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 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 dialog-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. |
