Difference between revisions of "JChemPaint/C3/Properties-of-JChemPaint/English-timed"
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| 00:07 | | 00:07 | ||
− | | In this tutorial, we will learn | + | | In this tutorial, we will learn: |
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| 00:09 | | 00:09 | ||
− | | | + | | '''Periodic table''' trends |
|- | |- | ||
| 00:11 | | 00:11 | ||
− | | | + | | Draw a reaction and Set-up '''R-Group query'''. |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
| 00:16 | | 00:16 | ||
− | | To record this tutorial I am using | + | | To record this tutorial, I am using: |
|- | |- | ||
| 00:19 | | 00:19 | ||
− | | | + | | '''Ubuntu Linux''' OS version '''12.04''' |
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| 00:23 | | 00:23 | ||
− | | | + | | '''JChemPaint''' version '''3.3-1210''' |
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| 00:29 | | 00:29 | ||
− | | | + | | '''Java''' version '''7'''. |
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| 00:31 | | 00:31 | ||
− | | To follow this tutorial you should be familiar with | + | | To follow this tutorial, you should be familiar with ''''JChemPaint' chemical structures editor'''. |
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| 00:39 | | 00:39 | ||
− | | | + | | If not, for relevant tutorials, please visit our website. |
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| 00:48 | | 00:48 | ||
− | | Recall that we had saved our '''.jar''' file on the '''Desktop'''. | + | | Recall that we had saved our ''''.jar'''' file on the '''Desktop'''. |
|- | |- | ||
| 00:54 | | 00:54 | ||
− | | Press ''' | + | | Press '''Ctrl+ALt''' and 'T' keys simultaneously to open the '''Terminal'''. |
|- | |- | ||
| 01:00 | | 01:00 | ||
− | | Type ''' | + | | Type: '''cd space Desktop''' and press '''Enter'''. |
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| 01:06 | | 01:06 | ||
− | | Type ''' | + | | Type: ''' java space -jar space ./jchempaint-3.3-1210.jar''' and press '''Enter'''. |
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| 01:24 | | 01:24 | ||
− | | Let's begin with '''Periodic Table | + | | Let's begin with '''Periodic Table''' trends. |
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| 01:28 | | 01:28 | ||
− | | The '''tool bar''' at the bottom shows buttons of some important | + | | The '''tool bar''' at the bottom shows buttons of some important elements. |
|- | |- | ||
| 01:35 | | 01:35 | ||
− | | The tool bar has two extra buttons towards the right. | + | | The tool-bar has two extra buttons towards the right. |
|- | |- | ||
| 01:40 | | 01:40 | ||
− | | | + | | '''Enter an element symbol via keyboard''' and |
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| 01:44 | | 01:44 | ||
− | | | + | | '''Select new drawing symbol from periodic table'''. |
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| 02:01 | | 02:01 | ||
− | | Here we can see a box with the text '''Periodic Table of elements'''. | + | | Here, we can see a box with the text '''Periodic Table of elements'''. |
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| 02:06 | | 02:06 | ||
− | | This is an information box. | + | | This is an '''information-box'''. |
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| 02:11 | | 02:11 | ||
− | | The information box displays the details of chosen | + | | The information-box displays the details of chosen Element. |
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| 02:21 | | 02:21 | ||
− | | Details about '''Oxygen''' are displayed in the information box. | + | | Details about '''Oxygen''' are displayed in the '''information-box'''. |
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| 02:26 | | 02:26 | ||
− | | Likewise, we can see the details of various | + | | Likewise, we can see the details of various Elements in the information-box. |
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| 02:45 | | 02:45 | ||
− | | '''Enter element''' text box opens. | + | | '''Enter element''' text-box opens. |
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| 02:48 | | 02:48 | ||
− | | We can type the symbol of the | + | | We can type the symbol of the Element in the text-box. |
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| 02:53 | | 02:53 | ||
− | | For example: I will type | + | | For example: I will type "Xe" for '''Xenon'''. |
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| 03:02 | | 03:02 | ||
− | | The symbol of | + | | The symbol of '''Xenon''' (Xe) is displayed on the '''Panel'''. |
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| 03:23 | | 03:23 | ||
− | | Uncheck '''Show Implicit hydrogens''' check box if it is checked. | + | | Uncheck '''Show Implicit hydrogens''' check-box, if it is checked. |
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| 03:46 | | 03:46 | ||
− | | Click and hold the left mouse button | + | | Click and hold the '''left mouse button''' |
|- | |- | ||
| 03:50 | | 03:50 | ||
− | | | + | | and then drag to draw two '''Xenon-Fluoride''' bonds. |
|- | |- | ||
| 03:56 | | 03:56 | ||
− | | Now I will explain about '''Xenon's Atom Popup Menu'''. | + | | Now, I will explain about '''Xenon''''s '''Atom Popup Menu'''. |
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| 04:07 | | 04:07 | ||
− | | '''Xenon's | + | | '''Xenon''''s '''Atom Popup Menu''' opens. |
|- | |- | ||
| 04:11 | | 04:11 | ||
− | | Here, I will explain about '''Isotopes, Change Element''' and '''Properties''' options. | + | | Here, I will explain about '''Isotopes, Change Element''' and '''Molecular Properties''' options. |
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| 04:21 | | 04:21 | ||
− | | A | + | | A sub-menu opens with a list of isotopes of Xenon. |
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| 04:30 | | 04:30 | ||
− | | A | + | | A sub-menu opens with various categories of elements. |
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| 04:36 | | 04:36 | ||
− | | I will scroll down to various categories. | + | | I will scroll-down to various categories. |
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| 04:52 | | 04:52 | ||
− | | We see that ''' | + | | We see that element '''Xenon''' is replaced by '''Calcium'''. |
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| 05:01 | | 05:01 | ||
− | | Right click on '''Calcium'''. | + | | Right-click on '''Calcium'''. |
|- | |- | ||
| 05:04 | | 05:04 | ||
− | | '''Calcium's Atom Popup Menu''' opens. | + | | '''Calcium''''s '''Atom Popup Menu''' opens. |
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| 05:11 | | 05:11 | ||
− | | '''Properties''' text box opens. | + | | '''Properties''' text-box opens. |
|- | |- | ||
| 05:14 | | 05:14 | ||
− | | Type the name of the compound as | + | | Type the name of the compound as "Calcium Fluoride" and click on '''OK''' button. |
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| 05:26 | | 05:26 | ||
− | | Click on '''Save''' button on the tool bar. | + | | Click on '''Save''' button on the tool-bar. |
|- | |- | ||
| 05:30 | | 05:30 | ||
− | | '''Save''' dialog box opens. | + | | '''Save''' dialog-box opens. |
|- | |- | ||
| 05:32 | | 05:32 | ||
− | | Type the file name as | + | | Type the file name as "Calcium-fluoride". |
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| 05:52 | | 05:52 | ||
− | | Here the reactants are '''Propene''' and '''Chlorine''' molecules and product is '''1,2-dicholoropropane'''. | + | | Here, the reactants are '''Propene''' and '''Chlorine''' molecules and product is '''1,2-dicholoropropane'''. |
|- | |- | ||
| 06:01 | | 06:01 | ||
− | | On the left side tool bar, click on the '''Reaction | + | | On the left side tool bar, click on the '''Reaction Arrow''' button. |
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| 06:13 | | 06:13 | ||
− | | We will now | + | | We will now align the structures properly in the reaction. |
|- | |- | ||
| 06:18 | | 06:18 | ||
− | | Click on '''Relayout the structures''' button on the top tool bar.Structures align properly | + | | Click on '''Relayout the structures''' button on the top tool bar. Structures align properly. |
|- | |- | ||
| 06:27 | | 06:27 | ||
− | | I will now discuss about how to set up an '''R group query'''. | + | | I will now discuss about how to set up an '''R-group query'''. |
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| 06:35 | | 06:35 | ||
− | | | + | | An '''R-group query''' involves '''Root structure''' and '''substituents'''. |
|- | |- | ||
| 06:41 | | 06:41 | ||
− | | | + | | It represents substitution on the same '''Root structure'''. |
|- | |- | ||
| 06:45 | | 06:45 | ||
− | | | + | | It can involve derivatives which differ in one or more substituents. |
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| 07:03 | | 07:03 | ||
− | | Click on the '''Panel''' to draw a | + | | Click on the '''Panel''' to draw a Carbon chain with three Carbon atoms. |
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| 07:17 | | 07:17 | ||
− | | Click on '''Benzene''' | + | | Click on '''Benzene ring''' on right side tool bar. |
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| 07:22 | | 07:22 | ||
− | | Click on the | + | | Click on the Panel. |
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| 07:24 | | 07:24 | ||
− | | Let's label the terminal '''Carbon''' atom as | + | | Let's label the terminal '''Carbon''' atom as 'R1' in the '''Carbon''' chain. |
|- | |- | ||
| 07:31 | | 07:31 | ||
− | | Right click on terminal '''Carbon''' atom. | + | | Right-click on terminal '''Carbon''' atom. |
|- | |- | ||
| 07:35 | | 07:35 | ||
− | | '''Atom | + | | '''Atom Popup menu''' opens. |
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| 07:42 | | 07:42 | ||
− | | A | + | | A sub-menu opens; select 'R1'. |
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| 08:22 | | 08:22 | ||
− | | An input box opens. | + | | An '''input-box''' opens. |
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| 08:24 | | 08:24 | ||
− | | Here, enter | + | | Here, enter '''R-group''' number as “1” and click on '''OK''' button. |
|- | |- | ||
| 08:30 | | 08:30 | ||
− | | The substituent will be numbered as | + | | The substituent will be numbered as 'R1'. |
|- | |- | ||
| 08:34 | | 08:34 | ||
− | | On the '''Root structure,''' the substituent | + | | On the '''Root structure,''' the substituent 'R1' will be marked with an asterisk(*) |
|- | |- | ||
| 08:41 | | 08:41 | ||
− | | The attaching '''Carbon''' atom of the substituent | + | | The attaching '''Carbon''' atom of the substituent 'R1' will also be marked with an asterisk(*). |
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| 09:03 | | 09:03 | ||
− | | '''Save''' dialog box opens. | + | | '''Save''' dialog-box opens. |
|- | |- | ||
| 09:06 | | 09:06 | ||
− | | Type the file name as | + | | Type the file name as "r-group", select the location as Desktop. |
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| 09:19 | | 09:19 | ||
− | | '''Open''' | + | | '''Open''' dialog-box opens. |
|- | |- | ||
| 09:22 | | 09:22 | ||
− | | In the “Files of Type”, select “All Files” | + | | In the “Files of Type”, select “All Files”. |
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| 09:29 | | 09:29 | ||
− | | Click '''Open'''; then select the saved | + | | Click '''Open'''; then select the saved "r-group" file. |
|- | |- | ||
| 09:34 | | 09:34 | ||
− | | Click on | + | | Click on '''Open''' button. |
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| 09:46 | | 09:46 | ||
− | | To | + | | To align the structure properly, click on '''Relayout the structure''' button on the tool bar. |
|- | |- | ||
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| 10:04 | | 10:04 | ||
− | | In this tutorial we have learnt | + | | In this tutorial, we have learnt: |
|- | |- | ||
| 10:06 | | 10:06 | ||
− | | | + | | '''Periodic table''' trends |
|- | |- | ||
| 10:09 | | 10:09 | ||
− | | | + | | Draw a reaction |
|- | |- | ||
| 10:11 | | 10:11 | ||
− | | | + | | Set up '''R-Group query'''. |
|- | |- | ||
| 10:14 | | 10:14 | ||
− | | As an assignment | + | | As an assignment- |
|- | |- | ||
| 10:16 | | 10:16 | ||
− | | | + | | Explore various Periodic table trends and |
|- | |- | ||
| 10:19 | | 10:19 | ||
− | | | + | | Draw reactions of your choice. |
|- | |- | ||
| 10:24 | | 10:24 | ||
− | | This video summarizes the Spoken Tutorial project | + | | This video summarizes the Spoken Tutorial project. |
|- | |- | ||
Line 553: | Line 549: | ||
|- | |- | ||
| 10:33 | | 10:33 | ||
− | | Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates. | + | | Spoken Tutorial team conducts workshops using '''Spoken Tutorials''' and gives certificates. |
|- | |- | ||
Line 561: | Line 557: | ||
|- | |- | ||
| 10:42 | | 10:42 | ||
− | | The Spoken Tutorial | + | | The Spoken Tutorial project is funded by NMEICT, MHRD Government of India. |
|- | |- | ||
| 10:49 | | 10:49 | ||
− | | | + | | More information on this mission is available at this link. |
|- | |- | ||
| 10:55 | | 10:55 | ||
− | | This is | + | | This is Madhuri Ganapathi from '''IIT Bombay''', signing off. Thank you for joining. |
|} | |} |
Latest revision as of 15:28, 28 October 2020
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. |