Avogadro/C2/Hydrogen-Bonding/English - Revision history

Madhurig at 05:54, 7 June 2017

2017-06-07T05:54:59Z

Madhurig: Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Warm greetings! Welcome to this tutorial on '''Hydrogen bonding in molecules'..."

2016-03-17T06:55:29Z

Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' ||Warm greetings! Welcome to this tutorial on '''Hydrogen bonding in molecules'..."

New page

{| border=1
||'''Visual Cue'''
||'''Narration'''
|-
|| '''Slide Number 1'''

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

Welcome to this tutorial on '''Hydrogen bonding in molecules'''.
|-
||'''Slide Number 2'''
'''Learning Objectives'''
||In this tutorial, we will learn to:
* Configure Avogadro
* Show hydrogen bonding in molecules
* Measure length of hydrogen bonds
* Show Force display type and
* Show dipole moments in molecules.
|-
||'''Slide Number 3'''
'''System Requirement'''
||Here I am using,

Ubuntu Linux OS version 14.04

Avogadro version 1.1.1. and

Working Internet connection.
|-
||'''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.

Structures used in this tutorial are provided as code files for your reference.
|-
||Cursor on the '''Panel'''.
||I have opened a new '''Avogadro''' window.
|-
||Click on '''Draw tool''', icon>> Click on the '''Panel'''.

Point to methane molecule.
||Click on '''Draw Tool''', icon and click on the '''Panel'''.

Methane is drawn on the '''Panel'''.
|-
||Cursor on the '''Panel'''.
||Now we will learn to configure '''Avogadro'''.
|-
||Go to '''Settings''' menu, click on '''Configure Avogadro'''.
||Go to '''Settings''' menu and click on '''Configure Avogadro'''.
|-
||'''Settings''' dialog box appears.
||'''Settings''' dialog box appears.
|-
||Cursor on dialog box.

Point to the side menu item.
||Dialog box has a side menu with three menu items:
* General

* Plugins

* Project tree.
|-
||Point to '''General''' menu.
||By default '''General''' menu is selected.
|-
||Point to '''Quality''' and '''Fog'''.
||'''General''' menu has two sliders:
'''Quality''' and '''Fog'''.
|-
||Drag the slider from '''Low''' to '''High'''.
||Quality of rendering increases as you drag the slider from '''Low''' to '''High'''.
|-
||Drag the '''Quality''' slider to '''Low''', click on '''Apply''' button.
||Drag the '''Quality''' slider to '''Low''' and click on '''Apply''' button.

Notice that structure is not properly rendered.
|-
||Drag the Quality slider to high.

Point to the molecule.
||Drag the '''Quality''' slider to '''Highv, and click on '''Apply''' button.

Notice that molecule appears bright with high quality rendering.
|-
||'''Slide Number 5'''

'''Quality'''

High quality rendering:
* is set for printing and publishing images
* uses more CPU power.
||High quality rendering:
* is set for printing and publishing images
* It uses more CPU power.
|-
||Drag the '''Quality''' slider to '''Medium'''.

Point to the molecule.
||Drag the '''Quality''' slider to '''Medium''' and click on '''Apply'''.

Medium quality setting works fine for general viewing purpose.
|-
||Point to '''Fog''' slider.
||Now to '''Fog''' slider.
|-
||Drag the '''Fog''' slider to '''Lots''', click on '''Apply''' button.

Point to the structure.
||Drag the '''Fog''' slider to '''Lots''' and click on '''Apply''' button.

Notice that structure is fogged.
|-
||Drag the '''Fog''' slider to '''Some''', click on '''Apply'''.

Point to the structure.
||Drag the '''Fog''' slider to '''Some''' and click on '''Apply'''.

Structure appears clearly.
|-
||Click on '''Plugins''' menu.
||Next to '''Plugins''' menu.
|-
||'''Display Types''' drop down appears.
||'''Display Types''' drop downs appear.
|-
||Point to '''Display Types''' check boxes.
||Notice that all the '''Display Types''' check boxes are enabled.
|-
||Click on '''Axes'''.

Point to '''Details''' text box.
||Click on '''Axes'''.

Details about '''Axes Display Type''' are displayed in '''Details''' text box.
|-
||Point to all '''Display Types'''.
(click on some display types and show the details)
||Similarly you can see the details of other '''Display Types'''.
|-
||un-check all the check boxes, click on '''Apply''' button.
||I will un-check all the check boxes and click on '''Apply''' button.
|-
||Point to '''Ball and Stick''' check box in '''Display Types'''.
||'''Ball and Stick''' check box alone is seen in the '''Display Types''' menu.
|-
||Uncheck the check box for '''Ball and Stick''' display.

Point to the structure on the '''Panel'''.
||Uncheck '''Ball and Stick Display Type''' checkbox.

If '''Ball and Stick''' is also disabled, molecule disappears from the '''Panel'''.
|-
||Click the check box.
||Click on '''Ball and Stick''' check box to enable the display.
|-
||Go to '''Plugins''' menu.
||To enable all the '''Display Types'''
go to '''Plugins'''.
|-
||Click on all check boxes '''Display Types''' drop down.
||Click on all check boxes in '''Display Types''' drop down.
|-
||Click on '''Apply''' button.
||Click on '''Apply''' button.
|-
||Cursor on '''Panel'''.
||All '''Display Types''' are displayed in the '''Display Types''' drop down.
|-
||Click '''OK'''.
||Click on '''OK''' to close the '''Settings''' dialog box.
|-
||Cursor on '''Display Types'''.

Click on '''Add''' button.
||If any of the '''Display Types''' is not activated in the '''Display Types''' menu:
click on '''Add''' button.
|-
||Point to '''Add Display Types''' dialog box.
||'''Add Display Type''' dialog box appears.
|-
||Click on '''Types''' drop down, choose the '''Display Types''' you need.

Choose '''Hydrogen Bond''', click '''OK'''.
||Click on '''Types''' drop down and choose the '''Display Type''' you need.

I will choose '''Hydrogen Bond''' and click '''OK'''.
|-
||Point to '''Hydrogen Bond Display Type''' in the '''Display Types''' menu.
||'''Hydrogen Bond Display Type''' appears in the '''Display Types''' menu.
|-
||Cursor on the '''Panel'''.
||Now I will demonstrate hydrogen bonding in '''polar''' methanol molecules.
|-
||Point to methane molecule on the '''Panel'''.
||We already have a methane molecule on the '''Panel''.

For demonstration I need a group of methane molecules.
|-
||Point to '''Draw tool'''.
||Easy method to draw methane molecules is, using '''Draw tool'''.
|-
||Point to '''Draw Settings''' menu.
||By default '''Draw Settings''' menu has,
* '''Element''' as '''Carbon''' and
* '''Bond Order''' as '''Single'''.

Click on the '''Panel'''.
|-
||Click on '''Element''' drop down>> select '''Oxygen'''.
||Click on '''Element''' drop down.

Select '''Oxygen'''.
|-
||Click on one of the Hydrogens of the methane molecules.

Point to Methanol molecules on the '''Panel'''.
||Then click on any one of the Hydrogens of the methane molecules.

We now have a group of Methanol molecules on the '''Panel'''.
|-
||Click on '''Hydrogen Bond''' check box in the '''Display types'''.
||Click on '''Hydrogen Bond''' check box in the '''Display Types'''.
|-
||Cursor on the '''Panel'''.
||Let's optimize the molecules for proper orientation.
|-
||Click on '''Auto Optimization Tool''' icon on the tool bar.
||Click on '''Auto Optimization Tool''' on the tool bar.
|-
||Point to the menu.
||'''Auto Optimization Settings''' menu appears on the left.
|-
||Click on '''Force Field''' drop down list, select '''MMFF94'''.
||In the '''Force Field''' drop down, select '''MMFF94'''.
|-
||Click on '''Start''' button.
||Click on '''Start''' button to optimize.
|-
||Point to the yellow dashed lines.

Click on '''Stop''' to close '''AutoOptimization Settings'''.
||You can see hydrogen bond formation as yellow dashed lines.

These lines are formed between hydrogen of one molecule and oxygen of other molecule.

Click on '''Stop''' to stop the '''Auto optimization'''.
|-
||Cursor on the '''Panel'''.
||I will now demonstrate intramolecular hydrogen bonding in '''ortho-nitrophenol'''.
|-
||Cursor on the '''Panel'''.
||For this I will fetch the molecule from '''Chemical structure database'''.
|-
||Cursor on the '''Panel'''
||Close all the previously opened windows and open a new window.
|-
||Click on '''File''' Menu navigate to '''Import'''.

Click on '''Fetch by Chemical name'''.
||Click on '''File''' menu navigate to '''Import'''.

Click on '''Fetch by Chemical name'''.
|-
||Point to the box.
||'''Chemical Name''' text box appears.
|-
||Type o-nitrophenol and click on OK.
||Type '''o-nitrophenol''' in lower case and click on OK button.

'''Ortho-nitrophenol''' molecule appears on the '''Panel'''.
|-
||Cursor on the '''Panel'''.
||To show hydrogen bonding,
* you need a group of '''Ortho-nitrophenol''' molecules on the '''Panel'''.
|-
||Cursor on the Panel.
||I have copied and pasted molecules on the Panel.
|-
||Point to selection tool on the tool bar.

Press '''CTRL''' +'C''' to copy, '''CTRL+ V''' to paste.
||Select the molecule using selection tool.

Press '''CTRL +C''' to copy and '''CTRL +V''' to paste.
|-
||Click on '''Hydrogen bond''' check box.
||Click on '''Hydrogen Bond''' check box.
|-
||Click on '''Start''' in '''Auto Optimization''' menu.
||Optimize the molecules for proper orientation if required.
|-
||Point to optimization process.

Point to '''Hydrogen bond'''.
||During optimization process, intra molecular Hydrogen bond is formed within the molecules.

Hydrogen bond is formed between, Oxygen of '''nitro''' group and Hydrogen of '''Hydroxy''' group in the molecule.
|-
||Cursor on the '''Panel'''.
||Now let's measure the length of hydrogen bond.
|-
||Click on '''Click to Measure''' icon on the tool bar.

Click on Oxygen atom and hydrogen atom.
||Click on '''Click to Measure''' icon on the tool bar.

Click on hydrogen atom and Oxygen atom .

Hydrogen bond length is displayed at the bottom of the Panel.
|-
||Slide
||This slide shows the importance of hydrogen bonding.
|-
||'''Slide Number 6'''
'''Significance of Hydrogen Bonding'''.
||Hydrogen bonds:
* determine unique solvent capabilities of water and stabilize crystal structure of ice.
* hold complementary strands of DNA together.
* determine and stabilize structures of proteins and nucleic acids.
* involve in the mechanism of enzyme catalysis.
|-
||'''Slide Number 7'''

'''Assignment'''
||As an
assignment, show Hydrogen bonding in
* Para-hydroxybenzoic acid.
* Nucleobases, adenine and uracil.

Your assignments should look as follows.

Observe inter molecular hydrogen bonding in '''Para-hydroxybenzoic acid''' molecules.

And '''adenine''' and '''uracil''' molecules.
|-
||Point to '''Display Types''' menu.
||We have an option in the '''Display Types''' to show force for the molecules.
|-
||Point to water molecules.
||I will open a new window with a few water molecules.
|-
||In the '''Display Types''' click on '''Force''' check box.
||In the '''Display Types''' click on '''Force''' check box.
|-
||Click on '''Hydrogen Bond''' check box.
||Click on '''Hydrogen Bond''' check box.
|-
||Click on '''Auto Optimization Tool''' icon.
||Click on '''Auto Optimization Tool''' icon on the tool bar.
|-
||Select '''MMFF94 Force Field'''.
||Select '''MMFF94 Force Field'''.
|-
||Click on '''Start''' button.
||Click on '''Start''' button.
|-
||Point to green arrows.
||During optimization process:
'''Force''' display type shows, forces acting on each atom with green arrows.

Arrows illustrate direction and amount of force.

When a molecule is close to its optimization, arrows become small and then vanish.
|-
||
||Now to '''dipole moment''' in a molecule.
|-
||'''Slide Number 8'''

'''Dipole Moment'''
||* '''Dipole moment''' is due to charge separation in '''polar''' molecules.
* Dipole moment(μ) = charge(Q) * distance of separation(r)
* Dipole moment is expressed in Debye units.
|-
||Cursor on the '''Panel'''.
||Now I will show dipole moment in hydrogen cyanide(HCN) and water molecules.
|-
||Point to Draw tool,
||Open a new window.

Using Draw tool, draw hydrogen cyanide(HCN) molecule on the Panel.

Select Hydrogen and draw bond to carbon.

Select Nitrogen, Select bond order as triple and draw a bond as shown.
|-
||Point to '''MMFF94 Force Field'''.
||Optimize the structure using '''MMFF94 Force Field'''.
|-
||Click on '''Dipole''' check box in '''Display Types'''.
||To show '''dipole moment''' click on '''Dipole''' check box in '''Display Types'''.
|-
||Point to red colored arrow
||'''Dipole''' is shown using a red colored arrow.
|-
|| Go '''View''' menu.

Navigate to '''Properties''' >> select '''Molecule Properties'''.

Point to the window.
||To view the estimated dipole moment, go to '''View''' menu.

Navigate to '''Properties''' and select '''Molecule Properties'''.

Molecule Properties window opens.
|-
||Point to the estimated dipole moment of hydrogen cynaide.
||Window shows estimated dipole moment of hydrogen cyanide as '''0.396D'''.
|-
||Point to estimated dipole moment of water.
||Similarly the estimated dipole moment of water is '''0.245D'''.
|-
||
||Let's summarize.
|-
||'''Slide Number'''
'''Summary'''
||In this tutorial we have learnt to:
* Configure Avogadro
* Show intermolecular hydrogen bonding in Methanol
* Show intramolecular hydrogen bonding in o-nitrophenol
* Measure length of hydrogen bonds
* Show Force display type in water molecules
* Show dipole moments in HCN and H2O molecules.
|-
||'''Slide Number 9'''

'''Assignment'''
||As an assignment,
* Show dipole moments for carbon dioxide and methyl chloride molecules.
*Show '''Force Display Type''' for ammonia molecules.
|-
||'''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.
|-
|}

@@ Line 12: / Line 12: @@
 ||'''Slide Number 2'''
 '''Learning Objectives'''
-||In this tutorial, we will learn to:
+||In this tutorial, we will learn to,
-* Configure Avogadro
-* Show hydrogen bonding in molecules
+Configure Avogadro
-* Measure length of hydrogen bonds
-* Show Force display type and
+Show hydrogen bonding in molecules
-* Show dipole moments in molecules.
 |-
 ||'''Slide Number 3'''
@@ Line 70: / Line 75: @@
 Point to the side menu item.
-||Dialog box has a side menu with three menu items:
+||Dialog box has a side menu with three menu items-
-* General
-* Plugins
+General
-* Project tree.
+Plugins
 |-
 ||Point to  '''General''' menu.
@@ Line 95: / Line 101: @@
 Point to the molecule.
-||Drag the '''Quality''' slider to '''Highv, and click on '''Apply''' button.
+||Drag the '''Quality''' slider to '''High''', and click on '''Apply''' button.
 Notice that molecule appears bright with high quality rendering.
@@ Line 106: / Line 112: @@
 * is set for printing and publishing images
 * uses more CPU power.
-||High quality rendering:
+||High quality rendering-
-* is set for printing and publishing images
-* It uses more CPU power.
+is set for printing and publishing images
 |-
 ||Drag the '''Quality''' slider to '''Medium'''.
@@ Line 218: / Line 226: @@
 ||Point to '''Draw Settings''' menu.
 ||By default '''Draw Settings''' menu has,
-* '''Element''' as '''Carbon'''  and
-* '''Bond Order''' as '''Single'''.
+'''Element''' as '''Carbon'''  and
 Click on the '''Panel'''.
@@ Line 254: / Line 264: @@
 |-
 ||Point to the yellow dashed lines.
@@ Line 297: / Line 306: @@
 ||Point to selection tool on the tool bar.
-Press '''CTRL''' +'C''' to copy,  '''CTRL+ V''' to paste.
+Press '''CTRL''' + C''' to copy,  '''CTRL+ V''' to paste.
 ||Select the molecule using selection tool.
-Press '''CTRL +C''' to copy and  '''CTRL +V''' to paste.
+Press '''CTRL + C''' to copy and  '''CTRL + V''' to paste.
 |-
 ||Click on '''Hydrogen bond''' check box.
@@ Line 311: / Line 320: @@
 Point to '''Hydrogen bond'''.
-||During optimization process, intra molecular Hydrogen bond is formed within the molecules.
+||During optimization process, Intra molecular Hydrogen bond is formed within the molecules.
 Hydrogen bond is formed between, Oxygen of '''nitro''' group and Hydrogen of '''Hydroxy''' group in the molecule.
@@ Line 332: / Line 341: @@
 ||'''Slide Number 6'''
 '''Significance of Hydrogen Bonding'''.
-||Hydrogen bonds:
+||Hydrogen bonds-
-* determine unique solvent capabilities of  water and stabilize crystal structure of ice.
-* hold complementary strands of DNA together.
+determine unique solvent capabilities of  water and stabilize crystal structure of ice.
-* determine and stabilize structures of proteins and nucleic acids.
-* involve in the mechanism of enzyme catalysis.
+hold complementary strands of DNA together.
 |-
 ||'''Slide Number 7'''
@@ Line 342: / Line 355: @@
 '''Assignment'''
 ||As an
-assignment, show  Hydrogen bonding in
+assignment, show  Hydrogen bonding in,
-* Para-hydroxybenzoic acid.
-* Nucleobases, adenine and uracil.
+. Para-hydroxybenzoic acid.
 Your assignments should look as follows.
@@ Line 387: / Line 402: @@
 '''Dipole Moment'''
-||* '''Dipole moment''' is due to charge separation in '''polar''' molecules.
+|| '''Dipole moment''' is due to charge separation in '''polar''' molecules.
-* Dipole moment(μ) = charge(Q) * distance of separation(r)
-* Dipole moment is expressed in Debye units.
+Dipole moment(μ) = charge(Q) * distance of separation(r)
 |-
 ||Cursor on the '''Panel'''.
@@ Line 434: / Line 451: @@
 ||'''Slide Number'''
 '''Summary'''
-||In this tutorial we have learnt to:
+||In this tutorial we have learnt to-
-* Configure Avogadro
-* Show intermolecular hydrogen bonding in Methanol
+Configure Avogadro
-* Show intramolecular hydrogen bonding in o-nitrophenol
-* Measure  length of hydrogen bonds
+Show intermolecular hydrogen bonding in Methanol
-* Show Force display type in water molecules
-* Show dipole moments in HCN and H2O molecules.
+Show intramolecular hydrogen bonding in o-nitrophenol
 |-
 ||'''Slide Number 9'''
@@ Line 446: / Line 469: @@
 '''Assignment'''
 ||As an assignment,
-* Show dipole moments for carbon dioxide and methyl chloride molecules.
+. Show dipole moments for carbon dioxide and methyl chloride molecules.
-*Show '''Force Display Type''' for ammonia molecules.
 |-
 ||'''Slide Number 10'''