Imagine having a cup of steaming hot black coffee at your fingertips. Molecules that have reached their boiling point are escaping into the air. The coffee itself is a homogenous solution of ground coffee beans containing about 40 milligrams of caffeine per 100 grams of coffee and water.

You pour in some cream and it disperses immediately, swirling through the black and ultimately becoming part of the homogenous mixture. The cream is abiding by the second law of thermodynamics and is tending towards entropy, as is the tendency of the universe. This doesn’t necessarily mean that the universe is becoming more disordered; rather, it means the energy that exists in the fluid is becoming more evenly distributed, with the creamer intermixing with the original black coffee, as well as the molecules given off by the coffee as steam.

The coffee is cooling as described by an exponential decay function, but adding cream to it has increased the viscosity and thereby slowed the rate of cooling. You put a cap on it in order to prevent further heat loss by evaporation.

But alas! You forget about your coffee, leaving it on your desk and then coming back to find it cold. You don’t want to throw it away; you may have spent several precious dollars on that coffee! Maybe even five or six dollars, if you went to Starbucks. Instead, why not pop it in the microwave for thirty seconds? As the coffee spins in the microwave, the molecules within the liquid are rotating too. Radiated microwaves permeate the coffee, exciting polar molecules within it to new rotational states, creating thermal energy through dialectric heating. The rotating molecules bump into other molecules, distributing energy (and therefore again increasing entropy) which appears as heat.

Finally, you’re ready to drink your coffee. You bring the cup to your mouth and take your first sip. Immediately, sensation fills your mouth. There’s the sensation of the hot, of course, and then the curious sensation of taste. Your taste buds are comprised of chiral (or asymmetric) molecules that bind to other asymmetric molecules and send signals to your brain through electrical impulses mediated by an electrochemical gradient of sodium and potassium channels maintained by your neurons. Perhaps they are sending a message of the familiar slightly acidic (due to the fifty identified acidic compounds found in coffee), strong taste that is currently confronting your taste buds.

In your stomach, the coffee will encounter fairly concentrated hydrochloric acid, one of the seven strongest acids known to man. The acid would burn you if it came into contact with your skin, but amazingly does not burn you from the inside out due to the mucous membrane lining your stomach. Through your stomach, as well as through your mouth and throat, caffeine from the coffee may be absorbed and taken into the bloodstream.

Now that it’s in the bloodstream, the caffeine has potential to do great things! It may cross the blood-brain barrier and bind to adenosine receptors. Adenosine is a molecule that gives the effects of sleepiness when bound to the receptors. Caffeine binding blocks out the adenosine, allowing you to stay awake and alert during your nine AM biochemistry lecture, thus allowing you to learn about adenosine itself!

Caffeine also causes the adrenal glands atop your kidneys to release everybody’s favorite hormone, adrenaline. Another interesting effect of caffeine is the relaxation of smooth muscle. This includes your colon! Which explains the mad rush to the bathroom shortly after consuming a cup of coffee. When no longer in a useful form, caffeine is broken down and filtered out by the kidneys.

Clearly, coffee is quite a versatile drink as it is able to illicit such a variety of effects. What is truly remarkable to me, however, is the chemistry behind all of these effects. From the molecules within the coffee and their individual energies, to the reactions they invoke, so much chemistry is involved in this one drink. And this drink is but a tiny, miniscule, infinitesimal (on a scale of picometers) example of the chemistry that surrounds us and defines us. And that’s why you should never trust atoms. They make up everything.