Avogadro/C2/Build-molecules/English
Visual Cue | Narration |
Slide Number 1
Title Slide |
Warm greetings everyone!!
Welcome to this tutorial on Build Molecules. |
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
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Slide Number 4
Pre-requisites |
To follow this tutorial you should have,
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Slide number 5
Download Link To download Avogadro use the link shown sourceforge.net/projects/avogadro. |
To download Avogadro please use the link shown
sourceforge.net/projects/avogadro. I have already downloaded Avogadro. |
Click on Dash home. | To open Avogadro, click on Dash home.
In the search bar, type avogadro. |
Cursor on the Avogadro icon. | Click on Avogadro icon to open the application. |
Let's begin by importing a xylene molecule from chemical structure database. | |
Cursor on the Panel. | To import a molecule, we need a working Internet connection. |
Click on File menu, navigate to Import.
Point to the sub-menu. |
Click on File menu, navigate to Import.
A sub-menu opens. |
Select Fetch by chemical name. | Select Fetch by chemical name. |
Point to Chemical name dialog box.
Type xylene in the search box, click OK button. |
Chemical name dialog box appears.
For demonstration I will type xylene in the search box. Click on OK button. |
Point to xylene. | We now have a xylene molecule on the Panel. |
Let's rotate the molecule on the Panel. | |
Click on Navigation tool on the tool bar.
Hold the left mouse button and drag. |
Click on Navigation tool on the tool bar.
Place the cursor on the molecule. Hold the left mouse button and drag. Notice the direction arrows indicating the drag. |
Show the translation. | To translate the molecule, use right mouse button and drag. |
Scroll the mouse wheel to zoom in and zoom out. | Scroll the mouse wheel to zoom in and zoom out the structure. |
Cursor on the Panel. | Let's learn how to create a molecule. |
Click on Draw Tool icon on the tool bar. | To create a molecule, click on Draw Tool icon on the tool bar. |
Point to Draw Settings menu.
Point to drop downs. |
Under Draw Settings menu, we can see
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uncheck adjust hydrogens check box | If you don't want hydrogens on the structure, un-check Adjust Hydrogens check box. |
Scroll down the list.
Click on Other see the Periodic table. Click on Close(X). |
Element drop down list shows list of elements.
Click on Other to view the entire Periodic table in a separate window. Click on Close(X) to close the window. |
Cursor on the Panel. | Lets draw structure of Aniline on the Panel. |
Click on Carbon.
Click on the Panel and drag. |
Select Carbon from Elementdrop down list.
Select Single from Bond Order drop down. Click on the Panel. Drag and drop to make a closed chain of six carbon atoms. |
Select Double from Bond Order.
Click on alternate positions. |
To show double bonds, select Double from Bond Order drop down.
Click on alternate bonds to obtain Benzene structure. |
Let's complete Aniline structure. | |
Select Nitrogen from Element drop down. | Select Nitrogen from Element drop down list.
Select Single from Bond Order drop down. |
Click on hydrogen atoms on the structure. | Click on any one of the carbon atoms on the structure and drag. |
Go to Build menu, select Add Hydrogens.
Point to Aniline structure. |
Go to Build menu and select Add Hydrogens.
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Point to Aniline structure. | To get a stable conformation, Aniline structure on the Panel needs to be optimized. |
Click on Auto Optimization Tool icon on the tool bar. | To optimize, click on Auto Optimization Tool on the tool bar. |
Point to the menu. | AutoOptimization Settings menu appears on the left. |
Click on Force Field drop down list, select MMFF94. | Click on Force Field drop down list, select MMFF94.
MMFF94 is generally used to optimize small organic molecules. |
Click on Start button.
Click on Stop to close AutoOptimization Settings. |
Click on Start button.
It will take a few seconds to complete the optimization. Click on Stop to close the Optimization Settings. |
Cursor on the Panel | Let's measure bond lengths, bond angles and dihedral angles of Aniline. |
Select Click to Measure icon on the tool bar.
Click on any two consecutive carbon atoms. Click on 3 consecutive atoms. Click on 4 successive atoms. Point to the values. |
Select Click to Measure icon on the tool bar.
To measure distance, click on any two consecutive carbon atoms. To measure angles, click on any 3 consecutive atoms. To measure dihedral angles, click on any 4 consecutive atoms. Measured values appear at the bottom of the Panel. |
Click on File and Save as. | To save the file, click on File and Save As. |
Point to the dialog box. | Save Molecule As dialog box appears. |
Type the File Name as Aniline.cml.
Choose file location as Desktop, click on Save button. |
Type the File Name as Aniline.cml.
Choose the location as Desktop and click on Save button. |
Cursor on the window. | Click on New icon to open a new window. |
Cursor on the Panel. | Avogadro software has a feature to build complex molecules using fragment library. |
Go to Build menu.
Navigate to Insert and select Fragment option. Point to the dialog box. |
Go to Build menu.
Navigate to Insert and select Fragment option. Insert Fragment dialog box opens. |
Point to the list of folders. | We can see list of folders having cml files of different chemical structures. |
Double click on the folder to see .cml files. | For example let's open alkenes folder.
Double click on the folder to view the contents of the folder. |
Select 2-methylbut-2-ene.cml.
Click on Insert button. Click on close to close the dialog box. |
Select 2-methyl-buta-1,3-diene.cml.
Click on Insert button. Click on Close to close the dialog box. |
Point to the structure. | 2-methyl-1,3-butadiene structure is displayed on the Panel.
It is commonly called as Isoprene. We can build many natural products using Isoprene. |
Press CTRL+SHIFT+A. | The molecule is in select mode.
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Show the images of Vitamin A and natural rubber.
Point to the structure. |
As an example:
I will show Vitamin A and natural rubber which were built using Isoprene. Vitamin A, natural rubber. I will translate Isoprene to a corner. |
Click on Build menu, select Fragment.
Scroll down to macrocycles, |
Click on Build menu, navigate to Insert and select Fragment.
Scroll down to macrocycles folder; double click to open. |
Select porphin fragment. | Select porphin fragment and click on Insert.
Close the dialog box. |
Show structure of chlorophyl molecule and Vitamin B12 molecules. | Using porphyrin fragment, we can build complex chemical structures:
Such as Chlorophyll and Vitamin B12. Chlorophyll Vitamin B12. |
Cursor on the Panel. | Complex molecules like DNA and peptides can be easily built using Avogadro.
Open a new window using New icon. |
Cursor on the menu bar.
Go to Build menu, Insert. Select DNA/RNA from sub-menu. |
To insert a DNA molecule, go to Build menu navigate to Insert
And click on DNA/RNA from the sub-menu. |
Point to the box. | Insert Nucleic Acids dialog box appears. |
Select DNA in DNA/RNA builder. | Select DNA from DNA/RNA Builder drop down. |
Click on buttons. | Four nucleic acid bases are shown as buttons.
Click on the buttons to choose the nucleic acid sequence. |
Point to the molecule. | You can choose your own sequence of acids.
For demonstration I will select A T G C A T G C. The order of selection of nucleic acids appear in the Sequence text box. |
Point to Bases Per Turn drop down, A, select "5":
Select Strands as Single, click on Insert button. |
In the Bases Per Turn drop down, select A, select "5": which is the number of base pairs per Helix.
Select Strands as Single and click on Insert button. |
Click on Close(X) to close the dialog box. | Click on Close(X) to close the dialog box. |
Point to the molecule. | We now have a single stranded DNA molecule on the Panel.
Zoom out the structure and drag to the centre of the Panel. |
press CTRL, Shift and A keys simultaneously. | To deselect the DNA molecule on the Panel,
press CTRL, Shift and A keys simultaneously. |
Click on New icon to open a new window. | We can also create a Peptide sequence using Peptide option in the Insert menu.
Again click on New icon to open a new window. |
Go to Build menu scroll down to, Insert, Peptide. | Go to Build menu scroll down to Insert and Peptide. |
Point to the box. | Insert Peptide dialog box appears. |
Select amino acid sequence as Gly-Val-Pro-Cys, click on Insert Peptide button. | Select amino acids for the Peptide sequence by clicking on the amino acids buttons.
For demonstration I will choose the sequence as Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys). |
Point to the Sequence text box.
Click on Insert Peptide button. |
The order of selection appear in the Sequence text box.
Click on Insert Peptide button. Close the Insert Peptide dialog box. |
Point to the Peptide chain.
To de-select the Peptide on Panel, press CTRL, Shift and A keys simultaneously. |
Peptide chain appears on the Panel.
To de-select the Peptide on Panel, press CTRL, Shift and A keys simultaneously. You can choose the amino acids of your choice and build the Peptide sequence. |
Let's summarize. | |
Slide Number 8
Summary |
In this tutorial we learnt to :
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Slide Number 9
Assignment 1 |
As an assignment
Glu, Leu, Asn, Cys, His.
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Slide Number 10
Assignment 2 |
Assignment:
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Slide Number 11
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. |
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Slide Number 12
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 13
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: |
Spoken Tutorial Project is funded by NMEICT, MHRD Government of India |
This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining. |