Fun Fact - Hydrocarbons, Smiles, and Stereochemistry

Hydrocarbons and carbohydrates should not be confused. Hydrocarbons contain hydrogen and carbon only. Carbohydrates contain these two elements, but they also contain oxygen. In fact the "ate" suffix in chemistry implies oxygen. I'm sure you've heard of: carbonate (CO3), sulfate (SO4), phosphate (PO4), nitrate (NO3), and silicate (SiO4). These are not complete molecules - they are fragments, polyatomic anions to be precise, that are typically paired with metals to make salts or minerals, or with hydrogen to produce acids. Thus calcium carbonate, the principal component of limestone, or marble when compressed and heated over geologic time, is CaCO3. This "ate" nomenclature may help you remember that carbohydrates contain oxygen, and are a much more complicated molecule. In fact carbohydrates, along with proteins and fats, form the basis of food. These are the three macronutrients, as described earlier.

Since hydrocarbons contain only hydrogen and carbon, their structure is much simpler. In fact, the properties of a hydrocarbon molecule are determined, primarily, by the number of carbons. The simplest example has one carbon, surrounded by four hydrogens, and is called methane. It is a small, light, symmetric molecule, hence it is a gas. It does not liquify until -161C, or -258F. You've probably been out in weather that is subzero, but temperatures this cold are simply unimaginable.

methane CH4
H
HCH
H

The above representation is somewhat misleading, because it squashes the methane molecule onto the 2 dimensional page. Most molecules have a 3 dimensional structure. The carbon atom has four electrons in its outermost shell, four valence electrons, four bonds that must be satisfied. Each of these electrons joins with an electron from a hydrogen atom, satisfying the four covalent bonds. For quantum mechanical reasons, electrons join together in pairs. With the hydrogen atoms contributing, there are four pairs of electrons in the outermost shell of carbon. Since electrons repel one another (having the same negative charge), the electron pairs push each other apart. Think of each electron pair as a single point with a negative charge. Pause for a moment and arrange four points on a sphere, so that they are as far apart as possible. Two points is easy; place them at the north pole and the south pole. Three points are arranged around the equator at 120 degree angles. Four points form a tetrahedron, one at the north pole and the others forming a triangle 19 degrees below the equator. Place hydrogen atoms on these points to find the 3 dimensional structure of methane. It looks a bit like a tripod with hydrogen feet and a hydrogen atom at the top. With some practice you can get pretty good at lifting a molecule off the page and moving the atoms around to realize the 3 dimensional structure.

The great thing about methane, and all the hydrocarbons, is that they burn, and release plenty of heat in the process. A typical home has a pipe running into the basement that carries methane, also known as natural gas. Methane burns in the furnace to heat the home in the winter, and it may also (optionally) fuel the hot water heater, the dryer, and the stove. The chemical reaction looks like this.

CH4 + 2O2 = CO2 + 2H2O

The combustion products are water and carbon dioxide, which are harmless in moderation. The furnace vents these products out of the home, but the hot water heater and the gas stove do not. Running a gas oven all morning, to cook a turkey dinner, adds humidity to your home, which may or may not be a good thing.

If an appliance is malfunctioning, methane could burn incompletely, creating carbon monoxide instead of carbon dioxide. The reaction looks like this.

2CH4 + 3O2 = 2CO + 4H2O

Carbon monoxide (CO) is a colorless odorless gas that clings to the hemoglobin in your blood more tightly than oxygen, thus blocking oxygen transport. Your brain is deprived of oxygen, and you might not realize it, especially if you are asleep. A carbon monoxide detector (built into many smoke detectors) sounds the alarm, whereupon you should leave the house immediately and call for help. A technician will let you know when it is safe to reenter the home. Fortunately, such CO events are rare. You can easily go your entire life without hearing the CO alarm, whereas a burnt piece of toast can trigger the smoke alarm.

The next hydrocarbon is ethane, with two carbons in the chain. The molecule is small and light, thus ethane is a gas. In fact the pipe that carries natural gas into your home contains (roughly) 90% methane and 10% ethane. Household appliances have no trouble burning ethane along with methane.

ethane C2H6
HH
HCCH
HH

This is once again a 2 dimensional representation; the molecule actually has a 3 dimensional structure, two connected carbons with a tripod of hydrogen on the end of each carbon.

The next hydrocarbon is propane, C3H8, and it is still a gas, but it becomes a liquid under 12 atmospheres of pressure. Small propane cylinders are used to fuel outdoor grills and cook stoves in campers and motorhomes. When a cylinder is empty, just throw it away and go to the hardware store and buy another one. Plug the new cylinder into the grill, and a small tube punctures the seal, allowing gas to flow freely into the stove, where it cooks the food. However, I recall one mishap that was almost a life-changing disaster.

My grandfather built an entire camper on top of a flat-bed truck. It was the fanciest camper I've ever seen, with cupboards and closets and a fold-down table and a fridge and a stove and in-built lights and electrical sockets and small windows and curtains and fold-out beds and another bed on top of the cab, which is where I slept. I could write an entire book about Pappy, (my grandfather), but that will have to wait for another day. When I was 14 we went camping in Idaho, and it was time for lunch. He pulled the cook stove out of the wall and noticed that the propane can was empty. He tossed the empty can into the waste basket and plugged a fresh cylinder into the stove. Just before this maneuver, he put out his cigarette. Pappy smoked from morning til night. If he was awake he was probably smoking. He went through almost three packs a day, starting in his twenties and continuing into his eighties, when his doctor finally said he had to quit. How the man lived to be ninety I'll never know! He was a medical anomaly. Anyways, I was sitting on the bed just behind the cab, he was seated at the stove in front of me, and then the two doors opened out the back of the camper, overhanging the tailgate. He pushed the new can of propane into the stove, and the seal broke. Propane jetted out of the broken seal like a fire hose. We could quibble about whether it was a liquid or a gas, but it doesn't really matter - as soon as it left the can and spilled out into the air it expanded and became a gas. Pappy threw the spouting can out the back of the camper as though it was a live grenade. It landed on the grass and continued to hiss for several minutes like an angry snake. What if he hadn't put that cigarette out? What if it was still lit in his left hand? The cloud of propane would have exploded in a flash, igniting the curtains and clothes and bedding that was all around us. The inside of the camper would have become a ball of fire. From where I sat there was only one exit, out the back, through the wall of flames. I don't know if I would be here to tell the tale. Fortunately Pappy had the good fortune, or the good sense, to extinguish his cigarette before changing the propane cylinder.

After the hissing stopped I went outside and touched the can. It was the coldest thing I had ever felt. Heat is required to turn a liquid into a gas, even if you are not raising its temperature. This is called the latent heat of vaporization. Therefore, when the propane was no longer under pressure, it was well above its boiling point, and as it boiled away it sucked heat out of the can. I don't know if the can was pulled all the way down to -40 degrees, the boiling point of propane under normal atmospheric pressure, but it sure felt like it. It seemed like it came from space, it was so cold, especially when compared to the hot summer day in Pocatello. This was the capper on an experience that was both frightening and surreal.

C4H10 is butane, a gas that becomes a liquid under just a couple of atmospheres of pressure. This is the fuel of choice for cigarette lighters.

After four carbons, we use the latin words for 5 6 7 etc to name the compounds: pentane C5H12, hexane C6H14, heptane C7H16, octane C8H18, etc. All these molecules are large enough to be liquid at room temperature and pressure. You are familiar with octane, the fuel you put into your car.

Chains of lengths 20 to 30, e.g. C30H62, are viscous liquids. This, along with other additives, is motor oil, which you put in your car to keep the engine lubricated.

Longer chains, from 30 to 45, form a solid. This is the wax in your candle. It is white or colorless; colors or scents can be added for effect. Paraffin wax is flammable, like its lighter hydrocarbon cousins, but it burns slowly, providing light for hours.

All these hydrocarbons are saturated, with as many hydrogen atoms as possible. However, when two adjacent carbon atoms are connected by a double bond, i.e. two bonds instead of one, there are two fewer bonds to hold hydrogen atoms, and the molecule is no longer saturated. An example is ethene, C2H4, with a double bond between the carbons, and two hydrogens on each end. another example is acetylene, C2H2, with a triple bond between the carbons, and a hydrogen on each end.

It would be nice if a molecule could be described, concisely and unambiguously, by an ascii string. Smiles, Simplified Molecular Input Line Entry System, was designed to fill this need. Various software packages can convert a .smi file, containing a Smiles description of a molecule, into a 2 or 3 dimensional representation. Other inline notations exist, but Smiles is perhaps easiest for a human to read and unravel. I find it fairly intuitive.

The idea is simple, march along the molecule, like a chain, and list each atom, and travel down each branch in parentheses. Dangling bonds are assumed to be filled with hydrogens. Thus water is represented as O, methane is C, and ammonia is N. Turning to chains, butane is CCCC, and octane is CCCCCCCC. However, there is another form of butane, called isobutane, that is not a straight chain. The central carbon is connected to three other carbons, and hydrogens fill in the rest. The aggregate formula is still C4H10, still 4 carbons and 10 hydrogens. This is ambiguous, but Smiles makes it clear. Start at one carbon and travel to the central carbon, and then to the third carbon, but along the way, take a trip down a branch of the tree, which is the fourth carbon. The Smiles representation is CC(C)C. Chloroform, traditionally CHCl3, can be written ClC(Cl)Cl, though it can also be written C(Cl)(Cl)Cl, which emphasizes the central carbon.

A double bond is indicated by = and a triple bond by #. Thus carbon dioxide is O=C=O, acetylene is C#C, and the poisonous gas hydrogen cyanide is C#N. Combine the double bond with branching to write butyric acid as CCCC(=O)O.

Other features of Smiles allow a molecule to form a loop, or retain an ionic charge, or present a specific chirality (left or right handed). The basic sugar molecule glucose starts out as a ring of five carbons and one oxygen, with the digit 1 telling you where to connect the ring.

C1OCCCC1

Decorate this ring with OH groups along the way, and CH2OH on the first carbon, as below. This gives the familiar formula C6H12O6.

OCC1OC(O)C(O)C(O)C1O

If you like, additional at signs can indicate whether the next three branches, in order, as you move towards the center of the carbon, run clockwise or counterclockwise. This establishes the 3 dimensional structure of the molecule. Consider alanine, one of the amino acids used to build protein. Start with nitrogen at the left, move to the central carbon, then put a methyl group on as a branch, then move on to the acid COOH, thus NC(C)C(=O)O. It's called an amino acid because it starts with an amine, NH2, and ends in an organic acid. As you start from N, the amine, and look towards the central carbon, do the three groups hydrogen, methyl, and carboxylate run clockwise or counterclockwise? Is the molecule left handed or right handed? Use @ to specify counter clockwise, right handed, so that D-alanine is N[C@H](C)C(=O)O. L-alanine, counterclockwise, is N[C@@H](C)C(=O)O. The latter is one of the 20 building blocks of protein, as used by all life on earth, whereas the former is fairly useless to us. We've talked about reflected molecules before. With this in mind, the complete representation of glucose, D-glucose that is, with its 3 dimensional structure, is:

OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O

Well that's enough stereochemistry for one day.

Further Reading

methane propane butane
Motor oil
Paraffin wax
SMILES
Glucose