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Time Narration
00:01 Hello everyone. Welcome to this tutorial on Properties of JChemPaint..
00:07 In this tutorial, we will learn:
00:09 Periodic table trends
00:11 Draw a reaction and Set-up R-Group query.
00:16 To record this tutorial, I am using:
00:19 Ubuntu Linux OS version 12.04
00:23 JChemPaint version 3.3-1210
00:29 Java version 7.
00:31 To follow this tutorial, you should be familiar with 'JChemPaint' chemical structures editor.
00:39 If not, for relevant tutorials, please visit our website.
00:44 Let's switch to JChemPaint window.
00:48 Recall that we had saved our '.jar' file on the Desktop.
00:54 Press Ctrl+ALt and 'T' keys simultaneously to open the Terminal.
01:00 Type: cd space Desktop and press Enter.
01:06 Type: java space -jar space ./jchempaint-3.3-1210.jar and press Enter.
01:21 JChemPaint window opens.
01:24 Let's begin with Periodic Table trends.
01:28 The tool bar at the bottom shows buttons of some important elements.
01:35 The tool-bar has two extra buttons towards the right.
01:40 Enter an element symbol via keyboard and
01:44 Select new drawing symbol from periodic table.
01:48 Click on Select new drawing symbol from periodic table button.
01:55 Choose an element window opens with an inbuilt Periodic Table.
02:01 Here, we can see a box with the text Periodic Table of elements.
02:06 This is an information-box.
02:11 The information-box displays the details of chosen Element.
02:16 For eg: I will place the cursor on Oxygen.
02:21 Details about Oxygen are displayed in the information-box.
02:26 Likewise, we can see the details of various Elements in the information-box.
02:34 Click on Close to close the window.
02:38 Click on Enter an element symbol via keyboard button.
02:42 Click on the Panel.
02:45 Enter element text-box opens.
02:48 We can type the symbol of the Element in the text-box.
02:53 For example: I will type "Xe" for Xenon.
02:58 Click on OK button.
03:02 The symbol of Xenon (Xe) is displayed on the Panel.
03:08 Now, let's draw the structure of Xenondifluoride (XeF2).
03:14 Go to Edit menu, navigate to Preferences and click on it.
03:20 Preferences window opens.
03:23 Uncheck Show Implicit hydrogens check-box, if it is checked.
03:29 Click OK to close the Preferences window.
03:33 Click on Fluorine(F) button and then click on Single bond button.
03:39 Move the cursor on Xenon atom.
03:42 Notice, a small blue circle appears on it.
03:46 Click and hold the left mouse button
03:50 and then drag to draw two Xenon-Fluoride bonds.
03:56 Now, I will explain about Xenon's Atom Popup Menu.
04:02 Move the cursor over to Xenon atom, right-click on it.
04:07 Xenon's Atom Popup Menu opens.
04:11 Here, I will explain about Isotopes, Change Element and Molecular Properties options.
04:18 Let's first move to Isotopes.
04:21 A sub-menu opens with a list of isotopes of Xenon.
04:26 Next, I will move the cursor to Change Element.
04:30 A sub-menu opens with various categories of elements.
04:36 I will scroll-down to various categories.
04:40 I will choose Alkali Earth Metals.
04:44 Alkali Earth Metals list opens.
04:48 Select Calcium(Ca) from the list.
04:52 We see that element Xenon is replaced by Calcium.
04:57 Now, we move on to Molecular Properties option.
05:01 Right-click on Calcium.
05:04 Calcium's Atom Popup Menu opens.
05:08 Click on Molecular Properties option.
05:11 Properties text-box opens.
05:14 Type the name of the compound as "Calcium Fluoride" and click on OK button.
05:20 Name of the compound is displayed below the structure.
05:24 Let us save the file now.
05:26 Click on Save button on the tool-bar.
05:30 Save dialog-box opens.
05:32 Type the file name as "Calcium-fluoride".
05:36 Click on Save button.
05:39 Next, we will learn how to create a reaction.
05:42 To draw a reaction, we need to draw the required structures.
05:48 I have opened a new window with required structures.
05:52 Here, the reactants are Propene and Chlorine molecules and product is 1,2-dicholoropropane.
06:01 On the left side tool bar, click on the Reaction Arrow button.
06:06 Click between reactants and products.
06:10 The reaction is created.
06:13 We will now align the structures properly in the reaction.
06:18 Click on Relayout the structures button on the top tool bar. Structures align properly.
06:27 I will now discuss about how to set up an R-group query.
06:31 What is an R-group query?
06:35 An R-group query involves Root structure and substituents.
06:41 It represents substitution on the same Root structure.
06:45 It can involve derivatives which differ in one or more substituents.
06:53 Click on Create a new file icon to open a new window.
07:01 Click on Draw a chain button.
07:03 Click on the Panel to draw a Carbon chain with three Carbon atoms.
07:09 Let's create a substituent that has to be attached to the Carbon chain.
07:14 For example, Benzene.
07:17 Click on Benzene ring on right side tool bar.
07:22 Click on the Panel.
07:24 Let's label the terminal Carbon atom as 'R1' in the Carbon chain.
07:31 Right-click on terminal Carbon atom.
07:35 Atom Popup menu opens.
07:38 Scroll down to Pseudo Atoms.
07:42 A sub-menu opens; select 'R1'.
07:45 Now let's define the Carbon chain as root structure.
07:50 Click on Selection button.
07:53 Select the Root structure by dragging over it.
07:57 Go to R-groups menu and select Define as Root Structure.
08:04 The substituent structure will be added as Not in R-Group.
08:10 Click on Selection button;
08:13 select the Substituent.
08:16 Go to R-groups menu and select Define as Substituent.
08:22 An input-box opens.
08:24 Here, enter R-group number as “1” and click on OK button.
08:30 The substituent will be numbered as 'R1'.
08:34 On the Root structure, the substituent 'R1' will be marked with an asterisk(*)
08:41 The attaching Carbon atom of the substituent 'R1' will also be marked with an asterisk(*).
08:49 Click on the Selection button, select Root Structure and substituent(R1).
08:56 Go to R-groups menu, select General Possible configurations(sdf).
09:03 Save dialog-box opens.
09:06 Type the file name as "r-group", select the location as Desktop.
09:12 Click on Save button.
09:15 Click on Open icon on the tool bar.
09:19 Open dialogue-box opens.
09:22 In the “Files of Type”, select “All Files”.
09:27 Click on Desktop.
09:29 Click Open; then select the saved "r-group" file.
09:34 Click on Open button.
09:37 A message pops up; click OK.
09:41 A new file opens with r-group query structure.
09:46 To align the structure properly, click on Relayout the structure button on the tool bar.
09:54 The structure shown is root structure along with attached R-group substituent Benzene.
10:02 Let's summarize.
10:04 In this tutorial, we have learnt:
10:06 Periodic table trends
10:09 Draw a reaction
10:11 Set up R-Group query.
10:14 As an assignment-
10:16 Explore various Periodic table trends and
10:19 Draw reactions of your choice.
10:24 This video summarizes the Spoken Tutorial project.
10:28 If you do not have good bandwidth, you can download and watch it.
10:33 Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates.
10:39 Please contact us.
10:42 The Spoken Tutorial project is funded by NMEICT, MHRD Government of India.
10:49 More information on this mission is available at this link.
10:55 This is Madhuri Ganapathi from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Ranjana, Sandhya.np14