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|| This is Madhuri Ganapathi singing off.  
 
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Revision as of 18:08, 16 June 2016

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.
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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.

Contributors and Content Editors

Madhurig, Nancyvarkey, PoojaMoolya

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