Posts Tagged ‘organic chemistry’

The last Organic-Biochemistry-Nutrition post presented the saturated hydrocarbons, which are familiar as gasolines and other fuels and oils.  The first step in getting control of organic chemistry is to be sure you can identify each compound which means recognizing (or assigning) a precise name.  From a theory standpoint, these compounds also provide the skeletons for nomenclature of the other classes of organic compounds.

The class of alcohols are those compounds that have a saturated carbon backbone and have one or more -OH groups attached.  The simplest alcohol is methanol CH3-OH.  Others are shown in the figure from the last post which emphasized that even if the backbone got very complicated, as in cholesterol, it was still an alcohol. The greater the percentage of the molecule that is -OH rather than hydrocarbon, the more they resemble water and the more they behave like water.  So, methanol, ethanol and propanol are soluble in water whereas butanol and higher alcohols are not.  Looking ahead, however, there are other chemical properties that are common to all alcohols: this is why it is so convenient to lump them together.

I received a comment on the last post that said “One wish, though: I don’t quite understand the graphic on cholesterol and how would that look when presented as the chemical symbols like all the other molecules in that last picture.”  I suggested the following exercise for understanding it by problem-solving. If you want to try this first, here is the exercise (answers follow):

  1. Draw the molecular formula for hexane.
  2. Connect the ends of the molecule by making a carbon-carbon bond.
  3. Recognize that now you have a hexagon-shaped objects all of whose vertices are CH-2. This molecule, not-surprisingly, is called cyclohexane.
  4. Since you know that all the points are CH-2, you can save time by just drawing the geometric figure.
  5. To make sure you have the idea, draw cyclopentane.
  6. Now draw a structure with two fused rings: two hexagons sharing a common side. This structure is called decalin (because it has ten carbons).
  7. Draw a C at each vertex or intersection. Now fill in hydrogens so that every carbon has four bonds. There should be 8 CH-2 and 2 CH.
  8. You can make a complex structure with three fused hexagons and one pentagon, as in the drawing. This structure is called cholestane and is the basis of the cholesterol in the drawing.
  9. If all this makes sense, Google “cholesterol structure” and click on “Image” in the top menu bar and you’ll see different representations.

The arrow is meant to show that the hexane molecule has no rigid structure and could be folded up. The relation to cyclohexane is formal, that is, pictorial.  (It is not that easy to convert one to the other in the laboratory). This has defined a new class of compounds, the cyclic hydrocarbons, that, rather than straight chains, are arranged in cyclic structures.  Before tackling questions 8 and 9, need to look at one more basic step.

Precise Names.

The allure of organic chemistry (to those who are attracted to it) is its precision and logic.  That’s why an important feature is the name game, giving precise names to organic compounds.  The idea is that if you order something from a chemical company, you want to know exactly what you are going to get.  Thinking about butanol, now, you might ask what you would call a compound that had exactly the same composition as butanol except that the -OH group was not at the end but rather attached to one of the other carbons.  To remove ambiguity in a case like this, the carbons are numbered. There are, in fact, two butanols: 1-butanol and 2-butanol.  There is no such thing as 3-butanol because, looking at the structures and remembering that we are trying to represent something from 3-D space, there is no difference between carbon-2 and carbon-3.

The big rule for numbering organic compounds: pick a numbering system that has the lowest numbers.  Even if, for some reason, the structure is written so that the hydroxyl group appears to be at the far end, you always pick the number so that is the lowest possible.  The next figure shows you some examples.  Make sure you are happy with this system.

More on Hydrocarbons.  Branched Chains.

The unique features of carbon atoms: the ability to form four chemical bonds and to form chemical bonds with other carbon atoms to form long chains. In addition to long linear chains, carbon can also form compounds with branches. Once you have 4 carbons in a chain (butane)there is more than one way to arrange the carbons. The figure below shows different representations of a compound called iso-butane, an isomer of what we originally wrote for butane. (Isomers are compounds that have the same type and number of atoms but a different arrangement). The straight chain form could be called normal butane, or n-butane but, once there is a precise name for isobutane, n-butane will just be called butane.


So, the problem is that there are literally millions of compounds and you can’t have a name for every one. Besides, chemists don’t really like to memorize things and pretty much feel that learning the names of the ten straight chain hydrocarbons should be enough and there must be a logical system for naming organic compounds by relating them to the simpler ones.

The Systematic Name Game.

The system in organic (called the IUPAC system after the International Union of Pure and Applied Chemists) starts from the straight chain hydrocarbons. Every compound is named as if it were derived from one of those.  To name a compound, then, find the longest possible continuous straight chain of carbon atoms.  For isobutane, this would be 3, that is propane.  What about the extra carbon atom?  That is assumed to come from a hydrocarbon too but is considered a substituent (substituting for a hydrogen atom), that is, an “add-on” and is given an adjective name “methyl,” and so a systematic name for isobutane is methyl-propane.  Similarly, there are two isomers for the 5-carbon hydrocarbon: pentane and methyl-butane.  For the 6-carbon compounds vatiation, methyl-pentane, there are two different isomers. Using the rule from the alcohols, the two must be called 2-methyl pentane (never  4-methylpentane) and 3-methylpentane. The examples at the end of this post should allow you to learn how to play the game.  A couple of questions are included.  Answers will be in the comments and the structures in the next post.  To find out what kind of substance they represent, for the simpler ones like isobutane, you can Google them but you should have a sense of power that you can give the precise chemical name for a large number of chemicals. First, two more rules.

Hydrocarbon names and substituent names.

Substituents can have more than 1 carbon (although obviously not more than the main chain to which they are attached. Why not?)

More than one substituent gets more than one number.

If there is more than one substituent, you use the prefix di-, tri-, tetra-, penta-, hexa- and indicate all numbers, even if they fall on the same carbon.  You should be able to follow the examples and you should be able to do the questions.

External links

For more information or to reinforce what you have here: Drawing organic molecules and Organic structures sites as well as Quiz on naming organic compounds.  Also, good intro as part of heavy-duty organic text (skip parts that are complicated).

Finally, cholestane

The hydrocarbon chains (and branches) can sometimes be written, like the cyclic hydrocarbons, just showing the geometry.  Recall the 3-D convention: a wedge represents atom coming out of the screen and a dotted line, an atom behind the plane of the screen.  Here it is.  Cholestane is the basic structure.  Cholesterol is an alcohol derivative as above.

The themes in my blog are the scientific issues in nutrition, how to interpret data in the literature and my take on policy issues like taxing fat and taxing sugar.  The most important thing, though, is the basic science because you really can’t understand nutrition without biochemistry and you really can’t do biochemistry without organic chemistry. Organic chemistry refers to the chemistry of carbon compounds. The term once referred to the chemistry of living organisms but now would includes polyethylene as much as fructose and, in the extreme case, the plastic bottles made from corn. I am going to try to present the science and I will start from scratch and make it very elementary. My experience is that chemists don’t mind very elementary — at professional seminars, it is the Nobel prize winner who asks the really simple question (because he doesn’t care what you think of him, he just wants to know the answer). I am interested in reader feedback as to whether this is what you want to know and if this and subsequent blogs help.

The good news is that, contrary to the college myth, organic chemistry is easy.  It is freshman chemistry that is hard (because it depends more on physical chemistry, that is, physics), so I think I can get you up to speed on biochemistry and nutrition pretty fast. I am duplicating some of the material on my YouTube presentation but people told me that that is not always the best format.  So, organic chemistry is easy. That’s the first thing.

The second thing is that chemistry is  structural, that is, visual and what a chemist sees in chemical formulas is visual objects.  I am going to show what a chemist is thinking about in dealing with chemical formulas.  It’s graphic, so I will try to use as few words as possible. Comments on the figures at the end of the post.


Start with H2O

What a chemist sees in the formula H2O is a diagram, or structural formula. What a chemist thinks of when they see that diagram is the ball and stick model  or maybe the so-called space-filling model which is supposed to be closer to what you would see if it weren’t that molecules of water  are too small to be seen.

Methane is the simplest organic compound – The formula is CH4 – carbon always forms 4 chemical bonds. Different views of methane below. Methane is a colorless, odorless gas, the major component of natural gas (the odor of cooking gas comes from an added compound as a safety warning). Various representations below. (The wedge (coming out of the paper) and dotted line (behind the plane of the paper) is a shorthand representation of the 3D structure

Carbon Forms bonds with Other Carbons and Carbon Atoms Can Form Chains – Think of two methane molecules tied together by replacing one of the carbon-hydrogen bonds in each with a carbon-carbon chemical bond.  The two carbon compound (C2H6) is called ethane. We can, similarly build up chains of carbon atoms. which will be the skeletons on which millions of organic compounds will be constructed.  Carbon always forms four chemical bonds.  A compound that has only carbon and hydrogen is called a hydrocarbon.  The series built up from ethane are called saturated hydrocarbons (other name: alkanes) meaning that they have as many hydrogens as possible.

There is a Family of Organic Compounds – everything is organized as if it came from the chain of carbons known as saturated hydrocarbons.  (IUPAC is the International Union of Pure and Applied Chemists who standardizes chemical names).  Propane is a gas but it can be compressed into a liquid and is used as a fuel for various kinds of engines or for barbecues or welding torches. The higher hydrocarbons are fuels; you recognize the name octane as a component of gasoline which is a mixture of the higher saturated hydrocarbons. Much larger hydrocarbons are the major constituent in industrial and motor oils. The first ten hydrocarbons are shown in this table:


STOP.  Are you with me so far? If so, you should commit to memory the names of the ten hydrocarbons.  Everything else depends on this.  Most organic compounds are given names based on this system.

The Secret of Organic Chemistry: Functional Groups

Organic compounds have two parts: a hydrocarbon backbone and a functional group, the non-hydrocarbon part that contains the chemically reactive part of the molecule, the functional groups. The assumption is that all compounds with the same functional group have similar chemistry. The millions of organic compounds are grouped into classes: alcohols, aldehydes, acids, sugars, amino acids, etc. based on which functional groups they contain. It’s easiest to understand by example.  Look at the alcohols.

What Alcohols Look Like

Start with the simplest functional group. The combination of oxygen and hydrogen as a functional group is called hydroxyl.  Any compound that has an hydroxyl group is called an alcohol.  The common term “alcohol” refers to ethanol, one specific type of chemical alcohol.  The simplest series of alcohols are those derived from the saturated hydrocarbons.  If the hydroxyl group is added at the end of the chain, the compound is called a primary alcohol.  To name such compounds, you count the number of carbons, use the name from the hydrocarbon, e.g., ethane and remove the “-e” at the end and add “-ol.”   The figure below shows you that no matter how complicated the hydrocarbon backbone, if there is an OH group, the compound is an alcohol.  Cholesterol is an alcohol (you can figure out that if you know that a structure has only CH groups, they can be indicated just with the geometry without writing the symbols, each vertex in the figure representing one carbon atom).

Next chemistry post:

Aldehydes, sugars and sugar alcohols.

Do I get it?  Answers in the comments.

  1. Can you write the structural formula for octanol?
  2. When there is more than one hydroxyl group, the number of groups may be indicated by “di-, tri-” etc. The common compound glycerol would be called propane triol.  What does it look like?