Difference between revisions of "Avogadro/C2/Build-molecules/English-timed"
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Latest revision as of 15:48, 5 July 2018
| Time | Narration |
| 00:01 | Warm greetings everyone!! Welcome to this tutorial on Build Molecules. |
| 00:07 | In this tutorial, we will learn to: Import molecules from database, |
| 00:11 | Rotate, zoom in and zoom out, |
| 00:15 | build molecules on the panel, |
| 00:17 | set up force field and optimize geometry, |
| 00:21 | measure bond lengths, bond angles, dihedral angles, |
| 00:25 | show fragment library, |
| 00:27 | build DNA molecules and Peptides. |
| 00:31 | Here I am using: Ubuntu Linux OS version 14.04 ,
Avogadro version 1.1.1, working internet connection. |
| 00:44 | To follow this tutorial, you should have knowledge of basic Chemistry.
To download Avogadro, please use the link shown sourceforge.net/projects/avogadro. |
| 00:53 | I have already downloaded Avogadro. |
| 00:56 | To open Avogadro , click on Dash home . |
| 01:00 | In the search bar, type avogadro . |
| 01:02 | Click on Avogadro icon to open the application. |
| 01:08 | Let's begin by importing a xylene molecule from chemical structure database . |
| 01:15 | To import a molecule, we need a working internet connection. |
| 01:19 | Click on File menu, navigate to Import . |
| 01:23 | A sub-menu opens. |
| 01:25 | Select Fetch by chemical name . |
| 01:28 | Chemical name dialog box appears. |
| 01:30 | For demonstration, I will type xylene in the search box. |
| 01:36 | Click on OK button. |
| 01:38 | We now have a xylene molecule on the Panel . |
| 01:42 | Let's rotate the molecule on the Panel . |
| 01:45 | Click on Navigation tool on the tool bar. |
| 01:49 | Place the cursor on the molecule. |
| 01:52 | Hold the left mouse button and drag. |
| 01:56 | Notice the direction arrows indicating the drag. |
| 02:00 | To translate the molecule, use right mouse button and drag. |
| 02:06 | Scroll the mouse wheel to zoom in and zoom out the structure. |
| 02:10 | Let's learn how to create a molecule. |
| 02:14 | To create a molecule, click on Draw Tool icon on the tool bar. |
| 02:19 | Under Draw Settings menu, we can see
Element drop down button, Bond Order drop down button, Adjust Hydrogens check box. |
| 02:30 | If you don't want hydrogens on the structure, un-check Adjust Hydrogens check box. |
| 02:37 | Element drop-down list shows list of elements. |
| 02:42 | Click on Other to view the entire Periodic table in a separate window. |
| 02:48 | Click on Close (X) to close the window. |
| 02:51 | Let's draw structure of Aniline on the Panel . |
| 02:55 | Select Carbon from Element drop down list. |
| 02:59 | Select Single from Bond Order drop down. |
| 03:03 | Click on the Panel . |
| 03:05 | Drag and drop to make a closed chain of six carbon atoms. |
| 03:10 | To show double-bonds, select Double from Bond Order drop-down. |
| 03:16 | Click on alternate bonds to obtain Benzene structure. |
| 03:21 | Let's complete Aniline structure. |
| 03:24 | Select Nitrogen from Element drop down list. |
| 03:29 | Select Single from Bond Order drop down. |
| 03:33 | Click on any one of the carbon atoms on the structure and drag. |
| 03:39 | Go to Build menu and select Add Hydrogens . |
| 03:45 | We have the structure of Aniline on the Panel. |
| 03:49 | To get a stable conformation, Aniline structure on the Panel needs to be optimized. |
| 03:56 | To optimize, click on Auto Optimization Tool on the tool bar. |
| 04:02 | AutoOptimization Settings menu appears on the left. |
| 04:06 | Click on Force Field drop-down list, select MMFF94 . |
| 04:13 | MMFF94 is generally used to optimize small organic molecules. |
| 04:20 | Click on Start button. |
| 04:23 | It will take a few seconds to complete the optimization. |
| 04:28 | Click on Stop to close the Optimization Settings. |
| 04:33 | Let's measure bond lengths, bond angles and dihedral angles of Aniline . |
| 04:40 | Select Click to Measure icon on the tool bar. |
| 04:44 | To measure distance, click on any two consecutive carbon atoms. |
| 04:49 | To measure angles, click on any 3 consecutive atoms. |
| 04:55 | To measure dihedral angles, click on any 4 consecutive atoms. |
| 05:02 | Measured values appear at the bottom of the Panel . |
| 05:07 | To save the file, click on File and Save As . |
| 05:13 | Save Molecule As dialog-box appears. |
| 05:17 | Type the File Name as Aniline.cml . |
| 05:21 | Choose the location as Desktop and click on Save button. |
| 05:28 | Click on New icon to open a new window. |
| 05:32 | Avogadro software has a feature to build complex molecules using fragment library. |
| 05:38 | Go to Build menu. |
| 05:40 | Navigate to Insert and select Fragment option. |
| 05:45 | Insert Fragment dialog box opens. |
| 05:49 | We can see list of folders having cml files of different chemical structures. |
| 05:55 | For example, let's open alkenes folder. |
| 06:00 | Double click on the folder to view the contents of the folder. |
| 06:04 | Select 2-methyl-buta-1,3-diene.cml . |
| 06:10 | Click on Insert button. |
| 06:13 | Click on Close to close the dialog box. |
| 06:17 | 2-methyl-1,3-butadiene structure is displayed on the Panel . |
| 06:22 | It is commonly called as Isoprene. |
| 06:26 | We can build many natural products using Isoprene . |
| 06:30 | The molecule is in select mode. |
| 06:33 | To de-select, press CTRL, SHIFT and A keys simultaneously. |
| 06:39 | As an example: I will show Vitamin A and natural rubber which were built using Isoprene . |
| 06:47 | Vitamin A, natural rubber . |
| 06:51 | I will translate Isoprene to a corner. |
| 06:56 | Click on Build menu, navigate to Insert and select Fragment . |
| 07:02 | Scroll down to macrocycles folder; double click to open. |
| 07:08 | Select porphin fragment and click on Insert . |
| 07:14 | Close the dialog box. |
| 07:16 | Using porphyrin fragment, we can build complex chemical structures such as: Chlorophyll and Vitamin B12 . |
| 07:25 | Chlorophyll |
| 07:27 | Vitamin B12. |
| 07:30 | Complex molecules like DNA and peptides can be easily built using Avogadro . |
| 07:37 | Open a new window using New icon. |
| 07:41 | To insert a DNA molecule, go to Build menu, navigate to Insert and click on DNA/RNA from the sub-menu. |
| 07:51 | Insert Nucleic Acids dialog box appears. |
| 07:55 | Select DNA from DNA/RNA Builder drop down. |
| 08:00 | Four nucleic acid bases are shown as buttons. |
| 08:05 | Click on the buttons to choose the nucleic acid sequence. |
| 08:10 | You can choose your own sequence of acids . |
| 08:14 | For demonstration, I will select A T G C A T G C. |
| 08:26 | The order of selection of nucleic acids appear in the Sequence text box. |
| 08:32 | In the Bases Per Turn drop down, select A, select "5" which is the number of base pairs per Helix . |
| 08:41 | Select Strands as Single and click on Insert button. |
| 08:47 | Click on Close to close the dialog box. |
| 08:51 | We now have a single stranded DNA molecule on the Panel . |
| 08:56 | Zoom out the structure and drag to the center of the Panel . |
| 09:01 | To deselect the DNA molecule on the Panel , press CTRL, Shift and A keys simultaneously. |
| 09:09 | We can also create a Peptide sequence using Peptide option in the Insert menu. |
| 09:16 | Again click on New icon to open a new window. |
| 09:21 | Go to Build menu, scroll down to Insert and Peptide . |
| 09:26 | Insert Peptide dialog box appears. |
| 09:29 | Select amino acids for the Peptide sequence by clicking on the amino acids button. |
| 09:36 | For demonstration, I will choose the sequence as Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys) . |
| 09:45 | The order of selection appears in the Sequence text box. |
| 09:50 | Click on Insert Peptide button. |
| 09:53 | Close the Insert Peptide dialog box. |
| 09:57 | Peptide chain appears on the Panel . |
| 10:00 | To de-select the Peptide on Panel , press CTRL, Shift and A keys simultaneously. |
| 10:07 | You can choose the amino acids of your choice and build the Peptide sequence. |
| 10:13 | Let's summarize. |
| 10:15 | In this tutorial, we learnt to : |
| 10:18 | import molecules from the database, |
| 10:21 | rotate, zoom in and zoom out, |
| 10:24 | build molecules on the panel, |
| 10:26 | set up force field and optimize geometry, |
| 10:30 | measure bond lengths, bond angles, dihedral angles, |
| 10:35 | show fragment library, |
| 10:37 | Build DNA molecules and Peptides . |
| 10:41 | As an assignment - Create a protein sequence using the following amino acid residues: |
| 10:49 | Optimize the geometry using UFF force field. |
| 10:53 | Save the image as .cml file. |
| 10:58 | Build RNA sequence using the Nucleic acids: AUGC . |
| 11:04 | Optimize geometry using MMFF94 force field. |
| 11:10 | Save the image as .cml file. |
| 11:14 | This video summarizes the Spoken Tutorial project. |
| 11:18 | If you do not have good bandwidth, you can download and watch it. |
| 11:23 | We conduct workshops using Spoken Tutorials and give certificates. Please contact us. |
| 11:30 | Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| 11:36 | This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining. |
