November 23, 2014

You Said Polar?

Alexis St-Gelais - Popularization

Polar: I am not reffering to the winter cold that has settled around here in Saguenay a few weeks ago... I am rather speaking of a concept that can be helpful to understand many chemical phenomena, to which I will certainly plentily refer to in the future on this blog. Polarity can indeed help to predict and explain the separation of molecules, their extraction, their volatility, their compatibility, and even some of their biological properties!

When atoms form chemical bonds, they do not share their electrons equally. Indeed, some elements attract electrons with more strength than others: they are more electronegative. The electrons are therefore more "concentrated" on one side of the bond. This in turn generates a slight difference in electric charges between the two sides, one becoming positive and the other negative. The more marked the difference is, the more polarized the bond becomes.

The four most frequent elements in natural organic molecules are ranked as follows, from the most to the least electronegative: oxygen (O) is the more electronegative, followed by nitrogen (N), and carbon (C) and hydrogen (H) are roughly equivalent. Of course, several other elements may be included in natural molecules, but they can introduce peculiar cases which I will not discuss now.

A C-H bond is relatively well balanced electronically, and the C-C bond features a perfect share of electrons. These bonds are nonpolar. Conversely, the O-H, O-C, N-H and N-C bonds imply the concentration of electrons on the O or N side, and are therefore polar. Figure 1 visually shows how this translates.
Figure 1. Approximate polarity schemes for a series of closely-related molecules. On isopropanol, the black arrow indicates the direction of the strong attraction of the electrons. The white arrows indicate a secondary attraction generated by the electron deficit in turn created at the CH. For all molecules, the red areas are rich in electrons, and thus partially negatively charged. The green areas are rather depleted of electrons, and thus slightly positive. Light gray indicates an electrically neutral region and dark gray a slight positive bias due to the positive charge of the neighboring atoms. BP: Boiling Point. 
Why is it useful to be able to get an idea of the polarity of a molecule? Figure 1 already gives a part of the answer by showing the boiling points of the molecules. You can notice that the more the molecule is polarized, the more the boiling point increases. This is because the polar molecules behave somehow like magnets: they possess two poles, which can attract the opposite pole of opposite sign on the neighbouring molecule. Thus, polar molecules tend to be very strongly retained to each other, so we must input a lot of energy to disrupt the intermolecular attraction, for example to enter the gas phase. Conversely, non-polar molecules do not attract eachother a lot. It is thus easier to induce a phase change. The same generally holds for the melting point.

This first property provides an excellent explanation for a phenomenon that we have discussed earlier for the analysis of essential oils. In general, in our tests, monoterpenes are eluted before the oxygenated monoterpenes, and sesquiterpenes before oxygenated sesquiterpenes. This is quite normal: molecules without oxygen are generally more volatile, given a similar molecular weight, than oxygenated molecules, because they are less polar. They therefore pass through the tubular columns at a lower temperature, and are detected earlier.

The polarity also helps to explain why essential oil and the water used to extract it form two distinct liquid phases. Indeed, in chemistry, "like dissolves like": polar environments easily mix together, and apolar media exclude polar media. Terpenes are composed mainly of non-polar C-C and C-H bonds, while water is highly polar. Therefore, the two groups reject each other and form non-miscible phases. In this regard, the essential oil has the same behavior as liquid hydrocarbons derived from petroleum and vegetable oils: all three groups feature molecules with a high proportion of non-polar bonds.

I also mentioned that polarity influenced the separation of molecules. Get a quick look back at my post about the basic principles of chromatography. The affinity which I was referring to in that text is often based on polarity. For example, solid silica, often used in chemistry to separate extracts, is a very polar material due to its silanol groups (Si-OH). It therefore retains strongly polar compounds, and only poorly non-polar compounds. A quick estimate of the polarity of a molecule allows the chemist to more easily target the chromatographic technique to use, and the conditions to be employed.

Finally, polarity affects how molecules interact with your body... Blood, lymph or cellular content form polar aqueous media. In contrast, cell membranes, skin, liver or fat cells, for example, are very rich in lipid derivatives and proteins exhibiting low polarity. This creates a wide range of possible interactions. For example, polar vitamins (B and C), which are water-soluble and can easily be excreted in urine, hardly ever cause overdoses, unless one takes huge amounts within a short period of time. In contrast, low polarity vitamins taken regularly in excess will accumulate in the environments for which they have affinity, including fat. They can then lead to hypervitaminosis (usually with vitamins A and D) with potentially serious, although rare, effects.

Another example: cosmetic creams are often made of a basis of molecules that are moderately to weakly polar, with a creamy or greasy texture, in order to penetrate the skin (which water, under normal circumstances, can not do). Thus, although we commonly speak of skin hydration, creams actually "fatten" the skin, a low-polarity environment where water is not welcome!

In short, "polar" is not only a matter of geography or temperature. It may even be useful to explain many phenomena we encounter daily.

November 9, 2014

Draw Me a Terpene

Alexis St-Gelais - Popularization

One of the strangest aspects of the life of a chemist is to constantly be working with something we can (almost) never see as a unit: a molecule. In fact, a considerable part of our job is to draw conclusions from data obtained indirectly in order to deduce the structure of the molecules that we study! Over time, it was therefore necessary to develop ways to represent molecular structures and thus build a collectively accepted and understood image for the compounds we encounter.

A molecule is, by definition, a set of two or more atoms held together by what is called chemical bonds. A bond is in fact a pair of electrons shared between two atoms, which keeps them close to each other. Without going into detail, one basic method of representation is therefore to indicate each of the atoms along with the electrons they share. To be stable, each atom must typically be surrounded by eight electrons, represented by dots, except for hydrogen, which only requires two electrons. Electrons always come in pairs. We call this representation the Lewis model (Figure 1).
Figure 1. Lewis structure of methanol.
This representation, however, is highly cumbersome, and is almost impossible to effectively use for larger molecules. Consequently, chemists have resorted to various simplifications to increase the flexibility of the representation of organic molecules, which often have dozens of atoms. The first simplification is to replace shared electronic pairs by a straight line representing a chemical bond. If several pairs of electrons are shared, the line is doubled or tripled. Pairs of free electrons, such as those of oxygen, are omitted. (Figure 2).
Figure 2. Developed structure of acetone, where electronic pairs are replaced by bonds represented as straight lines.
In organic chemistry, an overwhelming majority of the atoms that we represent are hydrogens and carbons. The simplification therefore continued to avoid having indicating them again and again. The carbons are therefore not shown, and by convention, a juction between chemical bonds, or a blank line tip, is automatically considered to be acarbon. Other atoms, called heteroatoms (other than carbon, C, and hydrogen, H) are still referred to by their chemical symbol (Figure 3).
Figure 3. Developed structure of isopropanol, where carbons have been omitted and are, by convention, situated at the junction of chemical bonds.
Hydrogen, finally, is omitted in molecular representations when it is bonded to a carbon. If we keep in mind that carbon must always have a total of four chemical bonds to be stable, missing bonds are implicitly filled with hydrogen atoms. Carbons showing three visible bonds include one hydrogen, whereas if the carbon has only one visible link, it rather bears 3 hydrogens. Figure 4 shows a complex molecule shown in this simplified manner, which is most commonly used by organic chemists daily.
Figure 4. To the left, the developed structure of  α-terpineol, with all atoms represented. To the right, the same molecule in its condensed form, as commonly used in organic chemistry. Junctions and tips are carbon atoms, and these are conventionnally "filled" with up to 4 links with hydrogens.
In 2013, a team successfully "saw" molecules using a technique of atomic microscopy: a carbon monoxide molecule interacts with the molecule previously deposited on a silver surface, and its oscillation is measured and converted to an image (Figure 5). Note that this is again an indirect representation of the molecule, and not an image obtained by a photographic method: it is rather a translation of the vibrations generated on the carbon monoxide molecule. But as the researchers themselves point out, the similarity between the picture and the molecular schemes is striking. In short, our representations, although simplified, reflect quite well the chemical reality as we currently understand it.
Figure 5. Molecular "pictures" obtained by atomic microscopy. Work of D. G. de Oteyza et al.
With this information, you should decipher more easily the structure of molecules represented in our blogposts and in most organic chemistry texts.