IUPAC Nomenclature and Organic Compounds

Imagine you are sitting a Chemistry exam.
The first question on the exam paper reads,

"Name the molecule shown below:"

How would you answer this question?

My first response is to name it Molly, short for molecule ofcourse. Not a very useful name, especially if I'm asked to name another molecule later on. It might get a bit confusing if I name every molecule Molly, even when the molecules are very different from each other.

So, the International Union of Pure and Applied Chemistry (IUPAC) has developed systems for naming compounds.
For this reason, you probably won't be asked to "name" the molecule, but you might be asked to "systematically name" the molecule, or to give the "systematic IUPAC name" for the molecule.

Even for the relatively simple molecule shown above, there is more than one way to systematically name the molecule using IUPAC nomenclature rules!

You could give a systematic IUPAC name based on the functional class of the compound. This molecule belongs to the functional class known as ketones (non-terminal C=O), two methyl (CH₃) groups are attached to the carbonyl carbon atom, so, according to the IUPAC rules for functional class nomenclature, I could systematically name it as dimethyl ketone.

I could give the same molecule a different systematic IUPAC name by applying the rules of substitutive nomenclature. In this case I name the parent hydride, propane, drop the final "e" and add a suffix denoting the non-terminal C=O functional group so that I get propanone, then I add in an infix which locates the functional group along the carbon chain, with the final name propan-2-one.

Because this is a simple molecule with just one functional group, I could use the infix as a prefix, so that the systematic IUPAC name would become 2-propanone. Or, because there is only one position for the C=O functional group to be in if this molecule is to be a ketone, I could drop the infix altogether and just systematically name the molecule as propanone.

So, some of the possible systematic IUPAC names for this molecule are:

• dimethyl ketone
• propan-2-one
• 2-propanone
• propanone

Because molecules can be named systematically in more than one way, there is a recommendation to adopt "preferred IUPAC names", or PINs. Usually the Preferred IUPAC Name is arrived at by using one of the recognized IUPAC systems for nomenclature, but not always.

If you were asked to give the Preferred IUPAC Name for the molecule shown above, the correct answer would be acetone ("Preferred names in the nomenclature of organic compounds" (Draft 7 October 2004) page 9), or, possibly propan-2-one ("Preferred names in the nomenclature of organic compounds" (Draft 7 October 2004) page 374). Acetone is the traditional name for this compound, literally meaning 'derived from acetic acid', and has been in use for more than 200 years, which is probably why the IUPAC would consider retaining the name "acetone" as the Preferred IUPAC Name for this compound.

Further Reading:
Introduction to Naming Organic Compounds

Nanoscopy

The Nobel Prize in Chemistry for 2014 has been awarded to Eric Betzig, Stefan W. Hell and William E. Moerner for the development of super-resolved fluorescence microscopy. This technique allows scientists to view objects at the nanometre scale and is therefore referred to as nanoscopy.

Since the 17^th century, we have been able to peer into the world of very small things using optical microscopes. In 1873, microscopist Ernst Abbe published an equation to show that optical microscopes could not be used to investigate things that were less than half the wavelength of light, that is, to be seen in an optical microscope the object must be greater than 0.2µm. An optical microscope can therefore be used to see some surface structure of a human hair, but you couldn't use it to see the actual protein building blocks making up the hair.

Stefan Hell was working on fluorescence microscopy, using fluorescent molecules to image parts of a cell. A brief pulse of light makes the fluorescent molecules glow temporarily, following the glow allows scientists to map where the molecules are in the cell. The technique can be used to tell where DNA is located for instance, but it could not be used to determined its structure. Stefan Hall proposed a new method, Stimulated Emission Depletion (STED) in which one pulse of light excites all the fluorescent molecules while another pulse quenches the fluorescence from all the molecules except those in a nanometre-sized volume in the middle. Only this volume is registered. An image is built up be sweeping along the sample and continually measuring light levels. In 2000 Stefan Hall was able to demonstrate the effectiveness of the STED microscope by imaging an E.coli bacterium at a resolution that could never be achieved using an optical microscope.

The nanoscopy method proposed independently by Eric Betzig and W E. Moerner, Single-Molecule Microscopy differs in that it relies on the the superposition of several images.

In 1989, W E. Moerner measured the light absorption of a single molecule for the first time.
W E. Moerner had found that one variant of green fluorescent protein (extracted from fluorescent jellyfish) could be made to fluoresce with light of 488nm wavelength, but that after awhile, the fluorescence faded and would not fluoresce again using 488nm light. The same protein, when hit by light of wavelength 405nm could be brought back to life, and then would fluoresce again when hit with light of 488nm.

In 2006 Eric Betzig demonstrated the usefulness of Single-Molecule Microscopy using a glowing protein coupled to a cell's lysosome. Using a weak light pulse, only some of the molecules were caused to fluoresce, and these were at distances greater than 0.2µm. This image was registered. When the fluorescence of these molecules died out, a new weak light pulse was used to initiate the fluorescence of a few more molecules.This new image was registered. This process was continued many times. When Betzig superimposed all the images, a super-resolution image of the cell's lysosome membrane was the result.