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

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Line 26: Line 26:
 
* Molecular contextual menu
 
* Molecular contextual menu
  
−
* Save the molecule in ''.mol'' format  
+
* Save the molecule in '''.mol''' format  
  
 
* Add and edit a reaction
 
* Add and edit a reaction
Line 54: Line 54:
 
|-
 
|-
 
||Switch to '''GChemPaint''' window
 
||Switch to '''GChemPaint''' window
−
||Let us open a new '''GChemPaint''' window.
+
||I have opened a new '''GChemPaint''' window.
 +
 
 
|-
 
|-
 
||Click on '''Use or manage templates''' tool.
 
||Click on '''Use or manage templates''' tool.
Line 60: Line 61:
  
 
'''Templates''' tool property page opens below.
 
'''Templates''' tool property page opens below.
 +
 
|-
 
|-
 
||Click on '''Amino Acids'''.
 
||Click on '''Amino Acids'''.
Line 65: Line 67:
  
 
Point to '''Alanine''' structure.
 
Point to '''Alanine''' structure.
−
||Click on the '''Templates''' drop-down button, which shows '''Amino acids''', by default.
+
||Click on '''Amino Acids''' on '''Templates''' drop down button.
  
 
Select '''Alanine''' from the list.  
 
Select '''Alanine''' from the list.  
  
 
Structure of '''Alanine''' is loaded onto the '''Templates''' property page.
 
Structure of '''Alanine''' is loaded onto the '''Templates''' property page.
 +
 
|-
 
|-
 
||Click on structure>>click on the '''Display area''' to load it.
 
||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.  
+
||Click on the structure and click on '''Display area''' to load it.  
 +
 
 
|-
 
|-
 
||
 
||
−
||Now, I will explain about contextual menu of '''Alanine''' molecule.
+
||I will explain about contextual menu of '''Alanine''' molecule.
 +
 
 
|-
 
|-
 
||Right click on molecule> Submenu opens>>  
 
||Right click on molecule> Submenu opens>>  
Line 84: Line 89:
 
A sub-menu opens.
 
A sub-menu opens.
  
−
Select '''Molecule'''; a contextual menu opens alongside.
+
Select '''Molecule'''; a contextual menu opens alongside.
 +
 
 
|-
 
|-
 
||Point to the menu items.
 
||Point to the menu items.
−
||This contextual menu contains different menu items.
+
||Contextual menu contains different menu items, of which, I will discuss about-
  
−
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'''
−
||Click on '''NIST''' webbook page for this molecule.
+
||Click on '''NIST Web page for this molecule'''
 +
 
 
|-
 
|-
 
||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'''.
+
Webpage shows all the details about '''Alanine'''.
 +
 
 
|-
 
|-
 
||Right click on '''Alanine''' to open '''PubChem''' page for this molecule.
 
||Right click on '''Alanine''' to open '''PubChem''' page for this molecule.
  
 
Come back to '''GChemPaint''' editor.
 
Come back to '''GChemPaint''' editor.
−
||Now right click on '''Alanine''' to open '''PubChem''' page for this molecule.
+
||Come back to '''GChemPaint''' editor.
 +
 
 +
Right click on '''Alanine''' to open the '''PubChem page for this molecule'''.
  
−
'''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 on 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''' 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 on 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.
 
Point to the '''Hydrogen''' atoms in white.
−
||On the same page, click on '''H''' icon to show hydrogens.
+
||On the same page, click on '''H''' icon to show '''hydrogens'''.
 +
 
 +
These are the '''Hydrogens'''.
  
−
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''';  choose the option '''Open in Calculator'''.  
  
−
'''Chemical calculator''' window will open, provided the '''Chemical calculator''' is installed.
+
'''Chemical calculator''' window opens.
 +
 
 +
If not, please install the same, using '''Synaptic Package Manager''', as 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.
−
||Window has two tabs at the bottom - '''Composition''' and '''Isotopic Pattern.'''
+
||This Window has two tabs at the bottom - '''Composition''' and '''Isotopic Pattern.'''
 +
 
 
|-
 
|-
 
||Move the cursor to all the components one by one.
 
||Move the cursor to all the components one by one.
Line 160: Line 176:
  
 
* '''Compound's elemental mass percentage(%) analysis'''.
 
* '''Compound's elemental mass percentage(%) analysis'''.
 +
 
|-
 
|-
 
||Click on '''Isotropic Pattern''' tab.
 
||Click on '''Isotropic Pattern''' tab.
  
 
Point to the graph and the peak.
 
Point to the graph and the peak.
−
||Click on '''Isotropic Pattern''' tab.
+
||Click on the '''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.
 
 
|-
 
|-
 
||'''Slide Number 5'''
 
||'''Slide Number 5'''
Line 176: Line 194:
  
 
2. Obtain their '''Composition''' and '''Isotropic pattern'''.  
 
2. Obtain their '''Composition''' and '''Isotropic pattern'''.  
 +
 
|-
 
|-
 
||Switch to GChemPaint window.
 
||Switch to GChemPaint window.
−
||Let's open a new GChemPaint window.
+
||I have opened a new '''GChemPaint''' window.
 +
 
 
|-
 
|-
 
||Click on '''Add a chain''' tool>> click and drag the chain to 4 carbons.
 
||Click on '''Add a chain''' tool>> click and drag the chain to 4 carbons.
Line 186: Line 206:
  
 
Click and drag the chain to 4 carbons.
 
Click and drag the chain to 4 carbons.
 +
 
|-
 
|-
 
||Click on '''Add a bond''' tool.
 
||Click on '''Add a bond''' tool.
−
||Click on '''Add a bond''' tool and  
+
||Click on '''Add a bond''' tool and click on first and third bonds, to form double bonds.
  
−
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.
 
||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 click 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 the current file''' icon in the tool bar.
+
||To convert '''1,3-butadiene''' 2D structure to 3D structure, click on the '''Save''' icon on 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.
 
Click on '''Save''' button.
−
||Type filename as '''1,3-butadiene'''.  
+
||Type the filename as '''1,3-butadiene'''.  
  
−
Select '''Desktop''' folder to save the file on '''Desktop'''.
+
Select '''Desktop''' to save the file on '''Desktop'''.
  
 
Then click on '''Save''' button.
 
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, type the filename as '''1,3butadiene.mol''' or '''.mdl'''
 +
 
 +
Click on '''Save''' button.
 +
 
 
|-
 
|-
 
||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 molecule.
  
−
Then select the option '''Open With Molecules viewer'''.
+
Select the option '''Open With Molecules viewer'''.
 +
 
 +
This is''' 1,3butadiene''' in 3D.
  
 
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 structure, place the cursor on the structure, hold and drag the mouse.  
 +
 
 
|-
 
|-
 
||'''Slide Number 6'''
 
||'''Slide Number 6'''
Line 234: Line 266:
 
'''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'''
Line 245: Line 280:
  
 
'''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.  
 
'''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.
−
||Open a new '''GChemPaint''' window.
+
||I have opened a new '''GChemPaint''' window.
 +
 
 
|-
 
|-
 
||
 
||
−
||Let's first draw the structure of '''Ethyl chloride.'''  
+
||Let's first draw structure of '''Ethyl chloride.'''  
 +
 
 
|-
 
|-
 
||Click on '''Add a chain''' tool.
 
||Click on '''Add a chain''' tool.
  
 
Click on the '''Display area.'''
 
Click on the '''Display area.'''
−
||Click on '''Add a chain''' tool and then click on '''Display area'''.
+
||Click on '''Add a chain''' tool.
 +
 
 +
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 bond positions.
−
||Right click on the chain to display atoms on first and second positions.
+
||Right click on the chain to display atoms on first and second bond positions.
 +
 
 
|-
 
|-
 
||Click on '''Current element''' drop down arrow button >> select '''Cl''' from table.
 
||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 '''Current element''' drop down arrow button.
 +
 
 +
Select '''Cl''' from table.
 
|-
 
|-
 
||Click on '''Add or modify an atom''' tool>>Click on the third position.
 
||Click on '''Add or modify an atom''' tool>>Click on the third position.
Line 268: Line 312:
 
||Click on '''Add or modify an atom''' tool.
 
||Click on '''Add or modify an atom''' tool.
  
−
Click on third position.
+
Click on the third bond position.
 +
 
 +
Structure  of '''Ethyl chloride''' is drawn.
  
−
'''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 the '''Display area'''>>Type '''Alc.KOH''' >>Click type '''Aq.KOH'''.  
 
||Click on '''Add or modify a group of atoms''' tool.  
 
||Click on '''Add or modify a group of atoms''' tool.  
−
Click on '''Display area''' and type '''Alc.KOH'''.  
+
 
 +
Click on the '''Display area'''. Type '''Alc.KOH'''.  
 +
 
 
Click again and type '''Aq.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.
 
||Click on '''Add an arrow for an irreversible reaction''' tool.
 
||Click on '''Add an arrow for an irreversible reaction''' tool.
 +
 
|-
 
|-
 
||Point to  '''Arrow length.'''
 
||Point to  '''Arrow length.'''
Line 284: Line 333:
  
 
I will increase the arrow length to 280.
 
I will increase the arrow length to 280.
 +
 
|-
 
|-
−
||On the '''Display area''' click beside '''Ethyl Chloride'''.  
+
||On the '''Display area''', beside '''Ethyl Chloride'''.  
−
||On the '''Display area''', click beside '''Ethyl Chloride'''.   
+
||Click on the '''Display area''', beside '''Ethyl Chloride'''.   
 +
 
 
|-
 
|-
−
||Click again below '''Ethyl Chloride'''.  
+
||Click below '''Ethyl Chloride'''.  
−
||Click again below '''Ethyl Chloride'''.  
+
||Click below '''Ethyl Chloride'''.
 +
 
 +
Hold the mouse and rotate the arrow to point downwards.
  
−
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 '''Selection''' tool>>Position '''Alc.KOH''' above the arrow>> '''Aq.KOH''' close to the arrow.
Line 299: Line 351:
  
 
Position '''Aqueous Potassium Hydroxide (Aq.KOH)''' close to second arrow.
 
Position '''Aqueous Potassium Hydroxide (Aq.KOH)''' close to second arrow.
 +
 
|-
 
|-
 
||Select '''Alc.KOH''' and right click on the arrow.
 
||Select '''Alc.KOH''' and right click on the arrow.
−
||Select '''Alcoholic Potassium hydroxide(Alc.KOH)''' and right click on the arrow.
+
||Select '''Alcoholic Potassium hydroxide(Alc.KOH)'''.
 +
 
 +
Right click on the arrow.
 +
 
 
|-
 
|-
 
||A submenu opens, select '''Arrow''' and click on '''Attach selection to arrow'''.
 
||A submenu opens, select '''Arrow''' and click on '''Attach selection to arrow'''.
Line 307: Line 363:
  
 
Select '''Arrow''' and click on '''Attach selection to arrow'''.
 
Select '''Arrow''' and click on '''Attach selection to arrow'''.
 +
 
|-
 
|-
−
||A dialogue box with heading '''Arrow associated''' opens.
+
||A dialog box with heading '''Arrow associated''' opens.
−
||A dialog box with the heading '''Arrow associated''' opens.
+
||A dialog box with heading '''Arrow associated''' opens.
 +
 
 
|-
 
|-
 
||Click on '''Role''' drop down list  
 
||Click on '''Role''' drop down list  
Line 317: Line 375:
  
 
Select '''Catalyst''' from the list. Click on '''Close'''.
 
Select '''Catalyst''' from the list. Click on '''Close'''.
 +
 
|-
 
|-
 
||Drag to see '''Alc.KOH''' attaches to the arrow as a '''Catalyst'''.
 
||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'''.
+
||Drag arrow to check if '''Alcoholic Potassium Hydroxide (Alc.KOH)''' attaches to the arrow, as a '''catalyst'''.
 +
 
 
|-
 
|-
 
||Point to '''(Aq.KOH)'''  
 
||Point to '''(Aq.KOH)'''  
−
||Let's repeat the process for '''Aqueous Potassium Hydroxide(Aq.KOH)''' to attach it to the arrow as a '''Catalyst'''.
+
||Let's repeat the process for '''Aqueous Potassium Hydroxide(Aq.KOH)'''.
−
|-
+
 
−
||
+
Drag to see the attachement as a '''catalyst'''.
−
||To obtain products, let's copy and paste '''Ethyl chloride''' structure.  
+
 
|-
 
|-
 +
 
||Click on '''Selection''' tool to select '''Ethyl chloride'''.  
 
||Click on '''Selection''' tool to select '''Ethyl chloride'''.  
−
||Click on '''Selection''' tool to select '''Ethyl chloride'''.
+
||Click on '''Selection''' tool to select '''Ethyl chloride''' structure.
−
|-
+
−
||Press '''CTRL + C''' to copy >>
+
  
−
press '''CTRL+V''' to paste the structures.
+
|-
−
||Press '''CTRL + C''' to copy and
+
||Press '''CTRL + C''' to copy >> press '''CTRL+V''' to paste the structures.
 +
||Press '''CTRL + C''' to copy and '''CTRL+V''' twice to paste the structures.
  
−
press '''CTRL+V''' twice to paste the structures.
 
 
|-
 
|-
 
||Cursor on the structures.
 
||Cursor on the structures.
 
||Place the structures at proper positions by dragging.
 
||Place the structures at proper positions by dragging.
 +
 
|-
 
|-
 
||Show the reaction slide
 
||Show the reaction slide
Line 344: Line 403:
  
 
'''Ethyl chloride''' reacts with '''Aqueous Potassium Hydroxide''' to give '''Ethanol'''.
 
'''Ethyl chloride''' reacts with '''Aqueous Potassium Hydroxide''' to give '''Ethanol'''.
 +
 
|-
 
|-
−
||Click on the '''Eraser''' tool, delete Cl bond.
+
||Click on the '''Eraser''' tool, delete '''Cl''' bond.
−
||To obtain '''Ethene''', click on '''Eraser''' tool and
+
||To obtain '''Ethene''', click on '''Eraser''' tool and delete '''Cl''' bond of  '''Ethyl chloride'''.
 +
 
 +
'''Ethane''' is formed.
  
−
delete Cl bond of  '''Ethyl chloride'''.
 
 
|-
 
|-
 
||Click on '''Current Element''' arrow.
 
||Click on '''Current Element''' arrow.
 
||In the Tool box, ensure that '''Current element''' is '''Carbon'''.
 
||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>>Click on the bond.
−
||Click on '''Add a bond''' tool and click on the bond to get a double bond.
+
||Click on '''Add a bond''' tool and click on the bond to obtain a double bond.
 +
 
 +
'''Ethene''' is formed.
 +
 
 
|-
 
|-
 
||Press '''O''' on the keyboard.
 
||Press '''O''' on the keyboard.
 
||To obtain '''Ethanol''', 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 an atom''' tool and then click on '''Cl'''.
−
||Click on '''Add or modify atom''' tool and then click on '''Cl''' of  '''Ethyl chloride'''.  
+
||Click on '''Add or modify an atom''' tool and then click on '''Cl''' of  '''Ethyl chloride'''.  
 +
 
 
|-
 
|-
 
||
 
||
 
||Now let's convert the reactants and products from 2D to 3D.  
 
||Now let's convert the reactants and products from 2D to 3D.  
 +
 
|-
 
|-
 
||Point to new '''GChemPaint''' file.
 
||Point to new '''GChemPaint''' file.
−
||Open a new file and copy '''Ethyl Chloride''' into it.
+
||Open a new file,  copy '''Ethyl Chloride''' and paste it into new file.
 +
 
 
|-
 
|-
−
||Click on '''Save the current file''' icon.
+
||Click on '''Save ''' button >> '''Save as''' dialog box opens.
 +
||Click on '''Save ''' button.
 +
 
 +
'''Save as''' dialog box opens.
  
−
'''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'''
−
||Type file name as '''Ethyl Chloride.mol'''  
+
||Type the 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.
−
||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 '''Ethene'''  
Line 391: Line 465:
 
Save as '''Ethanol.mol'''
 
Save as '''Ethanol.mol'''
  
−
I had already saved the files on my '''Desktop'''.
+
I have already saved the files on my '''Desktop'''.
 +
 
 
|-
 
|-
 
||
 
||
−
||I will minimize the current '''GChemPaint''' window.
+
||I will minimize the current window.
  
 
And I will go to '''Desktop''' folder where I had saved my files.
 
And I will go to '''Desktop''' folder where I had saved my files.
 +
 
|-
 
|-
 
||Right click on the  file '''Open with Molecules viewer'''.
 
||Right click on the  file '''Open with Molecules viewer'''.
−
||To view the compound in 3D, right click on the file, and
+
||To view the compound in 3D, right click on the file, choose '''Open with Molecules viewer'''.
  
−
choose '''Open with Molecules viewer'''.
+
Likewise, I will open all the files with '''Molecules viewer'''
  
 
Observe the compounds in 3D.  <Pause>
 
Observe the compounds in 3D.  <Pause>
 +
 
|-
 
|-
 
||
 
||
 
||Let's summarize what we have learnt.
 
||Let's summarize what we have learnt.
 +
 
|-
 
|-
 
||'''Slide Number 8'''
 
||'''Slide Number 8'''
 
'''Summary'''
 
'''Summary'''
−
||In this tutorial we have learnt about,
+
||In this tutorial we have learnt  
  
−
* NIST web book page for the molecule.
+
* '''NIST WebBook page for this molecule.'''
  
−
* Pub-Chem page for the  molecule
+
* '''Pub-Chem page for the  molecule'''
  
−
* Find molecular weight of the compound using Chemical calculator.
+
* Find molecular weight of the compound using '''Chemical calculator'''.
  
−
* Obtain graph of mass spectrum of a molecule
+
* Obtain graph of '''mass spectrum''' of a molecule
  
−
* Save the molecule in .mol format  
+
* Save the molecule in '''.mol''' format  
  
−
* Add reaction conditions and reagents onto the reaction arrow
+
* Add reaction conditions and reagents on the reaction arrow
  
 
* Add and edit a reaction
 
* Add and edit a reaction
  
−
* Convert reaction molecules into 3D structures.
+
* Convert reaction molecules into 3D structures
 +
 
 
|-
 
|-
 
||'''Slide Number 9'''
 
||'''Slide Number 9'''
  
 
'''Assignment'''
 
'''Assignment'''
−
||Here is an assignment  
+
||AS an assignment  
  
 
Draw chemical reaction of:
 
Draw chemical reaction of:
−
1)Propene (C3H6)(C<sub>3</sub>H<sub>6</sub>) and Bromine(Br-Br) molecule. with Carbon tetra chloride(CCl<sub>4</sub>) as a catalyst.
 
  
−
2)Benzene and Chlorine(Cl-Cl) molecule with Anhydrous Aluminum Chloride(AlCl<sub>3</sub>) as a catalyst.
+
1)'''Propene''' (C3H6)(C<sub>3</sub>H<sub>6</sub>) and '''Bromine'''(Br-Br) molecule with '''Carbon tetra chloride'''(CCl<sub>4</sub>) as a '''catalyst'''.
 +
 
 +
2)'''Benzene''' and '''Chlorine'''(Cl-Cl) molecule with '''Anhydrous Aluminum Chloride'''(AlCl<sub>3</sub>) as a '''catalyst'''.
  
 
Your completed assignment should look like this.
 
Your completed assignment should look like this.
 +
 
|-
 
|-
 
||'''Slide Number 10'''
 
||'''Slide Number 10'''

Latest revision as of 14:15, 13 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 I have opened 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 Amino Acids on Templates drop down button.

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 click on Display area to load it.
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. Contextual menu contains different menu items, of which, I will discuss about-
  • 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 Web page for this molecule
Move the cursor over the page. Alanine's NIST webpage opens.

Webpage shows all the details about Alanine.

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

Come back to GChemPaint editor.

Come back to GChemPaint editor.

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

Point to the structure on the webpage. Click on Alanine structure on 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 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 on 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 Hydrogens.

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; choose the option Open in Calculator.

Chemical calculator window opens.

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

Point to the tabs. This 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 the 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. I have opened 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 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 click 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 the Save icon on 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 the filename as 1,3-butadiene.

Select Desktop 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, type the filename as 1,3butadiene.mol or .mdl

Click on Save button.

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

Select the option Open With Molecules viewer.

This is 1,3butadiene in 3D.

Please note, we cannot make changes in the structure.

Move the mouse pointer over the structure To rotate the 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. I have opened a new GChemPaint window.
Let's first draw structure of Ethyl chloride.
Click on Add a chain tool.

Click on the Display area.

Click on Add a chain tool.

Click on the Display area.

Right click on the chain to display atoms on first and second bond positions. Right click on the chain to display atoms on first and second bond positions.
Click on Current element drop down arrow button >> select Cl from table. Click on Current element drop down arrow button.

Select Cl from table.

Click on Add or modify an atom tool>>Click on the third position.

Point to the structure.

Click on Add or modify an atom tool.

Click on the third bond position.

Structure of Ethyl chloride 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 the Display area. 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, beside Ethyl Chloride. Click on the Display area, beside Ethyl Chloride.
Click below Ethyl Chloride. Click below Ethyl Chloride.

Hold the mouse and 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).

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 dialog box with heading Arrow associated opens. A dialog box with 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 arrow to check if Alcoholic Potassium Hydroxide (Alc.KOH) attaches to the arrow, as a catalyst.
Point to (Aq.KOH) Let's repeat the process for Aqueous Potassium Hydroxide(Aq.KOH).

Drag to see the attachement as a catalyst.

Click on Selection tool to select Ethyl chloride. Click on Selection tool to select Ethyl chloride structure.
Press CTRL + C to copy >> press CTRL+V to paste the structures. Press CTRL + C to copy and 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.

Ethane is formed.

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 obtain a double bond.

Ethene is formed.

Press O on the keyboard. To obtain Ethanol, press O on the keyboard.
Click on Add or modify an atom tool and then click on Cl. Click on Add or modify an 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, copy Ethyl Chloride and paste it into new file.
Click on Save button >> Save as dialog box opens. Click on Save button.

Save as dialog box opens.

Type file name as Ethyl Chloride.mol Type the 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 have already saved the files on my Desktop.

I will minimize the current 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, choose Open with Molecules viewer.

Likewise, I will open all the files 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
  • NIST WebBook page for this 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 on the reaction arrow
  • Add and edit a reaction
  • Convert reaction molecules into 3D structures
Slide Number 9

Assignment

AS an assignment

Draw chemical reaction of:

1)Propene (C3H6)(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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