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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.
01:40 * 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 Properties options.
04:18 Let's first move to Isotopes.
04:21 A submenu opens with a list of Isotopes of Xenon.
04:26 Next, I will move the cursor to Change Element.
04:30 A submenu 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 allign 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 Pop menu opens.
07:38 Scroll down to Pseudo Atoms.
07:42 A submenu 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 an 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 allign 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