PoojaMoolya at 09:01, 23 June 2017

2017-06-23T09:01:15Z

Nancyvarkey at 14:42, 24 June 2016

2016-06-24T14:42:46Z

Madhurig at 12:38, 16 June 2016

2016-06-16T12:38:30Z

Madhurig: Created page with "{|border=1 |'''Time''' |'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''. |- ||..."

2016-06-15T06:14:32Z

Created page with "{|border=1 |'''Time''' |'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''. |- ||..."

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{|border=1
|'''Time'''
|'''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Warm greetings!

Welcome to this tutorial on '''General Features in Avogadro'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial we will learn about:
* Proton transfer in compounds by changing pH values
* Load crystal structures
* Show various miller planes
* Build super cells
* Show geometries in coordination compounds and
* Build nanotubes
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using,

Ubuntu Linux OS version 14.04

Avogadro version 1.1.1.
|-
|| '''Slide Number 4'''

'''Pre-requisties'''

You should be familiar with:

'''Avogadro''' interface.

For relevant tutorials, visit our website.

'''www.spoken-tutorial.org'''.
|| To follow this tutorial, you should be familiar with:

'''Avogadro''' interface.

If not, for relevant tutorials, please visit our website.

Example files used in this tutorial are provided as code files.
|-
||
|| I have opened a new '''Avogadro''' window.
|-
|| Cursor on the '''Panel'''.
|| I will demonstrate proton transfer in compounds by changing '''pH''' values.
|-
|| Cursor on the '''Panel'''.
|| For this I will load amino acids from '''fragment''' library.
|-
|| '''Build>>Insert>> Fragment'''
|| Using '''Build''' menu go to '''Fragment''' library.

In the fragment library double click on '''Amino acids''' folder.

|-
|| Select '''D-alanine.cml''' >> click on '''Insert'''.

Press CTRL+SHIFT+A to deselect the structure.
|| Select '''D-alanine.cml''' and click on '''Insert'''.

Close '''Insert Fragment''' dialog box.

Press '''CTRL''', '''SHIFT''' and '''A''' to deselect the structure.
|-
|| Point to '''Navigation''' tool.
|| Using '''Navigation''' tool rotate the structure for proper orientation.
|-
|| Go to '''Build''' menu >> click on '''Add Hydrogens for pH'''.
|| I will demonstrate proton transfer in amino acids by changing '''pH'''.

Go to '''Build''' menu and select '''Add Hydrogens for pH'''.
|-
|| Point to the text box.

In the text box change pH value to 7.0.

Click '''OK.'''
|| '''Add Hydrogens for pH''' text box opens with default value 7.4.

In the text box change pH value to 7.0.

Click '''OK'''.
|-
|| Point to hydrogens.
|| Notice the structure.

'''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''(COO-).

'''Amino''' group(NH2) gets protonated(NH3+) .
|-
|| Go to '''Build''' menu and click on '''Add Hydrogens for pH'''.

change pH to 2.0 >> click Ok.

Point to structure.
|| Go to '''Build ''' menu, and select '''Add Hydrogens for pH'''.

In the text box, change pH to 2.0 and click '''Ok'''.

'''Carboxylate ion'''(COO-) has been converted to '''Carboxylic group(COOH)'''.
|-
|| Go to Build menu, select '''Add Hydrogens for pH'''.

change the pH to 10.0>>click Ok.

Point to structure.
|| Go to '''Build''' menu and select '''Add Hydrogens for pH'''.

In the text box change '''pH''' to 10.0 and click Ok.

'''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''(COO-).

'''Amino''' group(NH2) is deprotonated.
|-
|| Press Delete key.
|| Press '''Delete''' key to delete the structure.
|-
|| Cursor on the '''Panel'''.
|| Now I will demonstrate proton transfer in amines by changing '''pH'''.
|-
|| Build>>Insert>>Fragment.
|| For this I will load '''ethylamine''' structure from '''Fragment''' library.

Close '''Insert Fragment''' dialog box.
|-
|| Press CTRL + SHIFT + A to deselect the structure.
|| Press '''CTRL, SHIFT''' and '''A''' to deselect the structure.
|-
|| Cusror on ''' Navigation''' tool.
|| Using '''Navigation ''' tool rotate the structure for proper orientation.
|-
|| Go to '''Build''' menu, click on '''Add Hydrogens for pH'''.
|| Go to Build menu, click on '''Add Hydrogens for pH'''.
|-
|| change pH value 7.0.

click on OK.

Point to the structure.
|| '''Add Hydrogens for pH''' text box opens.

In the text box change '''pH''' value to 7.0.

Click on '''OK'''.

Observe the structure.

'''Amino'''(NH2) group is protonated.

|-
|| Go to Build menu, click on '''Add Hydrogens for pH'''.

change the pH to 2.0 and click Ok.

Point to the structure.
|| Go to Build menu, click on '''Add Hydrogens for pH'''.

In the text box change pH to 2.0 and click OK.

Here we see no change in the structure.

As '''ethylamine''' shows proton transfer in basic medium only.
|-
|| Go to Build menu, click on '''Add Hydrogens for pH'''.

change the '''pH''' to 10.0 and click '''OK'''.

Point to the structure.
|| Go to Build menu, click on '''Add Hydrogens for pH'''.

In the text box, change '''pH''' to 10.0 and click '''OK'''.

'''Amino''' group gets deprotonated.
|-
|| Cursor on the Panel.
|| Now I will demonstrate:
* how to load crystal structures from crystal library and
* some crystal properties.
|-
|| Click on New icon on the tool bar.
|| Click on '''New''' icon on the tool bar to open a new window.
|-
|| Go to File menu,>> Import>> Crystal.
|| Go to '''File''' menu, navigate to '''Import''' and select '''Crystal'''.
|-
|| Point to the dialog box.

Scroll and show.

Double click on '''halides''' folder.

Select '''NaCl-Halite.cif''' file >>click on '''Insert''' button.
|| '''Insert Crystal''' dialog box opens.

Here we can see different folders.

Double click on '''halides''' folder.

Select '''NaCl-Halite.cif''' file and click on '''Insert'''.

Close '''Insert Crystal''' dialog box.
|-
|| Point to Tool Settings and Display Settings.
|| Here I will close '''Tool Settings''' and '''Display Settings''' for proper view.
|-
|| Point to crystal structure.

Point to cell parameters.
|| Crystal structure of '''sodium chloride''' is displayed on the '''Panel'''.

Along with the structure, its cell parameters are displayed.

On the top-left side of the '''Panel''' you can see:

'''Lattice Type'''

'''Spacegroup''' and

'''Unit cell volume''' of sodium chloride crystal.

|-
|| Cursor on the Panel.
|| Now I will show '''Miller''' planes for this crystal.
|-
||Cursor on the Panel.
|| Before that I will give a brief introduction about '''Miller indices'''.
|-
|| '''Slide Number 5'''

'''Miller Indices'''
|| Miller indices are a set of three numbers (hkl).

They are used to specify directions and internal planes in crystal systems.
|-
|| Cursor on the Panel.
|| Now to '''Miller planes''' in sodium chloride crystal.
|-
|| Go to View menu >> '''Crystal View options'''.

Point to the menu.
|| Go to '''View''' menu and click on '''Crystal View Options'''.

'''Crystal View Options''' menu, gets loaded on the right.
|-
|| Click on '''Miller indices''' radio button.
|| Click on '''Miller indices''' radio button.

I will change the values of 'h', 'k', 'l' to 2, 3, 2.

Notice the change in planes and position of atoms in the '''crystal'''.
|-
|| Cursor on the Panel.
|| Now I will explain how to build a super cell.
|-
|| Go to '''Build''' menu >> '''Super Cell Builder'''.

Point to the dialog box.
|| Go to '''Build''' menu and select '''Super Cell Builder'''.

'''Super Cell Parameters''' dialog box opens.
|-
|| Click on '''Generate cell'''.

Click on '''Close'''
|| Under '''Super Cell Options''' we can change unit cell parameters 'A', 'B' and 'C'.

I will change the field values of 'A', 'B' and 'C' to '2', '2', '2'.

Then click on '''Generate cell'''.

Click on '''Close''' to close the dialog box.
|-
|| Zoom the structure.
|| Zoom the structure as required for proper view.
|-
|| Point to super cell builder.
|| Crystal lattice is displayed on the Panel.
|-
|| Click on 'h', 'k', 'l' values.

Point to the dotted figure.
|| Now I will change '''Miller Indices''' to 3, 2, 3.

Rotate the cell using '''Navigation''' tool.

Here dotted figure shows the plane.
|-
|| Change 'h', 'k','l' values.
|| You can see various planes by changing 'h', 'k', 'l' values.
|-
|| Cursor on the Panel.
|| Now I will build '''octahedral''' geometry for '''Hexamminecobalt(III)'''.
|-
|| Click on '''New''' icon.
|| Click on '''New''' icon on the tool bar to open a new window.
|-
|| Cursor on the Panel.

Click on '''Draw''' tool icon.
|| To draw '''Hexammine cobalt(III)''', click on '''Draw''' tool icon.
|-
|| In the '''Element''' drop down select '''Other'''.

Point to Periodic table window.

Select Cobalt from the table.
|| In the '''Element''' drop down select '''Other'''.

'''Periodic table''' window opens.

Select '''Cobalt''' from the table.

Close '''Periodic table''' window.
|-
|| Click on the '''Panel'''.

Select '''Nitrogen''' from '''Element''' drop down.

|| Click on the '''Panel'''.

Select '''Nitrogen''' from '''Element''' drop down.
|-
|| Click and drag to draw six bonds on cobalt atom.

Select '''Hydrogen''' from '''Element''' drop down.

Click on all the Nitrogen atom.
|| Click and drag to draw six bonds on '''cobalt''' atom.

Notice that each '''Nitrogen''' has two attached hydrogens.

In '''hexamminecobalt(III)''' structure, each nitrogen has three attached hydrogens.

Select '''Hydrogen''' from '''Element''' drop down.

Click and drag on all Nitrogen atoms.
|-
|| Point to Hexammine cobalt(III) structure.
|| '''Hexamminecobalt(III)''' structure is drawn on the Panel.
|-
|| Click on '''Display Settings''' button.
|| Click on '''Display settings''' button to open '''Display Types''' menu.
|-
|| Cursor on the Panel.
|| Now I will show '''octahedral''' geometry of '''Hexamminecobalt(III)''' structure.

For this I will use '''Polygon Display Type'''.
|-
|| Point to '''Add''' button.
|| If '''Polygon Display Type''' is not activated use '''Add''' button to activate.

Click '''Polygon Display Type''' check box.
|-
|| Click on '''Auto Optimization Tool''' icon on the tool bar.
|| To optimize, click on '''Auto Optimization Tool''' on the tool bar.
|-
|| Click on '''Force Field''' drop down list, select '''UFF'''.
|| In the '''Force Field''' drop down, select '''UFF'''.
|-
|| Click on '''Start''' button.

Click on '''Stop''' to stop '''Auto Optimization''' process.
|| Click on '''Start''' button to optimize.

Click on '''Stop''' to stop the '''Auto optimization''' process.
|-
|| Cursor on Navigation tool.
|| Using '''Navigation''' tool rotate the structure to see '''octahedral''' geometry.
|-
|| Point to the structure.
|| Similarly this is '''pentagonal bipyramidal''' geometry of '''iodine heptafluoride'''.
|-
|| Point to '''Nanotube Builder'''.
|| Now we will see another feature in '''Build''' menu called '''Nanotube builder'''.
|-
|| '''Slide Number 6+7'''

'''Nanotube '''

|| A '''nanotube''' is a nanometer-scale tube-like structure.

Examples of different types of nanotubes are:

* Boron carbon nitrogen
* Boron carbon and
* Carbon.

A carbon nanotube,

* is a miniature cylindrical carbon structure
* that has hexagonal graphite molecules attached at the edges.
|-
|| Click on''' New''' icon.
|| Click on '''New''' icon on the tool bar to open a new window.
|-
|| Cursor on the Panel.
|| For a better view of the '''nanotube''', I will change background color to blue.
|-
||Go to '''View''' >> '''Set Background Color'''.

Point to the box.
|| Go to '''View''' and navigate to '''Set Background Color'''.

'''Select Color''' dialog box opens.
|-
|| Select blue colour >> click Ok.
|| In the box select blue colour and click '''Ok'''.
|-
|| Go to '''Build''' menu >> '''Nanotube Builder'''.

Point to the '''Builder menu'''.
|| Go to '''Build''' menu and select '''Nanotube Builder.'''

'''Nanotube Builder''' menu opens below the '''Panel'''.
|-
|| Resize the window
|| I will re-size '''Avogadro''' window to view '''Nanotube Builder''' menu.
|-
|| Point to n,m.
|| You can set '''chirality indexes n, m''' to determine the type of '''nanotube'''.
|-
|| Point to n,m

Point to '''Length'''.

Point to '''Unit''' Field.
|| I will set index values, '''n''' and '''m''' to 4 and 4.

Change '''Length''' to 4.00(four point zero and zero).

Set '''Unit '''field to '''Periodic units'''.
|-
|| Click on '''Find double bonds''' check box.

click on '''Build.'''
|| Click on '''Find double bonds''' check box to show double bonds in the '''nanotube'''.

Then click on '''Build'''.
|-
|| Press CTRL + SHIFT + A to deselect the structure.
|| Press CTRL + SHIFT + A to deselect the structure.
|-
|| Cusor on Navigation tool.
|| Using '''Navigation''' tool rotate and zoom the '''nanotube''' for proper view.
|-
|| Point n,m.

Click on '''Build'''.
|| Next I will build a nanotube with 6,6 index values.

Go to '''Build''' menu and select '''Nanotube Builder'''.

Change '''n '''and '''m''' values to 6 and 6.

Then click on '''Build'''.
|-
|| Point to the nanotubes.
|| Notice the two overlapping '''nanotubes'''.
|-
|| Click on '''Auto Optimization Tool '''icon on the tool bar.
|| To optimize the '''nanotubes''', click on '''Auto Optimization Tool'''.
|-
|| Click on '''Force Field''' drop down list, select '''MMFF94'''.
|| In the '''Force Field''' drop down, select '''MMFF94'''.
|-
|| Click on '''Start''' button.

Click on '''Stop''' to stop '''AutoOptimization''' process.
|| Click on '''Start''' button to optimize.

Click on '''Stop''' to stop the '''auto optimization''' process.
|-
|| Press CTRL + SHIFT + A to deselect the structure.
|| Press CTRL + SHIFT + A to deselect the structure.
|-
|| Point to the nanotubes.
|| A double-walled '''nanotube''' is displayed on the '''Panel'''.
|-
|| Cursor on Navigation tool.
|| Using '''Navigation tool''' rotate the '''nanotube''' for proper view.
|-
|| Cursor on the Panel.
|| Now I will show carbon hexagon rings in the '''nanotube'''.
|-
|| '''Display Types''' menu select '''Ring''' check box.
|| In the '''Display Types''' menu select ''' Ring''' check box.

Using '''Navigation''' tool rotate the '''nanotube''' to see carbon hexagons.
|-
||
|| Let's summarize.

|-
|| '''Slide Number 8'''

'''Summary'''
|| In this tutorial we have learnt about:
* Proton transfer in compounds by changing pH values
* Load crystal structures from crystal library
* Show various miller planes
* Build super cells
* Show geometries in coordination compounds and
* Build nanotubes
|-
|| '''Slide number 9'''

'''Assignment'''.
|| As an assignment

Load silver chloride(AgCl) crystal structure and its show '''Miller''' planes.

Load structures from coordination library and show geometries.

Build '''nanotube''' with chirality index 9,9.
|-
|| '''Slide Number 10'''

'''Acknowledgement '''

Watch the video available at

http://spoken-tutorial.org

/What is a Spoken Tutorial

It summarises the Spoken Tutorial

project.

If you do not have good bandwidth,

you can download and watch it.
|| This video summarises the Spoken Tutorial project
* If you do not have good bandwidth, you can download and watch it.
|-
|| '''Slide Number 11'''

The Spoken Tutorial Project Team

Conducts workshops using spoken

tutorials

Gives certificates to those who pass

an online test

For more details, please write to

'''contact@spoken-tutorial.org'''
|| * We conduct workshops using Spoken Tutorials and give certificates.
* Please contact us.
|-
|| '''Slide number 12'''

Spoken Tutorial Project is a part of

the Talk to a Teacher project

It is supported by the National

Mission on Education through ICT,

MHRD, Government of India

More information on this Mission is

available at:

'''http://spoken-tutorial.org'''

'''/NMEICT-Intro '''
|| The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.
|-
|| This is Madhuri Ganapathi singing off.

Thank you for joining.
|-
|}

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 || This is Madhuri Ganapathi singing off.

Avogadro/C3/General-Features-in-Avogadro/English - Revision history

PoojaMoolya at 09:01, 23 June 2017

Nancyvarkey at 14:42, 24 June 2016

Madhurig at 12:38, 16 June 2016

Madhurig: Created page with "{|border=1 |'''Time''' |'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''. |- ||..."