Difference between revisions of "Avogadro/C3/General-Features-in-Avogadro/English-timed"

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(Created page with "{|border=1 |'''Time''' |'''Narration''' |- |00:01 |Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''. |- |00:08 |In this tutorial we will learn...")
 
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|In this tutorial we will learn about:  '''Proton transfer''' in compounds by changing '''pH values'''
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|In this tutorial, we will learn about:  '''Proton transfer''' in compounds by changing '''pH values''',
  
 
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| Load crystal structures  
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| '''load''' crystal structures,
  
 
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| Show various '''Miller planes'''  
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|Build super cells  
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|build super cells,
  
 
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| Show geometries in coordination compounds and  Build '''nanotubes'''
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| show geometries in coordination compounds and  Build '''nanotubes'''.
  
 
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|Here I am using, '''Ubuntu Linux''' OS version 14.04
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|To follow this tutorial, you should be familiar with, '''Avogadro''' interface.
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|In the text box change '''pH value''' to 7.0.Click '''OK'''.
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|Notice the structure.  '''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''
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|Notice the structure.  '''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''.
  
 
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|Go to '''Build ''' menu, and select '''Add Hydrogens for pH'''.
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Revision as of 17:41, 5 June 2018

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.
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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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