Archive for the ‘Learn organic chemistry’ Category

Last post, we were running with the name game, which emphasizes one of the two features of organic chemistry, its precision and logic.  The other distinguishing feature, as in all chemistry, is the sense of cooking and transformation that  we only hinted at: we had only one group of compounds, the alcohols but we did predict that the more the structure looks like water (the greater the percentage contributed by the OH group) the more water-soluble the compound was.

The last post finished with a quiz, for which I will now provide answers.  If you already know the answers and want to see new stuff, you can jump ahead.


Q1. The rule: find the longest continuous chain of carbon atoms, five in this case.  Consider as if it were derived from the five-carbon hydrocarbon, pentane. (“As if” because the real compound may not have been derived from pentane). Look for substituents (attached to the main chain.  There is a one carbon substituent, that is, a methyl group. Which carbon is it attached to? Count the carbons, trying each end. Use the one with the lowest number : 2-methyl pentane (not 4-methyl pentane). The compound is an isomer of hexane but the name is unambiguous which is the idea.

Q2. Same rule.  Find the longest carbon chain. Four carbons = butane. Find the functional group, alcohol. Always use the lowest number so it is a 1-butanol (not 4-butanol).  One methyl groups, so this compound would be called: 2-methyl 1-butanol.

Q3. Find the longest carbon chain. Don’t be misled by how the structure is laid out on the page.  (The way it is written will be determined from the chemical context).  This is an 8-carbon compound, an octane backbone.  Find the functional group, an alcohol. Always use the lowest number so it is a 2-octanol.  The methyl groups on carbons 4 and 5 means this compound would be called: 4, 5-dimethyl 2-octanol.

Q4. The functional group (if there is only one) is always on carbon 1, so you do not have to specify that.  Note: carbon 3 is indicated twice.

Q5. The variation: propyl is the substituent on carbon 3 of the main structure, but this side chain itself has a substituent on carbon 2 (counting from the point of attachment to the main structure) so 2-methyl is the “adjective” that modifies “propyl.”

Q6, 7. Pretty much obvious variations on the standard rules.




Where we’re going.  The new functional group is the carbonyl, C=O, a group that has two chemical bonds between carbon and oxygen.

When the carbonyl group is at the 1-position, that is, at the end of the chain of carbon atoms, the compound is called an aldehyde.  When, someplace else in the chain, the compound is called a ketone.

The principle: compounds that have more than one functional group have a different classification — sometimes the properties of the compound are the sum of the properties of the functional groups and sometimes they interact to give totally new properties.

Compounds that have both a carbonyl group and an -OH group are called sugars, that is, the sugars are polyhydroxy aldehydes and ketones and are sometimes referred to as aldoses and ketoses.

Sugars and their polymers and derivatives are called carbohydrates. (Alcohol, that is, ethanol is not a carbohydrate).

Start with aldehydes: Once again, the name game is a good idea. If you can give a correct name for the compound, then you have identified where the functional groups are and that’s where the chemistry lives.  A compound with a C=O group at one end is called an aldehyde.

Formaldehyde.The simplest aldehyde could formally be named as if were a derivative of methane. Drop the final -e and add the suffix –al.  Methanal, however, is a very common substance and is always called formaldehyde.

Acetaldehyde. Drop the final -e from the 2-carbon hydrocarbon, ethane. Add the suffix -al.  Like formaldehyde, ethanal is a common compound, especially in biochemistry and it is always called by the familiar name acetaldehyde (accent on third syllable).  The conversion of ethanol to acetaldehyde is the first step in the liver’s processing of ingested alcohol.  Conversely, microorganisms that carry out alcoholic fermentation, convert sugar (in many steps) to acetaldehyde and then to ethanol (faites attention: you are making the transition from organic chemistry to biochemistry).  Aldehydes are chemically reactive; acetaldehyde can react with proteins of the body and is fairly toxic accounting for some of the side effects of excessive drinking.  In normal people it is cleared by the next step which incorporates the compound into metabolism; people with genetic abnormalities in metabolizing acetaldehyde (common in the Asian population) are pretty much incapable of drinking at all because of the severe physiologic responses.

The system of naming aldehydes is perfectly regular and it should be obvious how to name aldehydes of 3-carbon (propanal), 4-carbon (butanal), 5-carbon (pentanal) aldehydes, etc.  The rules for substituents are the same as before and you should be able to write the  structure of, for example, 3,3- dimethyl hexanal.

Aldehydes can be complicated and tend to have fruity or complex aromas and are, in fact, found in many natural products.  Cinnamaldehyde and citronellal smell just the way you think.  Veratraldehyde was probably first isolated from a plant called veratrum but from one of its common names, methyl-vanillin you can guess where it is used in the food industry.

If the carbonyl group appears in the middle of a chain or ring, the compound is called a ketone.  The simplest is the three carbon compound acetone; formal name would be derived by dropping the -e from propane and adding the suffix -one although this is never used.

Ketones should not be confused with the colloquial “ketones” meaning ketone bodies, the compounds produced during starvation or low-carbohydrate diets which include acetone, acetoacetic acid (a keto-acid) and β-hydroxybutyrate which does not have a keto group at all.


Sugars are polyhydroxy aldehydes and ketones. Organic compounds, in general, can have more than one functional group.  For names, there is a hierarchy: carbonyl compounds have precedence over alcohols.  In other words, in a compound containing both an -OH group and a carbonyl, the compound is named as an aldehyde or ketone and the hydroxyl group is treated as if it were a substituent along the lines of a methyl group as in previous exercises. The alcohol groups are called hydroxy– when a substituent in another compound.

The simplest sugars have three carbons.  The suffix -ose is common for sugars and these compounds are called trioses.  The one shown below is an aldose, or combining the classifications, it would be called an aldotriose.  The name of the common aldotriose is glyceraldehyde, a name indicating its relation to sugar but probably discovered before the “ose” terminology became common; the compound is called in German, glycerose (pr. glitzerose)

There is one ketotriose, dihydroxyacetone.

The hexoses.  Looking ahead, the major sugars of interest in biochemistry are glucose and fructose.  They are isomers (the same chemical formula) but glucose is an aldose and fructose is a ketose.  Structures are shown below but there is another level of complication, stereochemistry, that has to wait for the next organic post.

With some of the major players, however, we can start to put together some information on biochemistry.  Glycolysis: the lysis (breaking) part of glycolysis involves the cleavage of a hexose into two triodes.  Both glucose and fructose are connected throughout the triodes. Ingested fructose can be converted to derivatives of the trioses and these, in turn, can be turned into glucose.

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?