Difference between revisions of "Avogadro/C2/Create-Surfaces/English"

Latest revision as of 19:20, 30 April 2022

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: View properties of the molecule Label the atoms with partial charge Create Van der waals surface Color the surface according to the electrostatic potential energies.
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.
Cursor on the Avogadro window.	Here I have opened the Avogadro window.
Cursor on the Panel Click on Build menu then click on Insert ->fragment	Insert a molecule of butane from Insert Fragment Library. Click on Build menu then click on Insert ->fragment
Double click on alkanes folder to open. Select butane.cml.	Double click on alkanes folder to open. Select butane.cml.
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. Molecule Properties window opens with information such as, 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: Click on Atom properties option from the properties menu.
Atom properties table appears Cursor on the table	A table opens with values of properties such as: Element, Type, Valence, Formal charge etc for each atom in the molecule.
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.
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. Cursor on the Panel.	Click on Partial charge option from atom labels text drop down. Now all the atoms in the molecule are labeled with partial charge.
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. Click on bond length.	We have also an option to label the bonds. Click on the bond labels text box. The drop-down menu has options to label the bonds. Click on bond length. The bond lengths for all the bonds are displayed on the panel.
Click on Color option under bond labels drop down. Select the color from the Select atoms label color window. Click on OK button.	To change the color of the labels, click on the box filled with color. Select the color from the Select atoms label color window. Click on OK button.
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. Click on the increment or decrement buttons in the label shift menu. Close the dialog box.
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.
Cursor on the dialog box.	Surface type drop-down has two options: Van der waals and electro-static potential.
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. Close the dialog box.
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: Click on the spanner symbol corresponding to surfaces.
A surface setting dialog box opens. Drag the slider	A surface setting dialog box opens. Drag the slider to adjust the opacity.
Click on Render option	In the Render drop-down there are different display options to choose such as: Fill, lines and points. The default option is fill.
Click on the box filled with color next to positive option.	To change the color of the surface: Click on the box filled with color next to positive option. Select the color from the basic color chart by clicking on the color. Click on OK button.
Choose Electrostatic potential from the Color by drop-down.	Next from the Create surface window: Choose Electrostatic potential from the Color by drop-down.
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.	Electrostatic potential surface illustrates charge distributions of the molecule. They are also used in predicting the behavior of molecules By default, areas of high electronegativity are colored in red and least in blue.
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. The electron density on the Nitrogen of cyclohexylamine is more localized than it is in aniline. Hence cyclohexylamine is a stronger base.
Slide Number 7 Summary	Let's summarize. In this tutorial we have learnt to: View properties of the molecule. Label the atoms with partial charge. Create Van der waals surface Color the surface according to the electrostatic potential energies.
Slide Number 8 Assignment	As an assignment Compare the reactivity of acetaldehyde and formamide using electro-static potential surface. Label the atoms with partial charge.
Slide Number 9 Electrostatic potential surfaces.	Your completed assignment should look as follows. Negative charge indicated in red is more localized on the oxygen atom of acetaldehyde. The Negative charge is more delocalized in formamide. Hence Acetaldehyde is more reactive than Formamide.
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 summarizes 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 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 http://spoken-tutorial.org /NMEICT-Intro	The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India
	This tutorial is contributed by Viswa Janani Vasudhevan and Snehalatha Kaliappan. Thank you for joining.

Contributors and Content Editors

Madhurig, Visjan

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Difference between revisions of "Avogadro/C2/Create-Surfaces/English"

Latest revision as of 19:20, 30 April 2022

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