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

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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.

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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.

Molecular Monday: Liquid Water vs. Liquid Methane

September 5, 2016

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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 comparing some of the properties of:


So you’re a moon or other planetary body, and you want to get some biochemical action going on. First, you need some organic substances. Titan has set a great example with the tholin haze that forms spontaneously in its atmosphere.

Next, you need a liquid to dissolve that organic material in, in the hopes that the organic material will recombine as amino acids, peptide chains, and ultimately DNA. But which liquid should you choose? Liquid water (as seen on Earth) or liquid methane (as seen on Titan)?

Pick Water!

Water (H2O) makes an excellent solvent for our purposes because it’s a polar molecule. There are two big reasons for water’s polarity.

  • First, oxygen has an extremely high electronegativity, meaning oxygen atoms like to yank electrons away from other atoms. Within a water molecule, oxygen’s electron-hogging tendencies cause it to become negatively charged, while the two hydrogen atoms become positive.
  • Second, you know how water molecules have that Mickey Mouse shape? Because of that shape, with the two hydrogen atoms bent toward each other, the positive charges accumulate on one side of the molecule and the negative charge accumulates on the other.

Thus, water is a polar molecule, and it’ll go around interacting with other polar molecules, like tholins or amino acids.

Don’t Pick Methane

Unlike water, methane (CH4) is a nonpolar molecule. Why?

  • Carbon is slightly more electronegative than hydrogen, but not by much, so the atoms in a methane molecule share electrons almost equally. This minimizes the electric charges that might build up inside the molecule.
  • Methane molecules are symmetrical, with the carbon atom in the center and the four hydrogens evenly spaced around in, like the four corners of an equilateral pyramid.

Sp05 Methane vs Water

Any electrical charges in a methane molecule balance out, due to the molecule’s symmetry. And those charges are fairly weak anyway, due to the similar electronegativities of carbon and hydrogen.

I won’t be so bold as to say life can’t develop in a liquid methane environment, but the idea does seem a bit farfetched in light of the chemistry. Polar molecules like tholins just aren’t likely to dissolve in a methane lake, like the lakes found on Titan.

On the other hand, the universe keeps surprising us, and the giant lake monster I recently met on Titan might dispute my assessment of Titan’s biochemical potential.

P.S.: Titan’s lakes also contain liquid ethane, but that doesn’t really change anything. Ethane is also nonpolar.

Molecular Monday: Are There Amino Acids on Titan?

August 1, 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:


Captain’s Log

Stardate 8116.3

My spaceship has completed orbital insertion at Saturn. During last year’s Mission to the Solar System, I missed the opportunity to explore Saturn’s largest moon, Titan, in any detail. I intend to correct that error.

Titan may or may not support life, but one thing is certain: it is a chemically active world. And that chemical activity is vaguely reminiscent to the biochemistry found on Earth.

While my spaceship is still on approach to Titan, this seems like a good time to review what I’ve learned so far about amino acids.

Anatomy of an Amino Acid

  • Amino Group: a structure on one side of an amino acid that can serve as a base in acid/base chemistry.
  • Carboxyl Group: a structure on the opposite side of the amino acid that can serve as an acid for acid/base chemistry.
  • Alpha Carbon: A single carbon atom separating the amino and carboxyl groups, preventing them from accidentally reacting with each other. Some amino acids also include a beta carbon, a gamma carbon, or even a delta carbon, further separating the amino and carboxyl groups.
  • The Side Chain: A chain of atoms dangling from the alpha carbon. These side chains vary in composition and complexity, giving each amino acid its own unique flavor (sometimes literally).

Functionality of Amino Acids

  • Peptide Bonds: The amino group of one amino acid can link up with the carboxyl group of another, forming a peptide bond (a water molecule is produced as a byproduct). This process can be repeated over and over, forming incredibly long peptide chains.
  • Proteinogenic Amino Acids: While there are hundreds (perhaps thousands) of different amino acids, life on Earth uses only twenty-three of them in the formation of proteins. We humans use only twenty-one.
  • Chirality: Side chains can be attached to one side of an alpha carbon or the other. Life on Earth only uses amino acids with side chains on the “left” side. Right-sided side chains are incompatible with our DNA, and we can’t use them for the construction of proteins (though our bodies can use some of them for other purposes).

When I arrive on the surface of Titan, I do not know what I will find. Amino acids? Probably. Peptide bonding? Maybe. Long peptide chains, like some sort of proto-DNA? It’s possible.

We’ll just have to wait and see what happens when I get there.