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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
00:12 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 tutorial, 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.
01:32 * Enter an element symbol via keyboard and
01:35 * Select new drawing symbol from periodic table.
01:40 Click on Select new drawing symbol from periodic table button.
01:45 Choose an element window opens with an inbuilt Periodic Table.
01:49 Here we can see a box with the text Periodic Table of elements.
01:55 This is an information box.
01:57 The information box displays the details of chosen Element.
02:02 For eg: I will place the cursor on Oxygen.
02:06 Details about Oxygen are displayed in the information box.
02:10 Likewise, we can see the details of various Elements in the information box.
02:17 Click on Close to close the window.
02:20 Click on Enter an element symbol via keyboard button.
02:24 Click on the Panel.
02:26 Enter element text box opens.
02:28 We can type the symbol of the Element in the text box.
02:33 For example: I will type Xe for Xenon.
02:37 Click on OK button.
02:40 The symbol of Xenon(Xe) is displayed on the Panel.
02:44 Now, let's draw the structure of Xenondifluoride (XeF2).
02:47 Go to Edit menu, navigate to Preferences and click on it.
02:54 Preferences window opens.
02:57 Uncheck Show Implicit hydrogens check box if it is checked.
03:02 Click OK to close the Preferences window.
03:06 Click on Fluorine(F) button and then click on Single bond button.
03:12 Move the cursor on Xenon atom.
03:15 Notice, a small blue circle appears on it.
03:19 Click and hold the left mouse button.
03:22 And then drag to draw two Xenon-Fluoride bonds.
03:27 Now I will explain about Xenon's Atom Popup Menu.
03:31 Move the cursor over to Xenon atom, right-click on it.
03:36 Xenon's Atom Popup Menu opens.
03:40 Here, I will explain about Isotopes, Change Element and Properties options.
03:46 Let's first move to Isotopes.
03:49 A submenu opens with a list of Isotopes of Xenon.
03:54 Next, I will move the cursor to Change Element.
03:58 A submenu opens with various categories of elements.
04:02 I will scroll down to various categories.
04:06 I will choose Alkali Earth Metals.
04:09 Alkali Earth Metals list opens.
04:12 Select Calcium(Ca) from the list.
04:15 We see that element Xenon is replaced by Calcium.
04:19 Now, we move on to Molecular Properties option.
04:23 Right click on Calcium.
04:26 Calcium's Atom Popup Menu opens.
04:29 Click on Molecular Properties option.
04:33 Properties text box opens.
04:36 Type the name of the compound as Calcium Fluoride and click on OK button.
04:43 Name of the compound is displayed below the structure.
04:47 Let us save the file now.
04:49 Click on Save button on the tool bar.
04:53 Save dialog box opens.
04:56 Type the file name as Calcium-fluoride.
05:00 Click on Save button.
05:03 Next, we will learn how to create a reaction.
05:06 To draw a reaction, we need to draw the required structures.
05:10 I have opened a new window with required structures.
05:14 Here the reactants are Propene and Chlorine molecules and product is 1,2-dicholoropropane.
05:23 On the left side tool bar, click on the Reaction arrow button.
05:27 Click between reactants and products.
05:31 The reaction is created.
05:33 We will now allign the structures properly in the reaction.
05:37 Click on Relayout the structures button on the top tool bar.
05:42 I will now discuss about how to set up an R group query.
05:47 What is an R-group query?
05:50 * An R-group query involves Root structure and substituents.
05:55 * It represents substitution on the same root structure.
06:00 * It can involve derivatives which differ in one or more substituents.
06:06 Click on Create a new file icon to open a new window.
06:11 Click on Draw a chain button.
06:14 Click on the Panel to draw a Carbon chain with three Carbon atoms.
06:20 Let's create a substituent that has to be attached to the Carbon chain.
06:24 For example, Benzene.
06:27 Click on Benzene ring on right side tool bar.
06:30 Click on the Panel.
06:33 Let's label the terminal Carbon atom as R1 in the Carbon chain.
06:39 Right click on terminal Carbon atom.
06:42 Atom Pop menu opens.
06:45 Scroll down to Pseudo Atoms.
06:48 A submenu opens; select R1.
06:52 Now let's define the Carbon chain as root structure.
06:56 Click on Selection button.
06:58 Select the Root structure by dragging over it.
07:02 Go to R-groups menu and select Define as Root Structure.
07:09 The substituent structure will be added as Not in R-Group.
07:14 Click on Selection button;
07:17 select the Substituent.
07:19 Go to R-groups menu and select Define as Substituent.
07:26 An input box opens.
07:27 Here, enter an R-group number as “1” and click on OK button.
07:34 The substituent will be numbered as R1.
07:38 On the Root structure, the substituent R1 will be marked as asterisk(*)
07:44 The attaching Carbon atom of the substituent R1 will also be marked with an asterisk(*).
07:51 Click on the Selection button, select Root Structure and substituent(R1).
07:58 Go to R-groups menu, select General Possible configurations(sdf).
08:05 Save dialog box opens.
08:08 Type the file name as r-group, select the location as Desktop.
08:14 Click on Save button.
08:18 Click on Open icon on the tool bar.
08:21 Open dialogue box opens.
08:24 In the “Files of Type”, select “All Files”
08:28 Click on Desktop.
08:30 Click Open; then select the saved r-group file.
08:36 Click on “Open” button.
08:39 A message pops up; click OK.
08:43 A new file opens with r-group query structure.
08:48 To allign the structure properly, click on Relayout the structure button on the tool bar.
08:55 The structure shown is root structure along with attached R-group substituent Benzene.
09:02 Let's summarize.
09:03 In this tutorial we have learnt
09:05 * Periodic table trends
09:07 * Draw a reaction
09:08 * Set up R-Group query.
09:11 As an assignment,
09:12 * Explore various Periodic table trends and
09:16 * Draw reactions of your choice.
09:19 This video summarizes the Spoken Tutorial project
09:23 If you do not have good bandwidth, you can download and watch it.
09:28 Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates.
09:34 Please contact us.
09:37 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
09:44 More information on this Mission is available at this link.
09:49 This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

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