Avogadro/C3/General-Features-in-Avogadro/English-timed
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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 its show 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 summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
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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. |