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MOTIF-Z Interactive - Organic - Got Game? - Organic Reality - Molecular Visualization - All Things Creative

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Fractal Matrix - Mandelbrot Fractal

William Shakespeare
Romeo and Juliet [1597]

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Organic Reality...

Molecular Visualization

overviewconnectionssummary

   

aspirin (2-acetyloxybenzoic acid) C9H8O4
Molecular Visualization - Aspirin Molecule - Static Picture
Molecular Visualization - Aspirin Molecule - Static Picture

OverviewOverview

Explore the molecular landscape with Jmol, an interactive Java molecular visualization plugin. To help your viewing experience, practice a few basic techniques before trying to solve more diffcult problems:

  • To load a new molecule:
    • Select from the Select Molecule... menu.
    • Click on the square icon to the right of the menu.
  • To stop the rotation of a molecule:
    • Click on Jmol menu > Spin > Off.
  • To zoom (in/out) a molecule manually:
    • Hold the shift key down.
    • Hold the left mouse button down.
    • Drag the mouse.
  • To measure a bond distance:
    • Double click on the first atom center to change the mouse pointer into a cross-hair.
    • Move the mouse pointer to a second atom center.
    • The bond distance will appear on the display.
    • If the number is difficult to see, hold the left mouse button down and drag the mouse.
  • To assign a name to a molecule:
    • Select from the Assign Name... menu.
    • Click on the square icon to the left of the menu.
    • The answer (Yes/No) will appear on the display.
  • To rotate a molecule manually:
    • Hold the left mouse button down.
    • Drag the mouse.
  • To measure a bond angle:
    • Double click on the first atom center to change the mouse pointer into a cross-hair.
    • Move the mouse pointer to a second atom center and click once.
    • Then move the mouse pointer to a third atom center.
    • The bond angle will appear on the display.
    • If the number is difficult to see, hold the left mouse button down and drag the mouse.

ConnectionsConnections

Jmol allows you to view the atom-to-atom connections in a molecule; it shows the accurate bond distances and angles, but does not distinguish between single and multiple bonds. You will have to use your knowledge of chemical bonding to evaluate the actual bond type(s) on a specific atom. Try your hand at the following entrées.

antipasto due

Find the organic molecules with a total of two carbon atoms that have the following functional groups or properties. No molecule may be used more than once in this section.

  • Find the amide.
  • Find the amine.
  • Find the ketone.
  • Find the alcohol.
  • Find the aldehyde.
  • Find the carboxylic acid.
  • Find the saturated hydrocarbon.
  • Find the least unsaturated hydrocarbon.
  • Find the most unsaturated hydrocarbon.

gumbo gruppo

Find the organic molecules that provide the best match to solve these chemical conundrums (puzzles). No molecule may be used more than once in this section.

  • Find the boat.
  • Find the diene.
  • Find the bomb (TNT).
  • Find the beautiful one
  • Find the ring most strained.
  • Find the allotrope of carbon.
  • Find the prototypical aromatic.
  • Find the most common acid catalyst.
  • Find the 3° carbon (sp³) without a 3° hydrogen.

SummarySummary

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