JChemPaint/C3/Properties-of-JChemPaint/English-timed
From Script | Spoken-Tutorial
| 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. |
