Molecular Monday: Water Gets Freaky

July 3, 2017

After today’s post, you might never look at a glass of water the same way again.

The water molecule is made of two hydrogen atoms plus one oxygen atom, arranged in a Mickey Mouse shape, with the chemical formula H20. You already knew that, I’m sure. But you may not be aware of this: water’s chemical formula gives you a hint about water’s true nature.

Hydrogen ions play an important role in acid/base chemistry, so when you see hydrogen listed first in a chemical formula, that typically indicates that you’re looking at the chemical formula of an acid.

  • Acid: an acid is a chemical that can give up a proton (a.k.a. a hydrogen ion) to a base.
  • Base: a base is a chemical that can accept a proton from an acid.

Water can do both. It’s an acid. It’s also a base.

  • Acidic Water: a water molecule (H2O) can give up a proton to a base, transforming itself into a hydroxide ion (HO).
  • Basic Water: a water molecule (H2O) can accept a proton from an acid, transforming into a molecule called hydronium (H3O+).

Now this is where things get really freaky: because water is both an acid and a base, it can actually react with itself.


Image credit: Manuel Almagro Rivas – Own work, CC BY-SA 4.0, Link

In fact water is constantly reacting with itself. The result is that even “pure water” is really a mix of water, hydroxide, and hydronium in a proton-swapping party that never ends.

Something to think about the next time you drink a glass of water.

* * *

Today’s post is part of a special series here on Planet Pailly called Molecular Mondays.

On the first Monday of the month, we take a closer look at the atoms and molecules that make up our physical universe, both in reality and in science fiction.

Where Does Fat Go When You Exercise? (A Molecular Monday Post)

June 5, 2017

Exercise is good for you, I guess. It’s probably one of the better options for anyone who’s trying to lose weight. But when you exercise, where does the weight go, physically speaking?

The first time someone asked me this question, my best guess was that it had something to do with Einstein’s E = mc2 equation, the equation that allows matter to be converted into energy. But I knew that couldn’t be right. That’s more of a nuclear physics thing, and the human body is not a nuclear reactor.

The actual answer has to do with chemistry. Rather simple chemistry. This is a triglyceride molecule:

Okay, it is sort of a complicated-looking molecule. Don’t worry. Your body knows what to do with it, even if your brain doesn’t.

The important thing, in relation to today’s question, is that triglyceride is composed almost entirely out of carbon and hydrogen atoms, with a few oxygen atoms sprinkled in.

Now when your body exposes triglyceride to the oxygen you breathe in, that highly reactive oxygen starts breaking the triglyceride molecule apart. With each chemical bond that breaks, a little bit of energy is released (allowing you to keep exercising), and the broken pieces of triglyceride recombine with oxygen to make carbon dioxide (CO2) and water (H20).

It’s worth noting that chemical bonds do contribute marginally to the total mass of a molecule, so when you break them and turn them into energy, E = mc2 does apply, sort of. But that’s nowhere close to being a significant factor in terms of weight loss.

The vast majority of the weight you lose comes in the form of carbon dioxide, which you breathe out through your lungs, and water, which you sweat out or pee out or breathe out as water vapor. (If you want to get into the math and find out how many kilograms of oxygen you need to burn how many kilograms of triglyceride, producing how many kilograms of water and CO2, click here.)

When I started studying chemistry, this was not the kind of thing I was hoping to learn. I’m a science fiction writer. I’m interested in the type of chemistry that makes rocket engines go, or drives weather patterns on other worlds, or could make alien life possible.

But still, it’s exciting to me when I can connect all that outer space science to some of the mundane aspects of life here on Earth.

* * *

Today’s post is part of a special series here on Planet Pailly called Molecular Mondays.

On the first Monday of the month, we take a closer look at the atoms and molecules that make up our physical universe, both in reality and in science fiction.

Molecular Monday: Why Chemistry?

May 1, 2017

The first Monday of the month is Molecular Monday here on Planet Pailly!

We just wrapped up this year’s A to Z Challenge, and I ended up writing a lot about chemistry. A lot more than I expected. You’d think I must really love chemistry.

But I don’t.

I really don’t.

For a long time, I tried to avoid the subject completely due to bad memories from high school chemistry. My professor was extremely generous in giving me a just-barely-passing grade.

So when I made the commitment to include more science in my science fiction, I figured I could get by with just the “fun” sciences like physics and astronomy. Then in 2015, I did my yearlong Mission to the Solar System, and the planet Venus forced me to start learning this chemistry stuff.

As you can see in this totally legit actual Hubble image, Venus has some very special chemical activity going on.

There’s simply no way to understand what’s happening on Venus without getting into the weird sulfur chemistry of the Venusian atmosphere. But once you do make sense of that sulfur chemistry, a strange new world is suddenly open to you: a world of both heavenly beauty and acid rain hellfire death.

Since my experiences with Venus, I’ve come to realize that understanding chemistry, even at a basic level, makes my work as a science blogger and science fiction writer so much easier.

  • Is there life on Mars or Europa? What about life in other star systems, or silicon-based life? If alien life is out there, it will be the product of chemistry.
  • What about humans traveling to other worlds? What would be safe for us to eat or breathe? Chemistry can help answer that too.
  • Venus isn’t the only world defined by chemistry. Earth has been shaped in large part by the chemistry of oxygen and water; the gas giants by ammonia and methane; and then there’s a true oddball like Titan with its tholen chemistry.
  • And how am I going to get my rocket ship off the ground? By mixing rocket fuel. In other words, by doing chemistry.

Chemistry is by no means the most fundamental science, but for the kinds of things I write, it is the most applicable science. So even though I don’t enjoy the subject, I’ve forced myself to stick with it.

And if I’m being perfectly honest, in those aha-moments when complex chemical reactions suddenly makes sense to me, I may quietly murmur to myself, “Okay, chemistry is kind of fun.”

Molecular Monday: Superatoms

March 6, 2017

Molecular Mondays Header

Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. On the first Monday of the month, we take a closer look at the atoms and molecules that make up our physical universe, both in reality and in science fiction. Today, we’re talking about:


It’s a bird! It’s a plane! It’s a superatom!


Okay, Superman isn’t the right reference to make for this post. I should probably make a reference to the Power Rangers, or perhaps Captain Planet. “When your powers combine, I am Superatom!”

Superatoms vs. Molecules

Atoms combining together is nothing new. That’s called a molecule. You could say that a superatom is basically just a molecule that acts like a giant atom.

In normal molecules, each atom gets to hold on to its own electron cloud, more or less. Yes, the atoms do share electrons. Yes, some molecular structures allow electrons to travel freely between atoms. Yes, sometimes an atom ends up losing an electron and never gets it back.

But for the most part, each atom still has its own unique electron cloud or electron shell structure around it, and therefore each atom still retains its own distinct chemical identity on the periodic table of elements.

In a superatom, something wildly different happens. An entirely new electron cloud forms, not around any individual atoms but around the molecule as a whole. This supercloud even has layers or shells, and it can form chemical bonds, just like the electron cloud around an ordinary atom would.

So Much for the Periodic Table

Because superatoms have their own electron clouds and can form chemical bonds with other atoms—or other superatoms—we can use them to create new molecules: molecules that would not be possible using just the hundred-plus elements on the periodic table.

So if you’re a chemist or an engineer (or a science fiction writer) and you can’t find the chemical element you need on the periodic table, you now have more options. You might be able to find (or invent) a super-element to do the job instead.

P.S.: I wonder if Star Trek’s dilithium might be a super-element that incorporates two lithium atoms.

Molecular Monday: What Color Are Atoms?

December 5, 2016

Molecular Mondays Header

Welcome to Molecular Monday! On the first Monday of the month, we take a closer look at the atoms and molecules that make up our physical universe. Today, we’re looking at:

CPK Coloring

When I first introduced this Molecular Monday series, I knew I’d be drawing a lot of atoms and molecules, but I wasn’t sure if there was a right way or a wrong way to draw them. For starters, I wasn’t even sure what colors I should use.

Atoms and molecules do not really have colors, in the sense that they’re too small for visible light to reflect off them. At one point, I wondered if I should color them based on their spectroscopic signatures, but that line of research got complicated really fast.

Eventually I discovered that chemists have a (mostly) standardized color-coding system for modeling the atoms in a molecule. It’s called CPK coloring, in honor of Robert Corey, Linus Pauling, and Walter Koltun. Apparently Corey and Pauling created this system in the 1950’s, and Koltun improved it by adding more colors in the 1960’s (improving things by adding more colors is basically what the 60’s were all about).

So following the CPK coloring scheme, hydrogen atoms are white, and oxygen atoms are red. (Example: water molecule, H2O.)


Nitrogen atoms are blue. (Example: molecular nitrogen, N2.)


Sulfur atoms are yellow. (Example: hydrogen sulfide molecule, H2S.)


And carbon atoms are either black or grey. I draw them in grey because otherwise you couldn’t see their little smiley faces. (Example: benzene molecule, C6H6.)


Personally, I think it would make more sense to switch the colors of oxygen and nitrogen. That way, water molecules would have blue in them, rather than bright red. But otherwise, CPK coloring is a pretty good system.

Typically green is assigned to either chlorine or fluorine, or sometimes both. Beyond that, modern chemists seem to have strayed from the original psychedelic system Koltun invented. I guess the rarer an element is, the less we worry about sticking to a standardized color code.

For my purposes, that hasn’t been a problem. Almost every molecule I write about on this blog is composed of carbon, hydrogen, and maybe oxygen and/or nitrogen. Occasionally sulfur gets into the mix, but that’s basically it.

For next month’s Molecular Monday post, I think we’ll continue looking at some of the other issues involved with drawing molecules. I settled on ball-and-stick models, but that’s not the only way to do things.

Molecular Monday: Life in an Ammonia Ocean

November 7, 2016

Molecular Mondays Header

Welcome to Molecular Monday! On the first Monday of the month, we take a closer look at the atoms and molecules that make up our physical universe. Today, we’re looking at:


Water, Water Everywhere…

You know how water has that Mickey Mouse shape? That shape is really important. That slight asymmetry allows electrical charges to accumulate on opposites sides of the water molecule.


The polarization of water molecules makes water a good solvent for other polar molecules, like amino acids. This is a big reason why water is essential to life (or at least, life on Earth). Without the ability to dissolve amino acids, we’d have an awfully hard time getting them to form peptides or proteins or DNA molecules.

But could life on some alien planet substitute another chemical for water?

Ammonia, Ammonia Everywhere…

This is an ammonia molecule (chemical formula NH3).


At first glance, you might think ammonia molecules are symmetrical, with three hydrogen atoms evenly spaced around the central nitrogen atom. Symmetrical molecules have all their electrical charges perfectly balanced, and therefore are non-polar and do not act as good solvents for amino acids.

But when you turn the ammonia sideways, things look rather more promising.


The three hydrogen atoms bend toward each other, just as the two hydrogens in water do. There’s a slight asymmetry, meaning electrical charges can form. Ammonia is a polar molecule after all!

And ammonia has a few other things in common with water:

  • They’re both fairly common in the universe (though water is more common).
  • They both can be liquid under fairly ordinary temperature/pressure ranges (though water’s liquid phase is wider than ammonia’s).
  • They can both act as a base, meaning they can accept a proton from an acid (though ammonia is slightly more basic than water).
  • They can both act as an acid, meaning they can both donate a proton to a base (though water is slightly more acidic than ammonia).

The most noteworthy difference seems to be that ammonia burns easily in the presence of oxygen. That could pose serious challenges to the evolution of complex, multi-cellular organisms that need the extra kick of energy oxygen provides.

Still, water and ammonia are similar enough to attract the attention of astrobiologists, and a lot has been written about the possibility of life emerging on some distant planet in an ammonia sea.


Hypothetical Types of Biochemistry from Wikipedia.

Alternatives to Water from Xenology: An Introduction to the Scientific Study of Extraterrestrial Life, Intelligence, and Civilization.

Thalassogens from Xenology: An Introduction to the Scientific Study of Extraterrestrial Life, Intelligence, and Civilization.

* * *

A special thank you to Kirov99 for suggesting this topic. My research tends to focus on the planets and moons of the Solar System, rather than hypothetical environments we might find elsewhere in the universe, so without the recommendation I would have probably missed this.

Who’s Eating Titan’s Acetylene?

October 3, 2016

The first Monday of the month is Molecular Monday, the day I write about my least favorite subject from school: chemistry.

Molecular Mondays Header

I’d planned to write something about ammonia today. Ammonia might (might!) serve as a good substitute for water in some alien biochemistry.

But then I was reminded of something. Something important. Something I’m kicking myself for not covering before. So once again, let’s turn our attention to Saturn’s largest moon: Titan.


Making Acetylene on Titan

As we’ve discussed previously, methane gas and other chemicals break apart in Titan’s upper atmosphere. This allows carbon, hydrogen, nitrogen, and possibly other elements to recombine in new ways. The result is a mishmash of organic chemicals collectively refered to as tholins.

Tholins tend to be sticky, yucky, and orange. They slowly fall to Titan’s surface, covering the moon with sticky, yucky, orange sludge. One chemical in the tholin mix should be acetylene (C2H2). In fact, acetylene is a fairly simple molecule compared to the rest of the tholin gunk on Titan, so we should find lots of it.

But we don’t. We’ve detected little to no acetylene accumulation on Titan’s surface. Maybe this means there’s something wrong with our detection techniques. Or maybe some as-yet-unidentified chemical process breaks up acetylene molecules as they fall through Titan’s atmosphere.

Or maybe (maybe!) something eats the acetylene as soon as it touches the ground.

Eating Titan’s Acetylene

I first read about this a few years ago in Astrobiology: A Very Short Introduction. It came up again, in greater detail, in the book I’m currently reading: All These Worlds Are Yours. The case of Titan’s missing acetylene is a hot topic for astrobiologists.

There’s a rather simple chemical reaction that might (might!) explain what’s going on.

C2H2 + 3H2 –> 2CH4 + energy

That’s one acetylene molecule reacting with three hydrogen molecules to produce two methane molecules and some energy. The kind of energy that weird Titanian microorganisms could use to survive (maybe).

In my opinion, it still seems unlikely that life could have evolved on the surface of Titan, if only because liquid methane (Titan’s “water”) is not a good solvent for amino acids. But unlikely is not the same as impossible.

It’s worth noting at this point that a few other weird things are happening on Titan. Hydrogen gas seems to mysteriously disappear near Titan’s surface, and no one has adequately explained how Titan replenishes its atmospheric methane (all the methane should have turned into tholins by now).

If Titan does have an acetylene-eating, hydrogen-breathing microbe that expels methane as a waste product, that would conveniently solve three mysteries at once. I can’t help but think, though, that this might be a little too convenient to be true.