Difference between revisions of "JChemPaint/C3/Properties-of-JChemPaint/English"

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(Created page with "{| border=1 || '''Visual Cue''' || '''Narration''' |- ||'''Slide Number 1 Title Slide''' ||Hello everyone. Welcome to this tutorial on '''Properties of JChemPaint.'''. |-...")
 
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* Draw a reaction and
 
* Draw a reaction and
  
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* Set-up R-Group query
+
* Set-up '''R-Group query'''
 
|-
 
|-
 
||'''Slide Number 3
 
||'''Slide Number 3
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||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
 
||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
 
|-
 
|-
−
||Type '''“cd space Desktop”''' and press enter.
+
||Type '''“cd space Desktop”''' and press '''Enter'''.
 +
||Type ''''“cd space Desktop”''' and press '''Enter'''.
  
−
Type '''java  -jar ./jchempaint-3.3-1210.jar''' and press enter.
+
|-
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||Type ''''“cd space Desktop”''' and press enter.
+
||Type '''java  -jar ./jchempaint-3.3-1210.jar''' and press '''Enter'''.
 +
||Type ''' “java space -jar space ./jchempaint-3.3-1210.jar”''' and press '''Enter'''.
  
−
Type ''' “java space  -jar space ./jchempaint-3.3-1210.jar”''' and press enter.
 
  
 
'''JChemPaint''' window opens.
 
'''JChemPaint''' window opens.
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||I will choose '''Alkali Earth Metals'''.  
 
||I will choose '''Alkali Earth Metals'''.  
  
−
'''Alkali Earth Metals''' list opens.
+
'''Alkali Earth Metals''' list opens.
 
|-
 
|-
 
||Select the '''Calcium''' from the list.
 
||Select the '''Calcium''' from the list.
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|-
 
|-
 
||Click on '''Save''' button the tool bar.
 
||Click on '''Save''' button the tool bar.
−
|| Let's save the file now.
+
|| Let us save the file now.
  
 
Click on '''Save''' button on the tool bar.
 
Click on '''Save''' button on the tool bar.
 
|-
 
|-
 
||Point to the dialogue box.
 
||Point to the dialogue box.
−
||'''Save''' dialogue box opens.  
+
||'''Save''' dialog box opens.  
 
|-
 
|-
 
||Type the file name as '''Calcium-fluoride'''.
 
||Type the file name as '''Calcium-fluoride'''.
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||Right click on terminal '''Carbon''' atom.
 
||Right click on terminal '''Carbon''' atom.
  
−
'''Atom Pop menu''' opens.
+
'''Atom Pop menu''' opens.
 
|-
 
|-
 
||Point to the submenu.
 
||Point to the submenu.
 
||Scroll down to '''Pseudo Atoms'''.
 
||Scroll down to '''Pseudo Atoms'''.
  
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A submenu opens select '''R1'''.
+
A submenu opens; select '''R1'''.
 
|-
 
|-
 
||
 
||
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Go to '''R-groups''' menu and select '''Define as Substituent'''.
 
Go to '''R-groups''' menu and select '''Define as Substituent'''.
−
||Click on '''Selection''' button, select the '''Substituent'''.
+
||Click on '''Selection''' button; select the '''Substituent'''.
  
 
Go to '''R-groups''' menu and select '''Define as Substituent'''.
 
Go to '''R-groups''' menu and select '''Define as Substituent'''.
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|| An input box opens.
 
|| An input box opens.
  
−
Here enter an '''R-group''' number as “1” and click '''OK''' button.
+
Here, enter an '''R-group''' number as “1” and click '''OK''' button.
  
 
The substituent will be numbered as '''R1'''.
 
The substituent will be numbered as '''R1'''.
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Point to the substituent marked with asterisk(*)
 
Point to the substituent marked with asterisk(*)
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|| On the '''Root structure''' the substituent '''R1''' will be marked as asterisk(*)
+
|| On the '''Root structure,''' the substituent '''R1''' will be marked as asterisk(*)
  
−
The attaching '''Carbon''' atom of the substituent '''R1''' will also be marked with an asterisk(*)
+
The attaching '''Carbon''' atom of the substituent '''R1''' will also be marked with an asterisk(*).
 
|-
 
|-
 
||Click on '''Selection''' button>> select '''Root Structure''' and  '''substituent(R1)'''.
 
||Click on '''Selection''' button>> select '''Root Structure''' and  '''substituent(R1)'''.
−
||Click on the '''Selection''' button,  select  the '''Root Structure''' and  '''substituent(R1)'''.
+
||Click on the '''Selection''' button,  select  '''Root Structure''' and  '''substituent(R1)'''.
 
|-
 
|-
 
||Go to '''R-groups''' menu>>  select '''General Possible configurations(sdf)'''.
 
||Go to '''R-groups''' menu>>  select '''General Possible configurations(sdf)'''.
 
|| Go to '''R-groups''' menu,  select '''General Possible configurations(sdf)'''.
 
|| Go to '''R-groups''' menu,  select '''General Possible configurations(sdf)'''.
 
|-   
 
|-   
−
||Point to the dialogue box.
+
||Point to the dialog box.
−
||'''Save''' dialogue box opens.
+
||'''Save''' dialog box opens.
 
|-
 
|-
 
||Type the file name as '''r-group''' >>select the file location as '''Desktop'''.
 
||Type the file name as '''r-group''' >>select the file location as '''Desktop'''.
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||Click on '''Desktop''' folder.
 
||Click on '''Desktop''' folder.
  
−
Click '''Open''' then select the saved '''r-group''' file.
+
Click '''Open'''; then select the saved '''r-group''' file.
  
 
Click on “Open” button.
 
Click on “Open” button.
 
|-
 
|-
 
||Point to OK
 
||Point to OK
−
||A message pops up, click '''OK'''.
+
||A message pops up; click '''OK'''.
 
|-
 
|-
 
||Move the cursor on the file.
 
||Move the cursor on the file.
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* Draw a reaction
 
* Draw a reaction
  
−
* Set up R-Group query.
+
* Set up '''R-Group query'''.
 
|-
 
|-
 
||'''Slide Number 7
 
||'''Slide Number 7
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* Explore various Periodic table trends and
 
* Explore various Periodic table trends and
−
 
 
* Draw reactions of your choice.
 
* Draw reactions of your choice.
 
|-
 
|-

Revision as of 13:02, 7 January 2015

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Properties of JChemPaint..

Slide Number 2

Learning Objectives

In this tutorial, we will learn to change
  • Periodic table trends
  • Draw a reaction and
  • Set-up R-Group query
Slide Number 3

System Requirement

To record this tutorial I am using,
  • Ubuntu Linux OS version 12.04
  • JChemPaint version 3.3-1210
  • Java version 7
Slide Number 4

Pre-requisites

To follow this tutorial you should be familiar with,
  • JChemPaint chemical structures editor.
  • If not, for relevant tutorial, please visit our website.
Let's switch to JChemPaint window.
Point to .jar file Recall that we had saved our .jar file on the Desktop.
Press CTRl+ALt+T keys simultaneously to open the terminal. Press CTRl+ALt and T keys simultaneously to open the Terminal.
Type “cd space Desktop” and press Enter. Type '“cd space Desktop” and press Enter.
Type java -jar ./jchempaint-3.3-1210.jar and press Enter. Type “java space -jar space ./jchempaint-3.3-1210.jar” and press Enter.


JChemPaint window opens.

Let's begin with Periodic Table trends.
Point to the Tool bar at the bottom.

Point to the element buttons.

The tool bar at the bottom shows buttons of some important elements.
Point to the buttons. The tool bar has two extra buttons towards the right.
  • Enter an element symbol via keyboard and
  • Select new drawing symbol from periodic table.
Click on the button. Click on Select new drawing symbol from periodic table button.
Move the cursor towards the window. Choose an element window opens with an inbuilt Periodic Table.
Point to information box. Here we can see a box with the text Periodic Table of elements.

This is an information box.

Point to information box.

Move the cursor on to Oxygen.

The information box displays the details of the chosen Element.

For eg: I will place the cursor on Oxygen.

Point to the information box.

Point to different elements.

Details about Oxygen are displayed in the information box.

Likewise, we can see the details of various Elements in the information box.

Click on Close. Click on Close to close the window.
Click on Enter an element symbol via keyboard button >> click on the Panel. Click on Enter an element symbol via keyboard button.

Click on the Panel.

Point to the box. Enter element text box opens.

We can type the symbol of the Element in the text box.

Type Xe for Xenon in the box >> click on OK button. For example: I will type Xe for Xenon.

Click on OK button.

Point to the symbol. The symbol of Xenon(Xe) is displayed on the Panel.
Now, let's draw the structure of Xenondifluoride (XeF2).
Go to Edit menu and navigate to Preferences>> click on it. Go to Edit menu, navigate to Preferences and click on it.
Point to the Preferences window Preferences window opens.
Point to Show Implicit hydrogens check box.

Click Ok to close the Preferences window.

Uncheck Show Implicit hydrogens check box if it is checked.

Click OK to close the Preferences window.

Click on Fluorine(F) button >> click on Single bond button. Click on Fluorine(F) button and then click on Single bond button.
Move the cursor on Xenon atom.

Point to the blue circle.

Move the cursor on Xenon atom.

Notice, a small blue circle appears on it.

Click >> hold the left mouse button. Click and hold the left mouse button.

And then drag to draw two Xenon-Fluoride bonds.

Now I will explain about Xenon's Atom Popup Menu.
Right click on Xenon.

Point to Atom Popup Menu.

Move the cursor over to Xenon atom, right-click on it.

Xenon's Atom Popup Menu opens.

Point to Isotopes, Change Element and Properties. Here, I will explain about Isotopes, Change Element and Properties options.
Point to the submenu >>Isotopes of Xenon. Let's first move to Isotopes.

A submenu opens with a list of Isotopes of Xenon.

Move the cursor to Change Element. Next, I will move the cursor to Change Element.
Point to the submenu >>various categories of elements of elements. A submenu opens with various categories of elements.

I will scroll down to various categories.

Move the cursor to Alkali Earth Metals.

Point to the list.

I will choose Alkali Earth Metals.

Alkali Earth Metals list opens.

Select the Calcium from the list.

Point to the replaced element.

Select Calcium(Ca) from the list.

We see that element Xenon is replaced by Calcium.

Right click on Calcium.

Calcium's Atom Popup Menu opens.

Now, we move on to Molecular Properties option.

Right click on Calcium.

Calcium's Atom Popup Menu opens.

Move the cursor to Molecular Properties option.

Point to Properties text box.

Click on Molecular Properties option.

Properties text box opens.

Type compound's name.

Point to the displayed text.

Type the name of the compound as Calcium Fluoride and click OK button.

Name of the compound is displayed below the structure.

Click on Save button the tool bar. Let us save the file now.

Click on Save button on the tool bar.

Point to the dialogue box. Save dialog box opens.
Type the file name as Calcium-fluoride.

Click on Save button.

Type the file name as Calcium-fluoride.

Click on Save button.

Next, we will learn how to create a reaction.
To draw a reaction, we need to draw the required structures.
Point to the window.

Point to the reactants and products.

I have opened a new window with required structures.

Here the reactants are Propene and Chlorine molecules and product is 1,2-dicholoropropane.

Click on Reaction arrow button.

Click between reactants and products.

Point to the created reaction.

On the left side tool bar, click on the Reaction arrow button.

Click between reactants and products.

The reaction is created.

Click on Relayout the structures button on the tool bar. We will now allign the structures properly in the reaction.

Click on Relayout the structures button on the top tool bar.

I will now discuss about how to set up an R group query.
Slide Number 5

R-group query

What is an R-group query?
  • An R-group query involves Root structure and substituents.
  • It represents substitution on the same root structure.
  • It can involve derivatives which differ in one or more substituents.
Click on Create a new file icon. Click on Create a new file icon to open a new window.
Click on Draw a chain button.

Click on the Panel >> drag to draw a Carbon chain with three Carbons.

Click on Draw a chain button.

Click on the Panel and drag to draw a Carbon chain with three Carbon atoms.

Let's create a substituent that has to be attached to the Carbon chain.

For example, Benzene.

Click on Benzene ring on right side tool bar.

Click on the Panel.

Click on Benzene ring on right side tool bar.

Click on the Panel.

Point to the terminal Carbon atom Let's label the terminal Carbon atom as R1 in the Carbon chain.
Right click on terminal Carbon atom.

Move the cursor onto Atom Pop menu.

Right click on terminal Carbon atom.

Atom Pop menu opens.

Point to the submenu. Scroll down to Pseudo Atoms.

A submenu opens; select R1.

Now let's define the Carbon chain as root structure.
Click on Selection button. Click on Selection button.

Select the Root structure by dragging over it.

Go to R-groups menu and select Define as Root Structure.

Point to the substituents.

Go to R-groups menu and select Define as Root Structure.

The substituent structure will be added as Not in R-Group.

Click on Select button and select the Substituent.

Go to R-groups menu and select Define as Substituent.

Click on Selection button; select the Substituent.

Go to R-groups menu and select Define as Substituent.

Point to the input box.

Point to the substituent.

An input box opens.

Here, enter an R-group number as “1” and click OK button.

The substituent will be numbered as R1.

Point to the Root structure marked as asterisk(*)

Point to the substituent marked with asterisk(*)

On the Root structure, the substituent R1 will be marked as asterisk(*)

The attaching Carbon atom of the substituent R1 will also be marked with an asterisk(*).

Click on Selection button>> select Root Structure and substituent(R1). Click on the Selection button, select Root Structure and substituent(R1).
Go to R-groups menu>> select General Possible configurations(sdf). Go to R-groups menu, select General Possible configurations(sdf).
Point to the dialog box. Save dialog box opens.
Type the file name as r-group >>select the file location as Desktop.

Click on Save button.

Type the file name as r-group, select the file location as Desktop.

Click on Save button.

Click on Open icon on the tool bar Click on Open icon on the tool bar.

Open dialogue box opens.

Point to “Files of Type” field select “All Files”. In the “Files of Type”, select “All Files”
Click on Desktop folder>>select the saved r-group file.

Click on “Open”

Click on Desktop folder.

Click Open; then select the saved r-group file.

Click on “Open” button.

Point to OK A message pops up; click OK.
Move the cursor on the file. A new file opens with r-group query structure.
Click on Relayout the structures button on the tool bar. To allign the structure properly,

Click on Relayout the structure button on the tool bar.

Point to the structure. The structure shown is root structure along with attached R-group substituent Benzene.
Let's summarize.
Slide Number 6

Summary

In this tutorial we have learnt
  • Periodic table trends
  • Draw a reaction
  • Set up R-Group query.
Slide Number 7

Assignment.

As an assignment,
  • Explore various Periodic table trends and
  • Draw reactions of your choice.
Slide Number8

Acknowledgement

This video summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

Slide Number 9 Spoken Tutorial team conducts workshops using Spoken Tutorials and gives certificates.

Please contact us.

Slide number 10 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. 
More information on this Mission is available at this link.

http://spoken-tutorial.org/NMEICT-Intro ]

This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, Nancyvarkey, PoojaMoolya

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