JChemPaint/C3/Properties-of-JChemPaint/English-timed

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
00:12	* 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.
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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