Avogadro/C3/General-Features-in-Avogadro/English-timed

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.
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Contributors and Content Editors

PoojaMoolya, Sandhya.np14