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

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{|border=1
 
{|border=1
−
|'''Time'''
+
|'''Visual Cue'''
 
|'''Narration'''
 
|'''Narration'''
 
|-
 
|-
Line 14: Line 14:
 
'''Learning Objectives'''
 
'''Learning Objectives'''
 
|| In this tutorial we will learn about:
 
|| In this tutorial we will learn about:
−
* Proton transfer in compounds by changing pH values
+
* '''Proton transfer''' in compounds by changing '''pH values'''
 
* Load crystal structures  
 
* Load crystal structures  
−
* Show various miller planes  
+
* Show various '''Miller planes'''
 
* Build super cells  
 
* Build super cells  
 
* Show geometries in coordination compounds and
 
* Show geometries in coordination compounds and
−
* Build nanotubes
+
* Build '''nanotubes'''
 
|-
 
|-
 
|| '''Slide Number 3'''
 
|| '''Slide Number 3'''
Line 26: Line 26:
 
|| Here I am using,
 
|| Here I am using,
  
−
Ubuntu Linux OS version 14.04
+
'''Ubuntu Linux''' OS version 14.04
  
−
Avogadro version 1.1.1.
+
'''Avogadro''' version 1.1.1.
 
|-
 
|-
 
|| '''Slide Number 4'''
 
|| '''Slide Number 4'''
Line 34: Line 34:
 
'''Pre-requisties'''
 
'''Pre-requisties'''
  
−
You should be familiar with:
+
You should be familiar with '''Avogadro''' interface.
  
−
 
−
'''Avogadro''' interface.
 
  
 
For relevant tutorials, visit our website.  
 
For relevant tutorials, visit our website.  
  
 
'''www.spoken-tutorial.org'''.
 
'''www.spoken-tutorial.org'''.
−
|| To follow this tutorial, you should be familiar with:
+
|| To follow this tutorial, you should be familiar with, '''Avogadro''' interface.
−
 
+
−
'''Avogadro''' interface.
+
  
 
If not, for relevant tutorials, please visit our website.
 
If not, for relevant tutorials, please visit our website.
 +
  
 
Example files used in this tutorial are provided as code files.  
 
Example files used in this tutorial are provided as code files.  
Line 54: Line 51:
 
|-
 
|-
 
|| Cursor on the '''Panel'''.
 
|| Cursor on the '''Panel'''.
−
|| I will demonstrate proton transfer in compounds by changing '''pH''' values.
+
|| I will demonstrate '''proton transfer''' in compounds by changing '''pH values'''.
 
|-
 
|-
 
|| Cursor on the '''Panel'''.
 
|| Cursor on the '''Panel'''.
−
|| For this I will load amino acids from '''fragment''' library.
+
|| For this, I will load '''amino acids''' from '''Fragment library'''.
 
|-
 
|-
 
|| '''Build>>Insert>> Fragment'''
 
|| '''Build>>Insert>> Fragment'''
−
|| Using '''Build''' menu go to '''Fragment''' library.
+
|| Using '''Build''' menu, go to '''Fragment library'''.
  
−
In the fragment library double click on '''Amino acids''' folder.
+
In the '''Fragment library,''' double click on '''Amino acids''' folder.
  
 
|-
 
|-
Line 72: Line 69:
 
Close '''Insert Fragment''' dialog box.
 
Close '''Insert Fragment''' dialog box.
  
−
Press '''CTRL''', '''SHIFT''' and '''A''' to deselect the structure.
+
Press '''CTRL, SHIFT''' and '''A''' to deselect the structure.
 
|-
 
|-
 
|| Point to '''Navigation''' tool.
 
|| Point to '''Navigation''' tool.
Line 78: Line 75:
 
|-
 
|-
 
|| Go to '''Build''' menu >> click on '''Add Hydrogens for pH'''.
 
|| Go to '''Build''' menu >> click on '''Add Hydrogens for pH'''.
−
|| I will demonstrate proton transfer in amino acids by changing '''pH'''.
+
|| I will demonstrate '''proton transfer''' in '''amino acids''' by changing '''pH'''.
  
 
Go to '''Build''' menu and select '''Add Hydrogens for pH'''.
 
Go to '''Build''' menu and select '''Add Hydrogens for pH'''.
Line 89: Line 86:
 
|| '''Add Hydrogens for pH''' text box opens with default value 7.4.
 
|| '''Add Hydrogens for pH''' text box opens with default value 7.4.
  
−
In the text box change pH value to 7.0.
+
In the text box change '''pH value''' to 7.0.
 +
 
  
 
Click '''OK'''.
 
Click '''OK'''.
Line 98: Line 96:
 
'''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''(COO<sup>-</sup>).
 
'''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''(COO<sup>-</sup>).
  
−
'''Amino''' group(NH2) gets protonated(NH<sub>3</sub><sup>+</sup>)<sup> </sup>.
+
 
 +
'''Amino group(NH2)''' gets '''protonated(NH3+)'''.
 
|-
 
|-
 
|| Go to '''Build''' menu and click on '''Add Hydrogens for pH'''.
 
|| Go to '''Build''' menu and click on '''Add Hydrogens for pH'''.
Line 107: Line 106:
 
|| Go to '''Build ''' menu, and select '''Add Hydrogens for pH'''.
 
|| Go to '''Build ''' menu, and select '''Add Hydrogens for pH'''.
  
−
In the text box, change pH to 2.0 and click '''Ok'''.
+
In the text box, change '''pH''' to 2.0 and click '''Ok'''.
 +
 
 
   
 
   
 
'''Carboxylate ion'''(COO<sup>-</sup>) has been converted to '''Carboxylic group(COOH)'''.
 
'''Carboxylate ion'''(COO<sup>-</sup>) has been converted to '''Carboxylic group(COOH)'''.
Line 118: Line 118:
 
|| Go to '''Build''' menu and select '''Add Hydrogens for pH'''.
 
|| Go to '''Build''' menu and select '''Add Hydrogens for pH'''.
  
−
In the text box change '''pH''' to 10.0 and click Ok.
+
In the text box, change '''pH''' to 10.0 and click '''Ok'''.
  
−
'''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''(COO<sup>-</sup>).
+
'''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion(COO)'''.
  
−
'''Amino''' group(NH2) is deprotonated.
+
'''Amino''' group(NH2) is '''deprotonated'''.
 
|-
 
|-
 
|| Press Delete key.
 
|| Press Delete key.
Line 128: Line 128:
 
|-
 
|-
 
|| Cursor on the '''Panel'''.
 
|| Cursor on the '''Panel'''.
−
|| Now I will demonstrate proton transfer in amines by changing '''pH'''.
+
|| Now, I will demonstrate '''proton transfer''' in '''amines''' by changing '''pH'''.
 
|-
 
|-
 
|| Build>>Insert>>Fragment.
 
|| Build>>Insert>>Fragment.
−
|| For this I will load '''ethylamine''' structure from '''Fragment''' library.
+
|| For this I will load '''ethylamine''' structure from '''Fragment library'''.
  
 
Close '''Insert Fragment''' dialog box.
 
Close '''Insert Fragment''' dialog box.
Line 139: Line 139:
 
|-
 
|-
 
|| Cusror on ''' Navigation''' tool.
 
|| Cusror on ''' Navigation''' tool.
−
|| Using '''Navigation ''' tool rotate the structure for proper orientation.
+
|| 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'''.
−
|| 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.
 
|| change pH value 7.0.
Line 151: Line 151:
 
|| '''Add Hydrogens for pH''' text box opens.
 
|| '''Add Hydrogens for pH''' text box opens.
  
−
In the text box change '''pH''' value to 7.0.
+
In the text box, change '''pH''' value to 7.0.
 +
 
  
 
Click on '''OK'''.
 
Click on '''OK'''.
 +
  
 
Observe the structure.
 
Observe the structure.
  
−
'''Amino'''(NH2) group is protonated.
+
'''Amino(NH2)''' group is '''protonated'''.
  
 
|-
 
|-
Line 165: Line 167:
  
 
Point to the structure.
 
Point to the structure.
−
|| Go to Build menu, click on '''Add Hydrogens for pH'''.
+
|| Go to '''Build''' menu, click on '''Add Hydrogens for pH'''.
 +
 
 +
In the text box, change '''pH''' to 2.0 and click '''OK'''.
  
−
In the text box change pH to 2.0 and click OK.
 
  
 
Here we see no change in the structure.
 
Here we see no change in the structure.
  
−
As '''ethylamine''' shows proton transfer in basic medium only.
+
 
 +
As '''ethylamine''' shows '''proton transfer''' in basic medium only.
 
|-
 
|-
 
|| Go to Build menu, click on '''Add Hydrogens for pH'''.
 
|| Go to Build menu, click on '''Add Hydrogens for pH'''.
Line 178: Line 182:
  
 
Point to the structure.
 
Point to the structure.
−
|| Go to Build menu, click on '''Add Hydrogens for pH'''.
+
|| Go to '''Build''' menu, click on '''Add Hydrogens for pH'''.
  
 
In the text box, change '''pH''' to 10.0 and click '''OK'''.
 
In the text box, change '''pH''' to 10.0 and click '''OK'''.
  
−
'''Amino''' group gets deprotonated.
+
 
 +
'''Amino group''' gets '''deprotonated'''.
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
 
|| Now I will demonstrate:
 
|| Now I will demonstrate:
−
* how to load crystal structures from crystal library and
+
* how to load '''Crystal structures''' from '''Crystal Library''' and
−
* some crystal properties.
+
* some '''Crystal properties'''.
 
|-
 
|-
 
|| Click on New icon on the tool bar.
 
|| Click on New icon on the tool bar.
−
|| Click on '''New''' icon on the tool bar to open a new window.
+
|| Click on '''New''' icon on the tool bar, to open a new window.
 
|-
 
|-
 
|| Go to File menu,>> Import>> Crystal.
 
|| Go to File menu,>> Import>> Crystal.
Line 206: Line 211:
 
Here we can see different folders.
 
Here we can see different folders.
  
−
Double click on '''halides''' folder.  
+
Double-click on '''halides''' folder.  
 +
 
  
 
Select '''NaCl-Halite.cif''' file and click on '''Insert'''.
 
Select '''NaCl-Halite.cif''' file and click on '''Insert'''.
Line 218: Line 224:
  
 
Point to cell parameters.
 
Point to cell parameters.
−
|| Crystal structure of '''sodium chloride''' is displayed on the '''Panel'''.
+
|| '''Crystal''' structure of '''sodium chloride''' is displayed on the '''Panel'''.
  
−
Along with the structure, its cell parameters are displayed.
+
Along with the structure, its '''Cell Parameters''' are displayed.
  
 
On the top-left side of the '''Panel''' you can see:
 
On the top-left side of the '''Panel''' you can see:
Line 228: Line 234:
 
'''Spacegroup''' and  
 
'''Spacegroup''' and  
  
−
'''Unit cell volume''' of sodium chloride crystal.
+
'''Unit cell volume''' of '''sodium chloride crystal'''.
  
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
−
|| Now I will show '''Miller''' planes for this crystal.
+
|| Now I will show '''Miller planes''' for this '''crystal'''.
 
|-
 
|-
 
||Cursor on the Panel.
 
||Cursor on the Panel.
Line 240: Line 246:
  
 
'''Miller Indices'''
 
'''Miller Indices'''
−
|| Miller indices are a set of three numbers (hkl).
+
|| '''Miller Indices''' are a set of three numbers ('''hkl''').
  
−
They are used to specify directions and internal planes in crystal systems.
+
They are used to specify directions and internal '''planes''' in '''crystal systems'''.
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
−
|| Now to '''Miller planes''' in sodium chloride crystal.
+
|| Now to '''Miller planes''' in '''sodium chloride crystal'''.
 
|-
 
|-
 
|| Go to View menu >> '''Crystal View options'''.
 
|| Go to View menu >> '''Crystal View options'''.
Line 254: Line 260:
 
'''Crystal View Options''' menu, gets loaded on the right.
 
'''Crystal View Options''' menu, gets loaded on the right.
 
|-
 
|-
−
|| Click on '''Miller indices''' radio button.
+
|| Click on '''Miller Indices''' radio button.
−
|| 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.
+
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'''.
+
Notice the change in '''planes''' and position of '''atoms''' in the '''crystal'''.
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
Line 274: Line 280:
  
 
Click on '''Close'''  
 
Click on '''Close'''  
−
|| Under '''Super Cell Options''' we can change unit cell parameters 'A', 'B' and 'C'.
+
|| 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'.
+
I will change the field values of ''''A', 'B'''' and ''''C'''' to '2', '2', '2'.
  
 
Then click on '''Generate cell'''.
 
Then click on '''Generate cell'''.
 +
  
 
Click on '''Close''' to close the dialog box.
 
Click on '''Close''' to close the dialog box.
Line 286: Line 293:
 
|-
 
|-
 
|| Point to super cell builder.
 
|| Point to super cell builder.
−
|| Crystal lattice is displayed on the Panel.
+
|| '''Crystal lattice''' is displayed on the Panel.
 
|-
 
|-
 
|| Click on 'h', 'k', 'l' values.
 
|| Click on 'h', 'k', 'l' values.
Line 295: Line 302:
 
Rotate the cell using '''Navigation''' tool.
 
Rotate the cell using '''Navigation''' tool.
  
−
Here dotted figure shows the plane.
+
Here dotted figure shows the '''plane'''.
 
|-
 
|-
 
|| Change 'h', 'k','l' values.
 
|| Change 'h', 'k','l' values.
−
|| You can see various planes by changing 'h', 'k', 'l' values.
+
|| You can see various '''planes''' by changing ''''h', 'k', 'l'''' values.
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
Line 321: Line 328:
  
 
Select '''Cobalt''' from the table.
 
Select '''Cobalt''' from the table.
 +
  
 
Close '''Periodic table''' window.
 
Close '''Periodic table''' window.
Line 332: Line 340:
 
Select '''Nitrogen''' from '''Element''' drop down.
 
Select '''Nitrogen''' from '''Element''' drop down.
 
|-
 
|-
−
|| Click and drag to draw six bonds on cobalt atom.
+
|| Click and drag to draw six '''bonds''' on '''cobalt atom.'''
  
 
Select '''Hydrogen''' from '''Element''' drop down.
 
Select '''Hydrogen''' from '''Element''' drop down.
  
 
Click on all the Nitrogen atom.
 
Click on all the Nitrogen atom.
−
|| Click and drag to draw six bonds on '''cobalt''' atom.
+
|| Click and drag to draw six '''bonds''' on '''cobalt atom'''.
  
−
Notice that each '''Nitrogen''' has two attached hydrogens.
+
Notice that each '''Nitrogen''' has two attached '''hydrogens'''.
  
−
In '''hexamminecobalt(III)''' structure, each nitrogen has three attached hydrogens.
+
In '''hexamminecobalt(III)''' structure, each '''nitrogen''' has three attached '''hydrogens'''.
  
 
Select '''Hydrogen''' from '''Element''' drop down.
 
Select '''Hydrogen''' from '''Element''' drop down.
  
−
Click and drag on all Nitrogen atoms.
+
Click and drag on all '''Nitrogen atoms'''.
 
|-
 
|-
 
|| Point to Hexammine cobalt(III) structure.
 
|| Point to Hexammine cobalt(III) structure.
Line 351: Line 359:
 
|-
 
|-
 
|| Click on '''Display Settings''' button.
 
|| Click on '''Display Settings''' button.
−
|| Click on '''Display settings''' button to open '''Display Types''' menu.
+
|| Click on '''Display Settings''' button to open '''Display Settings''' menu.
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
−
|| Now I will show '''octahedral''' geometry of '''Hexamminecobalt(III)''' structure.
+
|| Now I will show '''octahedral geometry''' of '''Hexamminecobalt(III)''' structure.
  
−
For this I will use '''Polygon Display Type'''.
+
For this, I will use '''Polygon Display Type'''.
 
|-
 
|-
 
|| Point to '''Add''' button.  
 
|| Point to '''Add''' button.  
−
|| If '''Polygon Display Type''' is not activated use '''Add''' button to activate.
+
|| If '''Polygon Display Type''' is not activated, use '''Add''' button to activate.
  
−
Click '''Polygon Display Type''' check box.
+
Click on '''Polygon Display Type''' checkbox.
 
|-
 
|-
 
|| Click on '''Auto Optimization Tool''' icon on the tool bar.
 
|| Click on '''Auto Optimization Tool''' icon on the tool bar.
Line 377: Line 385:
 
|-
 
|-
 
|| Cursor on Navigation tool.
 
|| Cursor on Navigation tool.
−
|| Using '''Navigation''' tool rotate the structure to see '''octahedral''' geometry.
+
|| Using '''Navigation''' tool, rotate the structure to see '''octahedral geometry'''.
 
|-
 
|-
 
|| Point to the structure.
 
|| Point to the structure.
−
|| Similarly this is '''pentagonal bipyramidal''' geometry of '''iodine heptafluoride'''.  
+
|| Similarly, this is '''pentagonal bipyramidal geometry''' of '''iodine heptafluoride'''.  
 
|-
 
|-
 
|| Point to '''Nanotube Builder'''.
 
|| Point to '''Nanotube Builder'''.
Line 389: Line 397:
 
'''Nanotube '''
 
'''Nanotube '''
  
−
|| A '''nanotube''' is a nanometer-scale tube-like structure.
+
|| A '''nanotube''' is a '''nanometer-scale tube'''-like structure.
  
−
Examples of different types of nanotubes are:
+
Examples of different types of '''nanotubes''' are:
  
−
* Boron carbon nitrogen
+
* '''Boron carbon nitrogen'''
−
* Boron carbon and  
+
* '''Boron carbon''' and  
−
* Carbon.  
+
* '''Carbon'''.  
  
−
A carbon nanotube,
+
A '''carbon nanotube''',
  
−
* is a miniature cylindrical carbon structure
+
* is a miniature cylindrical '''carbon structure'''
−
* that has hexagonal graphite molecules attached at the edges.
+
* that has hexagonal '''graphite molecules''' attached at the edges.
 
|-
 
|-
 
|| Click on''' New''' icon.
 
|| Click on''' New''' icon.
Line 416: Line 424:
 
|-
 
|-
 
|| Select blue colour >> click Ok.
 
|| Select blue colour >> click Ok.
−
|| In the box select blue colour and click '''Ok'''.
+
|| In the box, select blue colour and click '''Ok'''.
 
|-
 
|-
 
|| Go to '''Build''' menu >> '''Nanotube Builder'''.
 
|| Go to '''Build''' menu >> '''Nanotube Builder'''.
Line 436: Line 444:
  
 
Point to '''Unit''' Field.
 
Point to '''Unit''' Field.
−
|| I will set index values, '''n''' and '''m''' to 4 and 4.
+
|| I will set '''index values n''' and '''m''' to 4 and 4.
  
 
Change '''Length''' to 4.00(four point zero and zero).
 
Change '''Length''' to 4.00(four point zero and zero).
Line 442: Line 450:
 
Set '''Unit '''field to '''Periodic units'''.
 
Set '''Unit '''field to '''Periodic units'''.
 
|-
 
|-
−
|| Click on '''Find double bonds''' check box.
+
|| Click on '''Find double bonds''' checkbox.
  
 
click on '''Build.'''
 
click on '''Build.'''
−
|| Click on '''Find double bonds''' check box to show double bonds in the '''nanotube'''.
+
|| Click on '''Find double bonds''' checkbox to show double bonds in the '''nanotube'''.
  
 
Then click on '''Build'''.
 
Then click on '''Build'''.
 
|-
 
|-
 
|| Press CTRL + SHIFT + A to deselect the structure.
 
|| Press CTRL + SHIFT + A to deselect the structure.
−
|| Press CTRL + SHIFT + A to deselect the structure.
+
|| Press '''CTRL + SHIFT + A''' to deselect the structure.
 
|-
 
|-
 
|| Cusor on Navigation tool.
 
|| Cusor on Navigation tool.
Line 458: Line 466:
  
 
Click on '''Build'''.
 
Click on '''Build'''.
−
|| Next I will build a nanotube with 6,6 index values.
+
|| Next I will build a nanotube with 6,6 '''index values'''.
  
 
Go to '''Build''' menu and select '''Nanotube Builder'''.
 
Go to '''Build''' menu and select '''Nanotube Builder'''.
Line 483: Line 491:
 
|-
 
|-
 
|| Press CTRL + SHIFT + A to deselect the structure.
 
|| Press CTRL + SHIFT + A to deselect the structure.
−
|| Press CTRL + SHIFT + A to deselect the structure.
+
|| Press '''CTRL + SHIFT + A''' to deselect the structure.
 
|-
 
|-
 
|| Point to the nanotubes.
 
|| Point to the nanotubes.
Line 489: Line 497:
 
|-
 
|-
 
|| Cursor on Navigation tool.
 
|| Cursor on Navigation tool.
−
|| Using '''Navigation tool''' rotate the '''nanotube''' for proper view.
+
|| Using '''Navigation tool,''' rotate the '''nanotube''' for proper view.
 
|-
 
|-
 
||  Cursor on the Panel.
 
||  Cursor on the Panel.
−
||  Now I will show carbon hexagon rings in the '''nanotube'''.  
+
||  Now I will show '''carbon hexagon rings''' in the '''nanotube'''.  
 
|-
 
|-
 
|| '''Display Types''' menu select '''Ring''' check box.  
 
|| '''Display Types''' menu select '''Ring''' check box.  
−
|| In the '''Display Types''' menu select ''' Ring''' check box.  
+
|| In the '''Display Types''' menu, select ''' Ring''' checkbox.  
  
−
Using '''Navigation''' tool rotate the '''nanotube''' to see carbon hexagons.
+
Using '''Navigation''' tool rotate the '''nanotube''' to see '''carbon hexagons'''.
 
|-
 
|-
 
||  
 
||  
Line 507: Line 515:
 
'''Summary'''
 
'''Summary'''
 
|| In this tutorial we have learnt about:
 
|| In this tutorial we have learnt about:
−
* Proton transfer in compounds by changing pH values
+
* '''Proton transfer''' in compounds by changing '''pH values'''
−
* Load crystal structures from crystal library
+
* Load '''crystal structures''' from '''crystal library'''
−
* Show various miller planes  
+
* Show various '''Miller planes'''
 
* Build super cells  
 
* Build super cells  
 
* Show geometries in coordination compounds and
 
* Show geometries in coordination compounds and
−
* Build nanotubes
+
* Build '''nanotubes'''
 
|-
 
|-
 
|| '''Slide number 9'''
 
|| '''Slide number 9'''
Line 519: Line 527:
 
|| As an assignment
 
|| As an assignment
  
−
Load silver chloride(AgCl) crystal structure and its show '''Miller''' planes.
+
Load '''silver chloride(AgCl) crystal structure''' and its show '''Miller planes'''.
  
 
Load structures from coordination library and show geometries.  
 
Load structures from coordination library and show geometries.  
  
−
Build '''nanotube''' with chirality index 9,9.  
+
Build '''nanotube''' with '''chirality index''' 9,9.  
 
|-
 
|-
 
|| '''Slide Number 10'''
 
|| '''Slide Number 10'''
Line 549: Line 557:
 
The Spoken Tutorial Project Team  
 
The Spoken Tutorial Project Team  
  
−
Conducts workshops using spoken  
+
Conducts workshops using spoken tutorials  
−
 
+
−
tutorials  
+
  
 
Gives certificates to those who pass  
 
Gives certificates to those who pass  
Line 584: Line 590:
 
|| The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.
 
|| The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.
 
|-
 
|-
 +
||
 
|| This is Madhuri Ganapathi singing off.  
 
|| This is Madhuri Ganapathi singing off.  
  

Latest revision as of 14:31, 23 June 2017

Visual Cue 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 Settings 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 on Polygon Display Type checkbox.

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 checkbox.

click on Build.

Click on Find double bonds checkbox 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 checkbox.

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.

Contributors and Content Editors

Madhurig, Nancyvarkey, PoojaMoolya

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