Difference between revisions of "GChemPaint/C3/Analysis-of-compounds/English"

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Line 91: Line 91:
 
I will discuss 3 of them in this tutorial, namely-
 
I will discuss 3 of them in this tutorial, namely-
  
−
* NIST webbook page for this molecule
+
* '''NIST''' webbook page for this molecule
  
−
* PubChem page for this molecule and
+
*''' PubChem''' page for this molecule and
  
−
* Open in Calculator
+
* '''Open in Calculator'''
 
|-
 
|-
 
||Click on '''NIST''' webbook page for this molecule.
 
||Click on '''NIST''' webbook page for this molecule.
Line 101: Line 101:
 
|-
 
|-
 
||Move the cursor over the page.
 
||Move the cursor over the page.
−
|'''|Alanine's NIST''' webpage opens.
+
||'''Alanine's NIST''' webpage opens.
  
 
It shows all the details about '''Alanine'''.
 
It shows all the details about '''Alanine'''.
Line 110: Line 110:
 
||Now right click on '''Alanine''' to open '''PubChem''' page for this molecule.
 
||Now right click on '''Alanine''' to open '''PubChem''' page for this molecule.
  
−
PubChem webpage opens.
+
'''PubChem''' webpage opens.
 
|-
 
|-
 
||Point to the structure on the webpage.
 
||Point to the structure on the webpage.
−
||Click on Alanine structure in this webpage.
+
||Click on '''Alanine''' structure in this webpage.
  
−
A new web-page with 2D Structure and 3D Conformer tabs, is seen.
+
A new web-page with '''2D Structure''' and '''3D Conformer''' tabs, is seen.
 
|-
 
|-
−
||Click on 3D Conformer tab to view the structure in 3 dimension
+
||Click on '''3D Conformer''' tab to view the structure in 3 dimension
−
||Click on 3D Conformer tab to view Alanine structure in 3 dimensions.  
+
||Click on '''3D Conformer''' tab to view '''Alanine''' structure in 3 dimensions.  
 
|-
 
|-
−
||Click on the 3D structure
+
||Click on the 3D structure.
 
||Click on the displayed 3D structure.
 
||Click on the displayed 3D structure.
  
 
This opens the structure in a separate window with some controls on the top and the left.
 
This opens the structure in a separate window with some controls on the top and the left.
 
|-
 
|-
−
||Click on the Rotation icon  
+
||Click on the '''Rotation''' icon  
−
||Click on the Rotation icon to rotate the structure in various directions.
+
||Click on the '''Rotation''' icon to rotate the structure in various directions.
 
|-
 
|-
−
||Click on H icon  
+
||Click on ''' H''' icon  
−
Point to the Hydrogen atoms in white.
+
 
−
||On the same page, click on H icon to show hydrogens.
+
Point to the '''Hydrogen''' atoms in white.
 +
||On the same page, click on '''H''' icon to show hydrogens.
 +
 
 
These are the Hydrogen atoms.
 
These are the Hydrogen atoms.
 
|-
 
|-
−
||Switch to GChemPaint.
+
||Switch to '''GChemPaint'''.
−
||Let's switch to GChemPaint window again.
+
||Let's switch to '''GChemPaint''' window again.
 
|-
 
|-
−
||Right click on Alanine to Open in Calculator.
+
||Right click on '''Alanine''' to '''Open in Calculator'''.
 
Move the cursor on Chemical calculator window.
 
Move the cursor on Chemical calculator window.
−
||Right-click on '''Alanine''' and choose '''Open in Calculator''' option.
+
||'''Right click''' on '''Alanine''' and choose '''Open in Calculator''' option.
  
 
'''Chemical calculator''' window will open, provided the '''Chemical calculator''' is installed.   
 
'''Chemical calculator''' window will open, provided the '''Chemical calculator''' is installed.   
  
−
If not, then please install the same, using '''Synaptic Package Manager''', as mentioned in the Overview tutorial.
+
If not, then please install the same, using '''Synaptic Package Manager''', as mentioned in the '''Overview''' tutorial.
 
|-
 
|-
 
||Point to the tabs.
 
||Point to the tabs.
Line 161: Line 163:
  
 
Point to the graph and the peak.
 
Point to the graph and the peak.
−
||Click on Isotropic Pattern tab.
+
||Click on '''Isotropic Pattern''' tab.
  
 
It shows a graph of mass spectrum with a peak at '''Molecular weight''' of the compound.
 
It shows a graph of mass spectrum with a peak at '''Molecular weight''' of the compound.
Line 192: Line 194:
 
||Right click at each position to show atoms.  
 
||Right click at each position to show atoms.  
  
−
Click on 'Atom' then on 'Display symbol'.  
+
Click on '''Atom''' then on '''Display symbol'''.  
 
|-
 
|-
−
||Click on Save the current file icon on the tool bar.
+
||Click on '''Save the current file''' icon on the tool bar.
−
||To convert 1,3-butadiene 2D structure to 3D structure, click on Save icon in the tool bar.
+
||To convert '''1,3-butadiene''' 2D structure to 3D structure, click on '''Save the current file''' icon in the tool bar.
 
|-
 
|-
−
||Save as dialog box opens.
+
||'''Save as''' dialog box opens.
−
||Save as dialog box opens.
+
||'''Save as''' dialog box opens.
 
|-
 
|-
−
||Point to  File type field>>select MDL Molfile Format.
+
||Point to  '''File type''' field>>select '''MDL Molfile''' Format.
−
||In the File type field, select MDL Molfile Format.
+
||In the '''File type''' field, select '''MDL Molfile''' Format.
 
|-
 
|-
−
||Type filename as 1,3-butadiene.
+
||Type filename as '''1,3-butadiene'''.
−
Click on Save button.
+
−
||Type filename as 1,3-butadiene.  
+
  
−
Select Desktop folder to save the file on Desktop.
+
Click on '''Save''' button.
 +
||Type filename as '''1,3-butadiene'''.  
  
−
Then click on Save button.
+
Select '''Desktop''' folder to save the file on '''Desktop'''.
 +
 
 +
Then click on '''Save''' button.
 
|-
 
|-
−
||Type and show 1,3-butadiene.mol and 1,3-butadiene.mdl
+
||Type and show '''1,3-butadiene.mol''' and '''1,3-butadiene.mdl'''
−
||Alternatively, you can also save the file with extension .mol or .mdl directly.
+
||Alternatively, you can also save the file with extension ''.mol'' or ''.mdl'' directly.
  
−
For example as 1,3-butadiene.mol and 1,3-butadiene.mdl
+
For example as '''1,3-butadiene.mol''' and '''1,3-butadiene.mdl'''
 
|-
 
|-
−
||Right click on saved file and Open With Molecules viewer.
+
||Right click on saved file and '''Open With Molecules viewer'''.
−
||To view the structure in 3D, right-click on the saved file.
+
||To view the structure in 3D, right click on the saved file.
  
−
Then select the option Open With Molecules viewer.
+
Then select the option '''Open With Molecules viewer'''.
  
 
Please note, we cannot make changes in the structure.
 
Please note, we cannot make changes in the structure.
 
|-
 
|-
 
||Move the mouse pointer over the structure
 
||Move the mouse pointer over the structure
−
||To rotate the 3D structure, place the cursor on the structure, hold and drag the mouse.  
+
||To rotate the 3D structure, place the cursor on the structure, hold and drag the mouse.  
 
|-
 
|-
−
||Slide Number 6
+
||'''Slide Number 6'''
−
Assignment
+
 
 +
'''Assignment'''
 
||As an assignment,  
 
||As an assignment,  
−
Convert Benzene structure from 2D to 3D.
+
Convert '''Benzene''' structure from 2D to 3D.
 
|-
 
|-
 
||
 
||
−
||
+
||Now let's learn to draw chemical reactions and reaction conditions.
−
Now let's learn to draw chemical reactions and reaction conditions.
+
 
|-
 
|-
−
||Slide Number 7
+
||'''Slide Number 7'''
 +
 
 
(Show Screen shot of the reaction)
 
(Show Screen shot of the reaction)
−
||This is a chemical reaction of Ethyl chloride (C2H5Cl) with Alcoholic Potassium hydroxide(Alc.KOH) and Aqueous Potassium hydroxide(Aq.KOH) to yield Ethene(C2H4) and Ethanol(C2H5OH) respectively.  
+
||This is a chemical reaction of '''Ethyl chloride'''  ('''C<sub>2</sub>H<sub>5</sub>Cl''') with Alcoholic Potassium hydroxide(Alc.KOH) and Aqueous Potassium hydroxide(Aq.KOH) to yield Ethene(C<sub>2</sub>H<sub>4</sub>) and Ethanol(C<sub>2</sub>H<sub>5</sub>OH) respectively.  
 
|-
 
|-
 
||Point to the new window.
 
||Point to the new window.

Revision as of 16:55, 4 March 2014

Title of the tutorial: Analysis Of Compounds

Author: Madhuri Ganapathi

Key words: Molecular contextual menu,Chemical calculator, Composition, Isotropic pattern, video tutorial


Visual Cue Narration

Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Analysis of Compounds in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn about,
  • Molecular contextual menu
  • Save the molecule in .mol format
  • Add and edit a reaction
  • Add reaction conditions and reagents on the reaction arrow
  • Convert reaction molecules into 3D
Slide Number 3

System Requirement

For this tutorial I am using

Ubuntu Linux OS version 12.04.

GChemPaint version 0.12.10.

You will also require Internet connectivity.

Slide Number 4

Pre-requisites

To follow this tutorial, you should be familiar with

GChemPaint.

If not, for relevant tutorials, please visit our website.

Switch to GChemPaint window Let us open a new GChemPaint window.
Click on Use or manage templates tool. Click on Use or manage templates tool.

Templates tool property page opens below.

Click on Amino Acids.

Select Alanine from the list.

Point to Alanine structure.

Click on the Templates drop-down button, which shows Amino acids, by default.

Select Alanine from the list.

Structure of Alanine is loaded onto the Templates property page.

Click on structure>>click on the Display area to load it. Click on the structure and then click on the Display area to load it.
Now, I will explain about contextual menu of Alanine molecule.
Right click on molecule> Submenu opens>>

select Molecule >> molecule's contextual menu opens.

Right click on the molecule.

A sub-menu opens.

Select Molecule; a contextual menu opens alongside.

Point to the menu items. This contextual menu contains different menu items.

I will discuss 3 of them in this tutorial, namely-

  • NIST webbook page for this molecule
  • PubChem page for this molecule and
  • Open in Calculator
Click on NIST webbook page for this molecule. Click on NIST webbook page for this molecule.
Move the cursor over the page. Alanine's NIST webpage opens.

It shows all the details about Alanine.

Right click on Alanine to open PubChem page for this molecule.

Come back to GChemPaint editor.

Now right click on Alanine to open PubChem page for this molecule.

PubChem webpage opens.

Point to the structure on the webpage. Click on Alanine structure in this webpage.

A new web-page with 2D Structure and 3D Conformer tabs, is seen.

Click on 3D Conformer tab to view the structure in 3 dimension Click on 3D Conformer tab to view Alanine structure in 3 dimensions.
Click on the 3D structure. Click on the displayed 3D structure.

This opens the structure in a separate window with some controls on the top and the left.

Click on the Rotation icon Click on the Rotation icon to rotate the structure in various directions.
Click on H icon

Point to the Hydrogen atoms in white.

On the same page, click on H icon to show hydrogens.

These are the Hydrogen atoms.

Switch to GChemPaint. Let's switch to GChemPaint window again.
Right click on Alanine to Open in Calculator.

Move the cursor on Chemical calculator window.

Right click on Alanine and choose Open in Calculator option.

Chemical calculator window will open, provided the Chemical calculator is installed.

If not, then please install the same, using Synaptic Package Manager, as mentioned in the Overview tutorial.

Point to the tabs. Window has two tabs at the bottom - Composition and Isotopic Pattern.
Move the cursor to all the components one by one. Composition tab has the following components-
  • Formula
  • Raw formula
  • Molecular weight in g.mol-1 ( gram.mole-inverse)
  • Compound's elemental mass percentage(%) analysis.
Click on Isotropic Pattern tab.

Point to the graph and the peak.

Click on Isotropic Pattern tab.

It shows a graph of mass spectrum with a peak at Molecular weight of the compound.

Slide Number 5

Assignment

As an assignment

1. Select other Amino Acids from Templates list.

2. Obtain their Composition and Isotropic pattern.

Switch to GChemPaint window. Let's open a new GChemPaint window.
Click on Add a chain tool>> click and drag the chain to 4 carbons. Let's draw 1,3-butadiene structure.

Click on Add a chain tool.

Click and drag the chain to 4 carbons.

Click on Add a bond tool. Click on Add a bond tool and

click on the first and third bonds, to form double bonds.

Right click at each position to show atoms. Right click at each position to show atoms.

Click on Atom then on Display symbol.

Click on Save the current file icon on the tool bar. To convert 1,3-butadiene 2D structure to 3D structure, click on Save the current file icon in the tool bar.
Save as dialog box opens. Save as dialog box opens.
Point to File type field>>select MDL Molfile Format. In the File type field, select MDL Molfile Format.
Type filename as 1,3-butadiene.

Click on Save button.

Type filename as 1,3-butadiene.

Select Desktop folder to save the file on Desktop.

Then click on Save button.

Type and show 1,3-butadiene.mol and 1,3-butadiene.mdl Alternatively, you can also save the file with extension .mol or .mdl directly.

For example as 1,3-butadiene.mol and 1,3-butadiene.mdl

Right click on saved file and Open With Molecules viewer. To view the structure in 3D, right click on the saved file.

Then select the option Open With Molecules viewer.

Please note, we cannot make changes in the structure.

Move the mouse pointer over the structure To rotate the 3D structure, place the cursor on the structure, hold and drag the mouse.
Slide Number 6

Assignment

As an assignment,

Convert Benzene structure from 2D to 3D.

Now let's learn to draw chemical reactions and reaction conditions.
Slide Number 7

(Show Screen shot of the reaction)

This is a chemical reaction of Ethyl chloride (C2H5Cl) with Alcoholic Potassium hydroxide(Alc.KOH) and Aqueous Potassium hydroxide(Aq.KOH) to yield Ethene(C2H4) and Ethanol(C2H5OH) respectively.
Point to the new window.

Open a new GChemPaint window.

Let's first draw the structure of Ethyl chloride.

Click on Add a chain tool.

Click on the Display area.

Click on Add a chain tool and then click on the Display area.
Right click on the chain to display atoms at first and second positions. Right click on the chain to display atoms on first and second positions.
Click on Current element drop down arrow button >> select Cl from table. Click on Current element drop down arrow button and select Cl from table.
Click on Add or modify a atom tool>>Click on the third position.

Point to the structure.

Click on Add or modify a atom tool.

Click on third position. Ethyl chloride structure is drawn.

Click on Add or modify a group of atoms tool >>Click on the Display area>>Type Alc.KOH >>Click type Aq.KOH. Click on Add or modify a group of atoms tool.

Click on Display area and type Alc.KOH. Click again and type Aq.KOH

Click on Add an arrow for an irreversible reaction tool. Click on Add an arrow for an irreversible reaction tool.
Point to Arrow length.

You can change the Arrow length using the scroller here.

I will increase the arrow length to 280.

On the Display area click beside Ethyl Chloride. On the Display area, click beside Ethyl Chloride.
Click again below Ethyl Chloride. Click again below Ethyl Chloride.

Now without releasing the mouse button, rotate the arrow to point downwards.

Click on Selection tool>>Position Alc.KOH above the arrow>> Aq.KOH close to the arrow. Click on the Selection tool.

Position Alcoholic Potassium Hydroxide (Alc.KOH) above first arrow. Position Aqueous Potassium Hydroxide (Aq.KOH) close to second arrow.

Select Alc.KOH and right click on the arrow. Select Alcoholic Potassium hydroxide(Alc.KOH) and right click on the arrow.
A submenu opens, select Arrow and click on Attach selection to arrow. A sub-menu opens.

Select Arrow and click on Attach selection to arrow.

A dialogue box with heading Arrow associated opens. A dialog box with the heading Arrow associated opens.
Click on Role drop down list

Select Catalyst from the list. Click on Close.

Click on Role drop down list.

Select Catalyst from the list. Click on Close.

Drag to see Alc.KOH attaches to the arrow as a catalyst. Drag the arrow to check if Alcoholic Potassium Hydroxide (Alc.KOH) attaches to arrow as a Catalyst.
Point to (Aq.KOH) Let's repeat the process for Aqueous Potassium Hydroxide (Aq.KOH) to attach it to the arrow as a Catalyst.

To obtain products, let's copy and paste Ethyl chloride structure.

Click on Select one or more objects tool to select Ethyl chloride. Click on Select one or more objects tool to select Ethyl chloride.
Press CTRL + C to copy >> press CTRL+V to paste the structures. Press CTRL + C to copy and press CTRL+V twice to paste the structures.
Cursor on the structures. Place the structures at proper positions by dragging.
Show the reaction slide In the reactions Ethyl chloride reacts with Alcoholic potassium Hyroxide to give Ethene.

Ethyl chloride reacts with Aqueous Potassium Hydroxide to give Ethanol.

Click on the Eraser tool,

delete Cl bond.

To obtain Ethene, click on Eraser tool and delete Cl bond of Ethyl chloride.
Click on Current Element arrow.

In the Tool box, ensure that Current element is Carbon.

Click on Add a bond tool>>Click on the bond. Click on Add a bond tool and click on the bond to get a double bond.
Press O on the keyboard. To obtain Ethanol, press O on the keyboard.
Click on Add or modify atom tool and then click on Cl. Click on Add or modify atom tool and then click on Cl of Ethyl chloride
Now let's convert the reactants and products from 2D to 3D.
Point to new GChemPaint file. Open a new file and copy Ethyl Chloride into it.
Click on Save the current file icon.

Save as dialogue box opens .

On clicking, Save the current file icon, Save as dialog box opens.
Type file name as Ethyl Chloride.mol Type file name as Ethyl Chloride.mol
Click on Desktop to save your file on your Desktop>> Click on Save button. Click on Desktop to save your file on your Desktop. Click on Save button.
Point to Ethene

Point to Ethanol Point to the files on the Desktop.

Likewise copy Ethene into a new file.

Save as Ethene.mol. Copy Ethanol into a new file. Save as Ethanol.mol I had already saved the files on my Desktop.

I will minimize the current Gchempaint window. And I will go to Desktop folder where I had saved my files.

Right click on the file Open with Molecules viewer. To view the compound in 3D, right click on the file, and choose Open with Molecules viewer.

Observe the compounds in 3D. <Pause>

Let's summarize what we have learnt.
Slide Number 8

Summary In this tutorial we have learnt about,

NIST web book page for the molecule. Pub-Chem page for the molecule Find molecular weight of the compound using Chemical calculator. Obtain graph of mass spectrum of a molecule Save the molecule in .mol format Add reaction conditions and reagents onto the reaction arrow Add and edit a reaction Convert reaction molecules into 3D structures.

Slide Number 9

Assignment

Here is an assignment

Draw chemical reaction of: 1)Propene (C3H6) and Bromine(Br-Br) molecule. with Carbon tetra chloride(CCl4) as a catalyst. 2)Benzene and Chlorine(Cl-Cl) molecule with Anhydrous Aluminum Chloride(AlCl3) as a catalyst. Your completed assignment should look like this.

Slide Number 10

Acknowledgement

Watch the video available at this URL.

http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial It summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it

Slide Number 11 The Spoken Tutorial Project Team:

Conducts workshops using spoken tutorials Gives certificates to those who pass an on-line test For more details, please write to contact@spoken-tutorial.org

Slide number 12

Spoken Tutorial Project is a part of the Talk to a Teacher project It is supported by the National Mission on Education through ICT, 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

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