Activation Energy

There is a barrier to any chemical reaction that is higher in energy than either the amount of energy found in the starting materials or the ending materials. This is called the activation energy.

It’s like a big hill that you have to climb to get from one place to another. Some reactions have higher activation energies than others. It takes a bit of activation energy to get out of bed in the morning. It takes even more energy to get out of bed in the morning to exercise. Activation energy is also like a personal seating license to buy season tickets to a sporting event. You have to spend money before you can even pay what you owe for the tickets. Chemistry is a real jerk that way.

Bond Dissociation Energy (BDE)

The amount of energy needed to separate two bonded atoms an infinite distance. We will relate BDE’s in terms of kcalories (or Calories) and Snickers bars (assuming that there are 271 Calories in a Snickers bar).

The Carbon Cycle

Image from

This carbon cycle diagram shows the storage and annual exchange of carbon between the atmosphere, hydrosphere and geosphere in gigatons – or billions of tons – of Carbon (GtC). Burning fossil fuels by people adds about 5.5 GtC of carbon per year into the atmosphere.

Carbon dioxide

Carbon dioxide (CO2) is required for photosynthesis in plants and is a byproduct of respiration. Jan Baptist van Helmont, the first person to observe CO2 termed it a wild spirit (spiritus sylvestre). Joseph Priestly (the eminent chemist) made the first soda water by reacting chalk with sulfuric acid. The resulting CO2 from his reaction was dissolved by a near-by bowl of water. CO2 is also a powerful greenhouse gas.


A catalyst is a chemical that reduces the activation energy of a reaction.

These chemicals make a reaction proceed much faster. For example: $100 would be a great catalyst to convince me to wake up each morning to exercise. (Alas, if life only worked like these silly little examples.)

CO2 Conversion

Simply put, CO2 conversion refers to any process that transforms carbon dioxide (CO2) into another chemical compound. This term is often used to describe transformations that lead to more “valuable” chemicals. For example, plants convert CO2 into carbohydrates (C6H12O6) for fuel through photosynthesis and chemists can convert CO2 into methanol (CH3OH), a more useful compound that can also be used for fuel. And clearly, carbs and alcohol are more valuable than some silly greenhouse gas! *Warning: do not drink methanol, it is toxic. Ethanol, however, is great!

Greenhouse effect

The Sun powers the Earth’s climate, radiating energy at very short wavelengths, predominately in the visible or ultraviolet part of the spectrum. Roughly 1/3 of the solar energy that reaches the top of Earth’s atmosphere is reflected back to space. The remaining 2/3 is absorbed by the surface and, to a lesser extent, to the atmosphere. To balance the absorbed incoming energy, the Earth must, on average, radiate the same amount of energy back into space. Because the Earth is much colder than the Sun, it radiates at much longer wavelengths, primarily in the infrared part of the spectrum. Much of this thermal radiation is absorbed by the atmosphere and reradiated back to Earth.


Methane has the chemical formula CH4. Atmospheric methane comes from natural gas fields, cows, and flatulence.

Nitrate (NO3-)

Nitrate is a negatively charged ion that has 3 oxygen atoms bound to a central nitrogen atom. Since it is negatively charged, it must be balanced with a positive counter-ion. Sodium nitrate and calcium nitrate are the most common forms used in fertilizers as plants directly uptake nitrate as an essential nutrient. Ammonium nitrates are also commonly used, however the ammonium ion must first be transformed into nitrate by certain microbes. Nitrates are great for plants, but unfortunately can pollute water supplies if over-used. Ammonium nitrate is also an oxidizing agent in explosives, so garden with care!


Nitrogen (N2) contains two nitrogen atoms connected by a triple bond. This triple bond is the reason why N2 is so stable and inert to chemical reactions. Nitrogen was discovered by Daniel Rutherford when he separated N2 from O2 and CO2 in air. Scientists observed that this gas could not support any life form and was thus given the name azote (from Greek, meaning lifeless).

Nitrogen Fixation

Nitrogen is a necessary nutrient for plant growth. Nitrogen is taken up from the soil in the chemical form nitrate (NO3-), which is a type of fixed nitrogen. As plants continue to grow, sources of fixed nitrogen are stripped from the soil. To continually sustain vegetation, the earth must replenish its fixed nitrogen. There are several natural methods for the fixation of atmospheric N2. But before we get to those we’ll offer a quick explanation why N2 is so difficult to fix.
N2, which makes up 78% of Earth’s atmosphere, is a molecule made of two nitrogen atoms. Each nitrogen has a “lone-pair” of electrons. The two nitrogens are held together by a triple bond. This just means that the two atoms like each other a lot. (Maybe they’re vain … that’s just how they roll.) In fact it takes a lot of energy to break that bond. The bond dissociation energy for N2 is roughly 3,662 Calories (or kcal) to dissociate 1 pound of N2. This is roughly equivalent to the number of Calories in 13.5 snickers bars. But it’s even more difficult than that. You still need to apply an
activation energy.
OK. So it’s tough to break up N2. How does Nature do it? Decaying plants and animals as well as animal excrement provide a source of ammonia that bacteria can turn into nitrate. Certain forms of bacteria that clump around the roots of beans and other legumes can take atmospheric N2 and turn it into nitrates. Also, a lightning strike provides enough energy to react N2 with O2 to form nitrates. Unfortunately, these sources of fixed nitrogen cannot keep up with agricultural demand. This is where chemical sources of fixed nitrogen and the Haber-Bosch process come in to play.

Nitrous oxide

Nitrous oxide contains a central nitrogen atom bound to a terminal nitrogen and a terminal oxygen. N2O regulates the ozone in the atmosphere and is a greenhouse gas. N2O makes cars go fast… and then explode. N2O makes people laugh and laugh and laugh and laugh and laugh and pass out.


Ozone is made up of three oxygen atoms(O3). Far away, it is good (ozone layer). Close up, it is bad (burning = ouch).

Parts per million (ppm)

This is a way of expressing very dilute concentrations of substances. Just as percent means out of a hundred, so parts per million means out of a million (and ppb means out of a billion). Usually describes the concentration of something in water, air, or soil. One ppm is equivalent to 1 milligram of something per liter of water (mg/l) or 1 milligram of something per kilogram soil (mg/kg). To put this in further context, if a two year old were to sit in an Olympic sized swimming pool all day, the resulting concentration of pee-pee would be approximately 72 ppb (granted, this depends greatly on the amount of juice boxes consumed).

PermafrostBasically it is
old frozen dirt.


The process by which plants and some bacteria are able to take CO2 out of the atmosphere and combine it with absorbed water to create oxygen and carbohydrates (mmm… bread). The cool thing about this reaction is that the entire process is driven by sunlight!
Net reaction: 6H2O + 6CO2 ———-> C6H12O6 + 6O2

Simplified view of the photosynthesis of lignin by trees (top) and cellulose by grasses (bottom).

Projected regional effects of global climate change:

(from the IPCC’s 4th Assessment Report)
-North America: decreasing snowpack in the western mountains and increased frequency and intensity of heat waves in certain cities.
-Latin America: replacement of tropical rainforest by savannah, significant biodiversity loss through extinction, and large scale changes in water availability for human consumption, agriculture and energy needs.
-Europe: increased risks of inland and coastal flooding, erosion from storms and sea level rise, glacial retreat, extensive species extinction and loss of crop productivity.
-Africa: 75-250 million people are projected to suffer from water stress, up to 50% loss of rain-fed agricultural productivity by the year 2020.
-Central, South, East and Southeast Asia: increased risk of coastal flooding, regional increases in death rate from drought-related disease and decreased freshwater availability by 2050.


The counter balance to photosynthesis. As animals, the energy we need to function comes from the carbohydrates produced by photosynthesis! The carbs that we ingest (mmmmm… Doritos) react with the oxygen we breathe. The useful byproduct of this reaction is Adenosine Triphosphate (ATP), which powers all of our cellular function. The really cool thing about respiration is that it is the mirror image of what happens in photosynthesis.
Net reaction: C6H12O6 + 6O2———-> 6H2O + 6CO2

Runaway greenhouse effect

No, this is not the speedy escape of your local florist … Rather, it is an extreme case of the normal greenhouse effect. The Earth has enormous amounts of two greenhouse gases: water vapor and carbon dioxide. However, for the Earth most of the water and carbon dioxide are not in the atmosphere. The water is mostly in the oceans, and the carbon dioxide is mostly bound chemically in rocks made from carbonates (limestone). If there is an increase in the amount of solar radiation or in the concentration of greenhouse gases in the atmosphere, the effectiveness of greenhouse heating would lead to the temperature rising. It would become a runaway greenhouse effect if that rising temperature approached the boiling point of water, because then the oceans would begin to convert to water vapor, the water vapor would increase the effectiveness of heat trapping and accelerate the greenhouse effect, this would cause the temperature to rise further, thus causing the oceans to evaporate faster, etc., etc. (This type of runaway is also called a “positive feedback loop”.) When the oceans were gone the atmosphere would finally stabilize at a much higher temperature and at much higher density, because all the water would now be in the atmosphere. This type of process is thought to be responsible for the inhospitable environment of Venus.

Snow day

For those readers residing in Southern California, a “snow-day” is the manifestation of every young boy, girl, or gradeschool teacher’s hopes and dreams. It is born out of bedtime prayers, a precise early morning snowfall and perhaps the deviant, yet noble act of hosing down the superindendent’s driveway… Essentially, it snows a lot and everyone stays home (or has a snowball fight). *Turns out, this also applies to the U.S. government!