. Then click on Build. |
| 11:40 | Notice the two overlapping nanotubes. |
| 11:44 | To optimize the nanotubes, click on Auto Optimization Tool. |
| 11:50 | In the Force Field drop down, select MMFF94. |
| 11:56 | Click on Start button to optimize. |
| 12:02 | Click on Stop to stop the auto optimization process. |
| 12:07 | Press CTRL + SHIFT + A to deselect the structure. |
| 12:11 | A double-walled nanotube is displayed on the Panel. |
| 12:16 | Using Navigation tool, rotate the nanotube for proper view. |
| 12:21 | Now I will show carbon hexagon rings in the nanotube. |
| 12:26 | In the Display Types menu, select Ring checkbox. |
| 12:31 | Using Navigation tool rotate the nanotube to see carbon hexagons. |
| 12:38 | Let's summarize. |
| 12:40 | In this tutorial, we have learnt about: |
| 12:43 | Proton transfer in compounds by changing pH values, |
| 12:48 | load crystal structures from crystal library, |
| 12:51 | show various Miller planes, |
| 12:54 | build super cells, |
| 12:56 | show geometries in coordination compounds and Build nanotubes. |
| 13:03 | As an assignment:
Load silver chloride(AgCl) crystal structure and show its Miller planes. |
| 13:09 | Load structures from coordination library and show geometries. |
| 13:14 | Build nanotube with chirality index 9,9. |
| 13:19 | This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
| 13:27 | We conduct workshops using Spoken Tutorials and give certificates. Please contact us. |
| 13:34 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| 13:41 | This is Madhuri Ganapathi singing off. Thank you for joining. |
