We mentioned how activation energy is like an energy hump a reaction has to go over. The first plot above shows an Sn2 reaction you might find in organic chemistry: OH- attacks a bromoethane molecule, kicking out the bromine and making ethanol. Here’s the important part: carbon (C) likes being bonded to 4 things, but in the transition state at the top of the hump, it’s kind of bonded to 5 things. It doesn’t like this, but has to go through it for the reaction to happen.

Notice I said the carbon doesn’t “like” something. In science-talk that means it “has high energy.” You can think of it like this: if your room is filthy, you might think “I’d be happier if I cleaned my room.” But to get to that happier state, you have to clean, which requires effort and generally doesn’t make you happy. If you just can’t seem to bring yourself to clean, it’s because the activation energy is high. You just can’t get over that hump.

Fossil fuels are a huge fraction of where we get energy. Some of these are used at power plants to make electricity (mainly coal and natural gas) or to power something like a car directly (mainly petroleum). Where does the energy come from in fossil fuels, and why do we use them so much?
Petroleum is a mixture of organic compounds, which are molecules based on carbon. Take octane as an example, shown above. Oct means eight, and octane is a molecule with 8 carbons. (Sometimes people get tired of drawing all the hydrogens in organic molecules, so they draw them as simple stick figures, with corners signifying carbons and the hydrogens implied but not drawn.) Coal (a solid) is mostly longer molecules, and natural gas is shorter molecules.
The energy in fossil fuels is stored in the bonds between the atoms. If you break these bonds, energy comes out. So we break them, and this is how the internal combustion engines in our cars run, as well as the external combustion engines in our power plants.

Fossil fuels are a huge fraction of where we get energy. Some of these are used at power plants to make electricity (mainly coal and natural gas) or to power something like a car directly (mainly petroleum). Where does the energy come from in fossil fuels, and why do we use them so much?

Petroleum is a mixture of organic compounds, which are molecules based on carbon. Take octane as an example, shown above. Oct means eight, and octane is a molecule with 8 carbons. (Sometimes people get tired of drawing all the hydrogens in organic molecules, so they draw them as simple stick figures, with corners signifying carbons and the hydrogens implied but not drawn.) Coal (a solid) is mostly longer molecules, and natural gas is shorter molecules.

The energy in fossil fuels is stored in the bonds between the atoms. If you break these bonds, energy comes out. So we break them, and this is how the internal combustion engines in our cars run, as well as the external combustion engines in our power plants.

We’ve been talking about organic chemistry, which is the chemistry of carbon compounds—molecules built around carbon atoms, much like the molecules found in life. Molecules undergo reactions, changing to new molecules, by rearranging bonds. The bonds are formed by electrons, which are shared between two atoms.
There is an interesting property of carbon bonded to 4 different things in a tetrahedral shape: if the four things are all different, the molecule will have a non-identical mirror image. In other words, two carbons can be bonded to the same four things, but the molecule turns out to be different. This is called stereochemistry. Stereo means "three-dimensionality," and is also used for the three-dimensionality of music you experience when the left and right channels in headphones are different.
The stereochemistry of carbon is shown above by the molecule looking in the mirror. The two mirror image forms are called enantiomers of each other. One of the most famous sets of enantiomers is the drug thalidomide, which has a carbon stereo-center in one of its rings. Thalidomide was sold to help alleviate morning sickness in pregnant women. R-thalidomide is effective in stopping morning sickness, but S-thalidomide causes birth defects, such as the baby with the extra toe shown above. Unfortunately, the drug contained both enantiomers, and was withdrawn from the market when the mistake was realized. 

We’ve been talking about organic chemistry, which is the chemistry of carbon compounds—molecules built around carbon atoms, much like the molecules found in life. Molecules undergo reactions, changing to new molecules, by rearranging bonds. The bonds are formed by electrons, which are shared between two atoms.

There is an interesting property of carbon bonded to 4 different things in a tetrahedral shape: if the four things are all different, the molecule will have a non-identical mirror image. In other words, two carbons can be bonded to the same four things, but the molecule turns out to be different. This is called stereochemistry. Stereo means "three-dimensionality," and is also used for the three-dimensionality of music you experience when the left and right channels in headphones are different.

The stereochemistry of carbon is shown above by the molecule looking in the mirror. The two mirror image forms are called enantiomers of each other. One of the most famous sets of enantiomers is the drug thalidomide, which has a carbon stereo-center in one of its rings. Thalidomide was sold to help alleviate morning sickness in pregnant women. R-thalidomide is effective in stopping morning sickness, but S-thalidomide causes birth defects, such as the baby with the extra toe shown above. Unfortunately, the drug contained both enantiomers, and was withdrawn from the market when the mistake was realized. 

We showed the structure of t-butyl bromide, and talked about how the bromine atom can pop off, leaving a planar, positively-charged group of 4 carbons (a t-butyl cation, it’s called). So what happens next is water attacks the t-butyl cation, as shown.
That’s the structure of water—H2O, as you see. The dots are “lone pairs” of electrons, which are normally cool with not doing anything, but the positive t-butyl is too much to pass up. Red arrows show the motion of electrons.
The water attaches, and the carbon becomes tetrahedral, having 4 bonds again. One of the hydrogen atoms leaves the attached water, and we now have a new molecule: t-butyl alcohol or tert-butanol. (Most molecules have more than one way to name them, which is okay.) tert-Butanol is used as an octane booster in gasoline, in paint remover, and for some other things.

We showed the structure of t-butyl bromide, and talked about how the bromine atom can pop off, leaving a planar, positively-charged group of 4 carbons (a t-butyl cation, it’s called). So what happens next is water attacks the t-butyl cation, as shown.

That’s the structure of waterH2O, as you see. The dots are “lone pairs” of electrons, which are normally cool with not doing anything, but the positive t-butyl is too much to pass up. Red arrows show the motion of electrons.

The water attaches, and the carbon becomes tetrahedral, having 4 bonds again. One of the hydrogen atoms leaves the attached water, and we now have a new molecule: t-butyl alcohol or tert-butanol. (Most molecules have more than one way to name them, which is okay.) tert-Butanol is used as an octane booster in gasoline, in paint remover, and for some other things.

We’re talking about organic chemistry, which is the chemistry of carbon compounds, and have brought up two general points about carbon:
It is usually has 4 bonds at a time
When those 4 bonds are to 4 separate things, it has a tetrahedral shape (which means that if the carbon were at the center of a 4-sided die, the 4 things it is bonded to would be at the points)
Above we see t-butyl bromide: a carbon with 3 methyl groups and 1 bromine bonded to it. (There is a logic to naming molecules in organic chemistry, and it relies on recognizing patterns about what to do when certain combinations of atoms appear.)
What makes organic chemistry (and life in general) interesting is how molecules change from one thing to another. They change by changing their bonds, meaning that electrons move from one place to another. Something you recognize once you’ve had some practice is that in a molecule like t-butyl bromide, the bromide has a tendency to pop right off when it’s dissolved in water. It takes its electrons with it, and you indicate this by a red arrow, pointing to where the electrons go.
Something interesting is that after this happens, the carbon only has 3 bonds, and it flattens out. Now something else is going to happen. What do you think it will be?

We’re talking about organic chemistry, which is the chemistry of carbon compounds, and have brought up two general points about carbon:

  • It is usually has 4 bonds at a time
  • When those 4 bonds are to 4 separate things, it has a tetrahedral shape (which means that if the carbon were at the center of a 4-sided die, the 4 things it is bonded to would be at the points)

Above we see t-butyl bromide: a carbon with 3 methyl groups and 1 bromine bonded to it. (There is a logic to naming molecules in organic chemistry, and it relies on recognizing patterns about what to do when certain combinations of atoms appear.)

What makes organic chemistry (and life in general) interesting is how molecules change from one thing to another. They change by changing their bonds, meaning that electrons move from one place to another. Something you recognize once you’ve had some practice is that in a molecule like t-butyl bromide, the bromide has a tendency to pop right off when it’s dissolved in water. It takes its electrons with it, and you indicate this by a red arrow, pointing to where the electrons go.

Something interesting is that after this happens, the carbon only has 3 bonds, and it flattens out. Now something else is going to happen. What do you think it will be?

Carbon likes to have four bonds to other elements. You can see from the periodic table that it is four spaces from both the left and right ends of the table. For this reason, it wants to share 4 electrons. In organic chemistry you draw a lot of structures that show the compositions of molecules. The letters represent atoms, and the lines represent bonds between atoms, holding them together. These are called covalent bonds, and each line is the sharing of 2 electrons.
Methane, the structure at the top, is the main component in natural gas, and is the simplest organic compound: CH4. Its shape is a tetrahedron, and the fat and dotted bonds simply show that those hydrogens are going into and coming out of the screen.
Ethanol is an “alcohol” and is the active component in alcoholic drinks. People have also experimented with using ethanol instead of gasoline as a fuel for cars. Formaldehyde is an important precursor for many industrial chemicals. You can see it has a double bond, which means the C and O are sharing 4 electrons instead of 2.

Carbon likes to have four bonds to other elements. You can see from the periodic table that it is four spaces from both the left and right ends of the table. For this reason, it wants to share 4 electrons. In organic chemistry you draw a lot of structures that show the compositions of molecules. The letters represent atoms, and the lines represent bonds between atoms, holding them together. These are called covalent bonds, and each line is the sharing of 2 electrons.

Methane, the structure at the top, is the main component in natural gas, and is the simplest organic compound: CH4. Its shape is a tetrahedron, and the fat and dotted bonds simply show that those hydrogens are going into and coming out of the screen.

Ethanol is an “alcohol” and is the active component in alcoholic drinks. People have also experimented with using ethanol instead of gasoline as a fuel for cars. Formaldehyde is an important precursor for many industrial chemicals. You can see it has a double bond, which means the C and O are sharing 4 electrons instead of 2.

Organic chemistry

We’ve mentioned organic chemistry a couple times in the last few weeks. Let’s talk about what organic chemistry is and what skills one uses solving organic chemistry problems. As we said before, this is a field of science that isn’t particularly mathematical, and is important in several other areas, such as biology, polymer science, and chemical engineering. Life on Earth is based on carbon, and carbon is the subject of organic chemistry. (Hence the name.)