Sandhya.np14 at 12:38, 8 July 2018

2018-07-08T12:38:12Z

Sandhya.np14 at 11:54, 5 June 2018

2018-06-05T11:54:35Z

PoojaMoolya: Created page with "{| border=1 |'''Time''' |'''Narration''' |- | 00:01 |Warm greetings! Welcome to this tutorial on '''Hydrogen bonding in molecules'''. |- |00:07 |In this tutorial, we will le..."

2017-09-02T05:41:31Z

Created page with "{| border=1 |'''Time''' |'''Narration''' |- | 00:01 |Warm greetings! Welcome to this tutorial on '''Hydrogen bonding in molecules'''. |- |00:07 |In this tutorial, we will le..."

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{| border=1
|'''Time'''
|'''Narration'''

|-
| 00:01
|Warm greetings! Welcome to this tutorial on '''Hydrogen bonding in molecules'''.

|-
|00:07
|In this tutorial, we will learn to, Configure Avogadro

|-
|00:11
|Show hydrogen bonding in molecules

|-
|00:14
|Measure length of hydrogen bonds

|-
|00:16
|Show Force display type and Show dipole moments in molecules.

|-
|00:22
|Here I am using, Ubuntu Linux OS version 14.04

|-
|00:27
|Avogadro version 1.1.1. and Working Internet connection.

|-
|00:34
|To follow this tutorial, you should be familiar with: '''Avogadro''' interface.

|-
|00:40
|If not, for relevant tutorials, please visit our website.

|-
|00:45
|Structures used in this tutorial are provided as code files for your reference.

|-
|00:52
|I have opened a new '''Avogadro''' window.

|-
|00:56
|Click on '''Draw Tool''', icon and click on the '''Panel'''.

|-
|01:01
|'''methane''' is drawn on the '''Panel'''.

|-
|01:04
|Now we will learn to configure '''Avogadro'''.

|-
|01:08
|Go to '''Settings''' menu and click on '''Configure Avogadro'''.

|-
|01:13
|'''Settings''' dialog box appears.

|-
|01:16
|Dialog box has a side menu with three menu items-

General

Plugins

Project tree.

|-
|01:24
|By default '''General''' menu is selected.

|-
|01:28
|'''General''' menu has two sliders: '''Quality''' and '''Fog'''.

|-
|01:34
|Quality of rendering increases as you drag the slider from '''Low''' to '''High'''.

|-
|01:41
|Drag the '''Quality''' slider to '''Low''' and click on '''Apply''' button.

|-
|01:47
|Notice that structure is not properly rendered.

|-
|01:51
|Drag the '''Quality''' slider to '''High''', and click on '''Apply''' button.

|-
|01:56
|Notice that molecule appears bright with high quality rendering.

|-
|02:02
|High quality rendering- is set for printing and publishing images

|-
|02:07
|It uses more CPU power.

|-
|02:11
|Drag the '''Quality''' slider to '''Medium''' and click on '''Apply'''.

|-
|02:16
|Medium quality setting works fine for general viewing purpose.

|-
|02:21
|Now to '''Fog''' slider.

|-
|02:24
|Drag the '''Fog''' slider to '''Lots''' and click on '''Apply''' button.

|-
|02:28
|Notice that structure is fogged.

|-
|02:32
|Drag the '''Fog''' slider to '''Some''' and click on '''Apply'''. Structure appears clearly.

|-
|02:40
|Next to '''Plugins''' menu.

|-
|02:43
|'''Display Types''' drop downs appear.

|-
|02:46
|Notice that all the '''Display Types''' check boxes are enabled.

|-
|02:51
|Click on '''Axes'''. Details about '''Axes Display Type''' are displayed in '''Details''' text box.

|-
|02:59
|Similarly you can see the details of other '''Display Types'''.

|-
|03:04
|I will un-check all the check boxes and click on '''Apply''' button.

|-
|03:11
|'''Ball and Stick''' check box alone is seen in the '''Display Types''' menu.

|-
|03:16
|Uncheck '''Ball and Stick Display Type''' checkbox.

|-
|03:20
|If '''Ball and Stick''' is also disabled, molecule disappears from the '''Panel'''.

|-
|03:26
|Click on '''Ball and Stick''' check box to enable the display.

|-
|03:30
|To enable all the '''Display Types''' go to '''Plugins'''.

|-
|03:33
|Click on all check boxes in '''Display Types''' drop down.

|-
|03:39
|Click on '''Apply''' button.

|-
|03:41
|All '''Display Types''' are displayed in the '''Display Types''' drop down.

|-
|03:46
|Click on '''OK''' to close the '''Settings''' dialog box.

|-
|03:50
|If any of the '''Display Types''' is not activated in the '''Display Types''' menu: click on '''Add''' button.

|-
|03:58
|'''Add Display Type''' dialog box appears.

|-
|04:02
|Click on '''Types''' drop down and choose the '''Display Type''' you need.

|-
|04:07
|I will choose '''Hydrogen Bond''' and click '''OK'''.

|-
|04:11
|'''Hydrogen Bond Display Type''' appears in the '''Display Types''' menu.

|-
|04:16
|Now I will demonstrate hydrogen bonding in '''polar methanol''' molecules.

|-
|04:22
|We already have a '''methane''' molecule on the '''Panel''.

|-
|04:26
|For demonstration I need a group of '''methane''' molecules.

|-
|04:31
|Easy method to draw '''methane''' molecules is, using '''Draw tool'''.

|-
|04:36
|By default '''Draw Settings''' menu has, '''Element''' as '''Carbon''' and '''Bond Order''' as '''Single'''.

|-
|04:43
|Click on the '''Panel'''.

|-
|04:46
|Click on '''Element''' drop down. Select '''Oxygen'''.

|-
|04:50
|Then click on any one of the Hydrogens of the '''methane''' molecules.

|-
|04:56
|We now have a group of '''Methanol''' molecules on the '''Panel'''.

|-
|05:00
|Click on '''Hydrogen Bond''' check box in the '''Display Types'''.

|-
|05:04
|Let's optimize the molecules for proper orientation.

|-
|05:08
|Click on '''Auto Optimization Tool''' on the tool bar.

|-
|05:12
|'''Auto Optimization Settings''' menu appears on the left.

|-
|05:17
|In the '''Force Field''' drop down, select '''MMFF94'''.

|-
|05:22
|Click on '''Start''' button to optimize.

|-
|05:26
|You can see '''hydrogen''' bond formation as yellow dashed lines.

|-
|05:31
|These lines are formed between '''hydrogen''' of one molecule and '''oxygen''' of other molecule.

|-
|05:38
|Click on '''Stop''' to stop the '''Auto optimization'''.

|-
|05:42
|I will now demonstrate intramolecular '''hydrogen''' bonding in '''ortho-nitrophenol'''.

|-
|05:48
|For this I will fetch the molecule from '''Chemical structure database'''.

|-
|05:54
|Close all the previously opened windows and open a new window.

|-
|05:59
|Click on '''File''' menu navigate to '''Import'''.Click on '''Fetch by Chemical name'''.

|-
|06:06
|'''Chemical Name''' text box appears.

|-
|06:09
|Type '''ortho-nitrophenol''' in lower case and click on OK button.

|-
|06:15
|'''Ortho-nitrophenol''' molecule appears on the '''Panel'''.

|-
|06:19
|To show '''hydrogen''' bonding, you need a group of '''Ortho-nitrophenol''' molecules on the '''Panel'''.

|-
|06:26
|I have copied and pasted molecules on the Panel.

|-
|06:30
|Select the molecule using selection tool.

|-
|06:34
|Press '''CTRL + C''' to copy and '''CTRL + V''' to paste.

|-
|06:39
|Click on '''Hydrogen Bond''' check box.

|-
|06:42
|Optimize the molecules for proper orientation if required.

|-
|06:46
|During optimization process, Intra molecular Hydrogen bond is formed within the molecules.

|-
|06:54
|Hydrogen bond is formed between, Oxygen of '''nitro''' group and Hydrogen of '''Hydroxy''' group in the molecule.

|-
|07:02
|Now let's measure the length of hydrogen bond.

|-
|07:06
|Click on '''Click to Measure''' icon on the tool bar.

|-
|07:10
|Click on hydrogen atom and Oxygen atom .

|-
|07:14
|Hydrogen bond length is displayed at the bottom of the Panel.

|-
|07:19
|This slide shows the importance of hydrogen bonding.

|-
|07:23
|Hydrogen bonds- determine unique solvent capabilities of water and stabilize crystal structure of ice.

|-
|07:32
|Hold complementary strands of DNA together.

|-
|07:36
|Determine and stabilize structures of proteins and nucleic acids.

|-
|07:41
|Involve in the mechanism of enzyme catalysis.

|-
|07:46
|As an assignment, show Hydrogen bonding in,

1. Para-hydroxybenzoic acid.

2. Nucleobases- adenine and uracil.

|-
|07:56
|Your assignments should look as follows.

|-
|08:00
|Observe inter molecular hydrogen bonding in '''Para-hydroxybenzoic acid''' molecules.

And '''adenine''' and '''uracil''' molecules.

|-
|08:10
|We have an option in the '''Display Types''' to show force for the molecules.

|-
|08:15
|I will open a new window with a few water molecules.

|-
|08:19
|In the '''Display Types''' click on '''Force''' check box.

|-
|08:23
|Click on '''Hydrogen Bond''' check box.

|-
|08:26
|Click on '''Auto Optimization Tool''' icon on the tool bar.

|-
|08:30
|Select '''MMFF94 Force Field'''. Click on '''Start''' button.

|-
|08:36
|During optimization process: '''Force''' display type shows, forces acting on each atom with green arrows.

|-
|08:45
|Arrows illustrate direction and amount of force.

|-
|08:49
|When a molecule is close to its optimization, arrows become small and vanish.

|-
|08:55
|Now to '''dipole moment''' in a molecule.

|-
|08:59
| '''Dipole moment''' is due to charge separation in '''polar''' molecules.

|-
|09:04
|Dipole moment(μ) = charge(Q) times distance of separation(r)

|-
|09:09
|Dipole moment is expressed in Debye units.

|-
|09:13
|Now I will show dipole moment in hydrogen cyanide(HCN) and water molecules.

|-
|09:20
|Open a new window.

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

|-
|09:27
|Select Hydrogen and draw a bond to carbon.

|-
|09:31
|Select Nitrogen, Select bond order as triple and draw a bond as shown.

|-
|09:38
|Optimize the structure using '''MMFF94 Force Field'''.

|-
|09:44
|To show '''dipole moment''' click on '''Dipole''' check box in '''Display Types'''.

|-
|09:50
|'''Dipole''' is shown using a red colored arrow.

|-
| 09:54
|To view the estimated dipole moment, go to '''View''' menu.

|-
|09:57
|Navigate to '''Properties''' and select '''Molecule Properties'''.

Molecule Properties window opens.

|-
|10:05
|Window shows estimated dipole moment of hydrogen cyanide as '''0.396D'''.

|-
|10:13
|Similarly the estimated dipole moment of water is '''0.245D'''.

|-
|10:21
|Let's summarize.

|-
|10:23
|In this tutorial we have learnt to-

Configure Avogadro

|-
|10:27
|Show intermolecular hydrogen bonding in Methanol

|-
|10:31
|Show intramolecular hydrogen bonding in ortho-nitrophenol

|-
|10:35
|Measure length of hydrogen bonds

|-
|10:38
|Show Force display type in water molecules

|-
|10:42
|Show dipole moments in HCN and water molecules.

|-
|10:48
|As an assignment,
1. Show dipole moments for carbon dioxide and methyl chloride molecules.

2. Show '''Force Display Type''' for ammonia molecules.

|-
|10:59
|This video summarises the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.

|-
|11:06
|We conduct workshops using Spoken Tutorials and give certificates.

Please contact us.

|-
|11:12
|The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.

|-
|11:18
|This is Madhuri Ganapathi singing off. Thank you for joining.
|-
|}

@@ Line 21: / Line 21: @@
 |-
 |00:16
-|show Force display type and show dipole moments in molecules.
+|show '''Force display''' type and show '''dipole moment'''s in molecules.
 |-
 |00:22
-|Here I am using: Ubuntu Linux OS version 14.04,
+|Here I am using: '''Ubuntu Linux OS''' version '''14.04''',
 |-
 |00:27
-|Avogadro version 1.1.1. and working internet connection.
+|'''Avogadro''' version '''1.1.1''' and working internet connection.
 |-
 |00:34
-|To follow this tutorial, you should be familiar with '''Avogadro''' interface.
+|To follow this tutorial, you should be familiar with ''''Avogadro' interface'''.
 |-
 |00:40
-|If not, for relevant tutorials, please visit our website.
+|If not, for relevant tutorials, please visit our '''website'''.
 |-
 |00:45
-|Structures used in this tutorial are provided as code files for your reference.
+|Structures used in this tutorial are provided as '''code file'''s for your reference.
 |-
@@ Line 57: / Line 57: @@
 |-
 |01:04
-|Now we will learn to configure '''Avogadro'''.
+|Now, we will learn to configure '''Avogadro'''.
 |-

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

Sandhya.np14 at 12:38, 8 July 2018

Sandhya.np14 at 11:54, 5 June 2018

PoojaMoolya: Created page with "{| border=1 |'''Time''' |'''Narration''' |- | 00:01 |Warm greetings! Welcome to this tutorial on '''Hydrogen bonding in molecules'''. |- |00:07 |In this tutorial, we will le..."