Sandhya.np14 at 12:34, 8 July 2018

2018-07-08T12:34:40Z

Sandhya.np14 at 11:16, 5 June 2018

2018-06-05T11:16:31Z

PoojaMoolya: Created page with " {| border=1 ! Time ! Narration |- |00:01 | Warm greetings everyone. Welcome to this tutorial on '''Create surfaces.''' |- | 00:07 | In th..."

2017-07-21T11:41:44Z

Created page with " {| border=1 ! <center>Time</center> ! <center>Narration</center> |- |00:01 | Warm greetings everyone. Welcome to this tutorial on '''Create surfaces.''' |- | 00:07 | In th..."

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{| border=1
! <center>Time</center>
! <center>Narration</center>

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|00:01
| Warm greetings everyone. Welcome to this tutorial on '''Create surfaces.'''

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| 00:07
| In this tutorial, we will learn to: View properties of the molecule

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| 00:13
| Label the atoms with '''partial charge'''

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| 00:17
| Create '''Van der waals '''surface

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| 00:20
| Color the surface according to the '''electrostatic potential''' energies.

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| 00:25
| Here I am using '''Ubuntu Linux '''OS version. 14.04

'''Avogadro''' version 1.1.1.

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|00:35
| To follow this tutorial, you should be familiar with: '''Avogadro '''interface.

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| 00:41
|If not, for relevant tutorials, please visit our website.

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| 00:47
| Here I have opened the '''Avogadro''' window.

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| 00:51
| Insert a molecule of '''butane''' from '''Insert Fragment Library.'''

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| 00:57
|Click on '''Build''' menu then click on '''Insert ->fragment'''

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| 01:04
| Double click on '''alkanes''' folder to open. Select '''butane.cml.'''

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| 01:11
| Click on '''Insert''' button.

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| 01:14
| Close the dialog box.

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| 01:17
| A model of '''n-butane''' is displayed on the panel.

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| 01:21
|Clear the selection using '''Select none''' option from the '''Select''' menu.

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| 01:26
| Let us display molecular properties of the molecule.

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| 01:30
| Click on '''View '''menu, select '''Properties''' option.

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| 01:35
| From the sub-menu, click on '''Molecule Properties.'''

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| 01:39
|'''Molecule Properties''' window opens with information such as,

'''IUPAC Molecule Name''', '''Molecular weight''', '''Chemical Formula''', '''Dipole moment''' etc.

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| 01:54
| Click on '''OK''' to close the window.

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| 01:57
| Similarly to view the '''Atom Properties''': Click on '''Atom properties''' option from the '''properties''' menu.

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| 02:04
| A table opens with values of properties such as: '''Element''', '''Type''', '''Valence''', '''Formal charge''' etc for each atom in the molecule.

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| 02:17
| Close the dialog box.

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| 02:20
| Explore other properties like '''Angle''', '''Torsion''' and '''Conformer''' from the list.

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| 02:27
| Let us now learn to label the atoms in the molecule with '''partial charge'''.

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| 02:33
| Click on '''Display settings''': From the '''Display Types''' list, check the box against '''Label.'''

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| 02:43
| Click on the '''Spanner''' symbol on the right side of '''Label''' check box.

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| 02:48
| '''Label Settings''' window opens.

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| 02:51
| Click on '''Partial charge''' option from '''atom labels''' text drop down. Now all the atoms in the molecule are labeled with '''partial charge'''.

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| 03:01
| The '''partial charge''' distribution helps to predict the reactivity of the carbon atoms.

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| 03:07
| '''Inductive effect''' can be explained by labeling the atoms with '''partial charge'''.

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| 03:14
| Replace a '''hydrogen''' with '''chlorine'''. Notice the change in the value of '''partial charge''' along the''' carbon''' chain.

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| 03:22
| Because of the '''inductive effect''' '''carbons''' close to '''chlorine''' become more positive.

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| 03:28
| We have also an option to label the bonds. Click on the '''bond labels '''text box.

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| 03:35
|The drop-down menu has options to label the bonds.

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| 03:39
|Click on '''bond length'''. The '''bond lengths''' for all the bonds are displayed on the panel.

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| 03:46
| To change the color of the labels, click on the box filled with color.

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| 03:51
|Select the color from the '''Select atoms label color''' window. Click on '''OK '''button.

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| 03:59
| We can shift the labels in '''X, Y '''and '''Z''' direction.

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| 04:04
|Click on the '''increment or decrement buttons''' in the '''label shift''' menu.
Close the dialog box.

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| 04:12
| Another very useful feature of '''Avogadro''', is the ability to create surfaces.

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| 04:18
|The option for creating surfaces is available in the '''extensions''' menu.

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| 04:24
| Click on '''extensions''' menu, then click on '''create surfaces''' option.

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| 04:30
|A '''create surface '''dialog box''' '''opens on the screen.

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| 04:34
| Surface type drop-down has two options: '''Van der waals''' and '''electro-static potential'''.

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| 04:42
| '''Electrostatic potential surfaces''' are not yet supported in '''Avogadro'''.

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| 04:48
| Choose '''Van der waals '''option. In the '''Color By''' drop down select '''Nothing'''.

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| 04:55
| Set '''Resolution''' to '''Medium'''

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| 04:58
|'''Iso value '''to zero. Click on '''Calculate''' button.

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| 05:04
|Close the dialog box.

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| 05:07
| The '''van der waals''' surface is displayed on the Panel.

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| 05:11
| '''Van der waals '''surface is a representation of surface through which a molecule interacts with other molecules.

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| 05:19
| To change the surface settings: Click on the spanner symbol corresponding to surfaces.

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| 05:26
| A surface setting dialog box opens. Drag the '''slider''' to adjust the '''opacity'''.

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| 05:34
| In the '''Render '''drop-down there are different display options to choose such as:

'''Fill''',''' lines''' and '''points'''.

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| 05:42
|The default option is '''fill'''.

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| 05:45
| To change the color of the surface: Click on the box filled with color next to '''positive''' option.

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| 05:52
|Select the color from the basic color chart by clicking on the color. Click on''' OK''' button.

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| 06:00
| Next from the '''Create surface''' window: Choose '''Electrostatic potential''' from the '''Color by''' drop-down.

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| 06:07
| Set the '''resolution''' to '''medium'''. Set the '''Iso value''' to 0.02.

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| 06:14
|Setting low '''Iso value''' gives a finer surface.

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| 06:18
| Click on '''Calculate button.'''

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| 06:21
| On the '''panel '''we see the surface of '''1-chloro butane''' Colored according to the '''electro-static potential values''' of atoms.

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| 06:31
| '''Electrostatic potential surface''' illustrates '''charge distributions''' of the molecule.

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|06:37
|They are also used in predicting the behavior of molecules

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|06:42
|By default, areas of high '''electronegativity''' are colored in red and least in blue.

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|06:49
| Here are a few more examples of molecules with '''electro-static potential surfaces.'''

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| 06:56
| '''Aniline and cyclohexylamine.'''

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|07:00
|The '''electron density''' on the '''Nitrogen''' of '''cyclohexylamine''' is more localized than it is in '''aniline'''.

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|07:08
|Hence '''cyclohexylamine''' is a stronger base.

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| 07:12
| Let's summarize. In this tutorial we have learnt to: View properties of the molecule.

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| 07:20
| Label the atoms with '''partial charge'''.

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|07:24
| Create '''Van der waals '''surface

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|07:27
|Color the surface according to the '''electrostatic potential''' energies.

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| 07:33
| As an assignment : Compare the reactivity of '''acetaldehyde''' and '''formamide''' using '''electro-static potential surface'''.

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|07:43
|Label the atoms with '''partial charge'''.

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|07:47
| Your completed assignment should look as follows.

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|07:51
|Negative charge indicated in red is more localized on the '''oxygen''' atom of '''acetaldehyde'''.

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|07:58
|The Negative charge is more delocalized in '''formamide'''.

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|08:02
|Hence '''Acetaldehyde''' is more reactive than '''Formamide'''.

|-
| 08:07
| This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.

|-
| 08:15
| We conduct workshops using Spoken Tutorials and give certificates. Please contact us.

|-
|08:22
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India

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| 08:29
| This tutorial is contributed by Viswa Janani Vasudhevan and Snehalatha Kaliappan.
Thank you for joining.

|}

@@ Line 26: / Line 26: @@
 |-
 | 00:25
-| Here, I am using '''Ubuntu Linux '''OS version. 14.04,
+| Here, I am using '''Ubuntu Linux OS''' version. '''14.04''',
-'''Avogadro''' version 1.1.1.
+'''Avogadro''' version '''1.1.1'''.
 |-
 |00:35
-| To follow this tutorial, you should be familiar with '''Avogadro '''interface.
+| To follow this tutorial, you should be familiar with ''''Avogadro' interface'''.
 |-
@@ Line 52: / Line 52: @@
 |-
 |  01:04
-| Double click on '''alkanes''' folder to open. Select '''butane.cml.'''
+| Double-click on '''alkanes''' folder to open. Select '''butane.cml.'''
 |-

Avogadro/C2/Create-Surfaces/English-timed - Revision history

Sandhya.np14 at 12:34, 8 July 2018

Sandhya.np14 at 11:16, 5 June 2018

PoojaMoolya: Created page with " {| border=1 ! Time ! Narration |- |00:01 | Warm greetings everyone. Welcome to this tutorial on '''Create surfaces.''' |- | 00:07 | In th..."