Avogadro/C2/Create-Surfaces/English
Visual Cue | Narration |
Slide Number 1
Title Slide |
Warm greetings everyone.
Welcome to this tutorial on Create surfaces. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to:
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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:
For relevant tutorials, visit our website. www.spoken-tutorial.org. |
To follow this tutorial, you should be familiar with:
Avogadro interface.
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Cursor on the Avogadro window. | Here I have opened the Avogadro window. |
Cursor on the Panel
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Insert a molecule of butane from Insert Fragment Library.
Insert ->fragment |
Double click on alkanes folder to open.
Select butane.cml. |
Double click on alkanes folder to open.
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Click on Insert button. | Click on Insert button. |
Close the dialog box. | Close the dialog box. |
Point to n-butane | A model of n-butane is displayed on the panel.
Clear the selection using Select none option from the Select menu. |
Cursor on molecule | Let us display molecular properties of the molecule. |
Click on View menu.
Navigate down and click on properties. |
Click on View menu, select Properties option. |
A sub menu appears
Cursor on the sub menu Molecule Properties dialog box appears. |
From the sub-menu, click on Molecule Properties.
IUPAC Molecule Name, Molecular weight, Chemical Formula, Dipole moment etc. |
Click on OK . | Click on OK to close the window. |
Click on Atom properties option from the properties menu. | Similarly to view the Atom Properties:
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Atom properties table appears
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A table opens with values of properties such as:
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Click on X | Close the dialog box. |
Cursor on Panel. | Explore other properties like Angle, Torsion and Conformer from the list. |
Cursor on Panel | Let us now learn to label the atoms in the molecule with partial charge. |
Click on Display settings | Click on Display settings:
From the Display Types list, check the box against Label.
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Click on the Spanner symbol on the right side of Label check box. | Click on the Spanner symbol on the right side of Label check box. |
Label Settings window opens. | Label Settings window opens. |
Click on Partial charge option from atom labels text drop down.
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Click on Partial charge option from atom labels text drop down.
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Cursor on the Panel. | The partial charge distribution helps to predict the reactivity of the carbon atoms. |
Cursor on the Panel. | Inductive effect can be explained by labeling the atoms with partial charge. |
Cursor on the Panel. | Replace a hydrogen with chlorine.
Notice the change in the value of partial charge along the carbon chain. |
Cursor on the Panel. | Because of the inductive effect carbons close to chlorine become more positive. |
Cursor on Label settings dialog box.
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We have also an option to label the bonds.
Click on bond length.
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Click on Color option under bond labels drop down.
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To change the color of the labels, click on the box filled with color.
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Click on the increment/decrement buttons in the label shift menu.
Close the dialog box. |
We can shift the labels in X, Y and Z direction.
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Cursor on the Panel | Another very useful feature of Avogadro, is the ability to create surfaces.
The option for creating surfaces is available in the extensions menu. |
Click on extensions, click on create surfaces
A create surface dialog box opens on the screen. |
Click on extensions menu, then click on create surfaces option.
A create surface dialog box opens on the screen.
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Cursor on the dialog box. | Surface type drop-down has two options:
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Cursor on the dialog box. | Electrostatic potential surfaces are not yet supported in Avogadro. |
Choose Van der waals option.
In the Color By drop-down choose nothing option. |
Choose Van der waals option.
In the Color By drop down select Nothing. |
Click on Medium in resolution drop down
Set Iso value 0 Click on Calculate button. Close the dialog box |
Set Resolution to Medium
Iso value to zero. Click on Calculate button.
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Cursor on the Panel. | The van der waals surface is displayed on the Panel. |
Cursor on the Panel. | Van der waals surface is a representation of surface through which a molecule interacts with other molecules. |
Click on the spanner symbol corresponding to surfaces in label check box. | To change the surface settings:
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A surface setting dialog box opens.
Drag the slider |
A surface setting dialog box opens.
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Click on Render option | In the Render drop-down there are different display options to choose such as:
Fill, lines and points.
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Click on the box filled with color next to positive option. | To change the color of the surface:
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Choose Electrostatic potential from the Color by drop-down. | Next from the Create surface window:
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Set the resolution to medium.
Set the Iso value to 0.02. |
Set the resolution to medium.
Set the Iso value to 0.02. Setting low Iso value gives a finer surface. |
Click on Calculate. | Click on Calculate button. |
Point to molecule | On the panel we see the surface of 1-chloro butane:
Colored according to the electro-static potential values of atoms. |
Slide Number 5
Electrostatic potential surface.
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Electrostatic potential surface illustrates charge distributions of the molecule.
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Slide number 6
Electrostatic-potential surfaces-images |
Here are a few more examples of molecules with electro-static potential surfaces. |
Cursor on slide number 6.
Point to molecules |
Aniline and cyclohexylamine.
Hence cyclohexylamine is a stronger base. |
Slide Number 7
Summary |
Let's summarize. In this tutorial we have learnt to:
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Slide Number 8
Assignment |
As an assignment
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Slide Number 9
Electrostatic potential surfaces. |
Your completed assignment should look as follows.
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Slide Number 10
Acknowledgement Watch the video available at /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 summarizes the Spoken Tutorial project
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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
Acknowledgement 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 /NMEICT-Intro
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The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India
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This tutorial is contributed by Viswa Janani Vasudhevan and Snehalatha Kaliappan.
Thank you for joining.
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