Realistic alternatives to oxygen-based respiration?

Question

Background
I'm developing 6 to 10 sapient alien races for a short story.

Basic Story Setting
The short story takes place in the Milky Way sometime in the next 1000 years. These races will be at roughly a Star-Trek / Star Wars / Pandora's Star level of technology, i.e., circumnavigation of the galaxy still takes a "long time", but any species worth talking about has FTL capability of some kind.

All sapient alien races will have their original, naturally evolved biological forms, because strong genetic engineering / nanotech / digital immortality will be impossible (by hypothesis) in this particular story. However, other than that, I would like to write these alien races as realistically as feasible in a short story.

My Concerns
If I had to sum up my concerns about my story in one sentence, it would be this:
I want to write this short story as with as much scientific realism as practical.

I anticipate the story exploring 6 to 10 specific alien races, though hundreds or thousands more will exist in the background setting. I've heard that most life is likely to be carbon-based, because of the unique chemical properties of carbon compared to other elements (if that's wrong, please tell me!). So most or all of the races in the story will be carbon-based. However, it doesn't feel "right" to make all the races both carbon-based and oxygen breathers.

Some of them will probably breath oxygen, but I worry that having all of the primary 6-10 species breathe oxygen would feel too "same-y", or would break the reader's suspension of disbelief. It would be odd that they all breath exactly the same, despite having radically different bodies and minds. And no, there is no galaxy-scale "panspermia" process in this setting, so they wouldn't all have similar biochemistry due to a shared origin.

They don't need to all be completely different chemically, but it just "feels responsible" to have maybe two or three of them (at least) be based on something completely alien to Earth biochemistry.

Research I've done so far
I've already done a little bit of research on this. In particular, I've read the Xenology entry on respiration. It largely convinced me that gas-breathing beings using an oxidizing chemistry are the way to go. In particular, the entry mentions oxygen, chlorine, and fluorine as possible gaseous oxidizers. I've also read What's the difference between Oxidation and Reduction and Alternative elements for oxygen transport in an alien blood. I know there's many more things I could read, but that's a rabbit hole I could spend months going down, only to end up at the same place I started.

I've come here because I'm not confident about my grasp of chemistry, or my grasp of available options for biochemistry models (oxygen/non-oxygen), or my ability to effectively research the right things to learn more without wasting a ton of time and effort. I took chemistry in both high school and university. While I found it interesting and enjoyable, I've forgotten most of it since I don't use it day-to-day. I retain just enough to know that 1) chemistry is really complicated yet extremely well-understood by many people and 2) it's extremely easy to look like a moron when discussing chemistry unless you really know what you are talking about. So I'm concerned about using a gas I'm not particularly familiar with. I worrying about questions like: If a being breathes chlorine, what might they exhale? How would a cabin of their ship need to be constructed so as not to be damaged by constant exposure to both chlorine and the waste product of respiration?

Questions
I know I asked some inline questions above. Those can be taken either as flavor questions, or ignored. I think these are the questions whose answers will have the biggest impact on my story:

1. Is my conclusion well-founded? That is, am I plausibly correct that gaseous oxidizing respiration chemistry is the most plausible energy source for complex life?
   If not, what else should I consider?
2. The Xenology post mentions oxygen, chlorine, fluorine. Are there other gaseous oxidizers that would be likely to occur in natural biological processes? other ones that would make sense?
3. If I indeed choose a non-oxygen gaseous oxidizer, what secondary effects should I consider?
   For example:
   What effect would it have on the building materials / biology of the races?
   if a race breathes chlorine like we breathe oxygen, could their planet of origin have plants?
   What materials would they use to construct their dwellings?
   Is a photosynthesis-like chemical reaction which produces chlorine or fluorine even possible?

Closing remarks
Not all these details will actually make their way into the story, but I'd like to have at least thought through them before I settle on details to include. I don't want to say something ill-considered like "They breathe chlorine" if I don't know what they exhale, or where the chlorine in the atmosphere comes from, or how the ecosystem can stay balanced.

Information I would find most helpful
I don't need answers at the level of chemical reaction diagrams, (although if you feel like providing them, that would be amazing!). I'm more interested in knowing potential "unknown unknowns" about basic chemistry reactions involving oxidizers. Here's a list of things I just made up as examples of possible unknown unknowns that I would want to know about; these are the sorts of things I would want to be told, but wouldn't necessarily know to ask:

• "vertebrates that breathe fluorine would need [x] instead of calcium in their bones because fluorine would dissolve calcium"
• "vertebrates that breathe chlorine would likely exhale [compound Y] because of {the molecular binding energies (or something)}, and plants that metabolize [compound Y] would also need [compound Z] in order to be able to output chlorine again"
• "complex life that respires using chlorine wouldn't breathe pure chlorine. instead, it would need to breathe [chlorine compound] because elemental or molecular chlorine [wouldn't work / wouldn't be present in the atmosphere]"
• A planet with a high fluorine content in its atmosphere would constantly be on fire due to the reactivity of fluorine [unless such and such condition is met].
• etc.

Feel free to answer any subset of my questions if that's easier than answering all of them. I know I'm asking a lot, but I really I don't want to make stupid oversights in my description of alien biology. This is starting as a short story but it might turn into a series if there's interest, and I don't want to have to retcon a basic chemistry error. If a world with a fluorine atmosphere would be constantly on fire, then I'd rather know that before writing about it. Thanks!

Answer 1

I'm going to approach this more as a primer for xenobiology so that you can get the basics down and then figure out just how 'scientific' you want to make your story. There are several aspects to organic chemistry that will help you in setting out your species. I'll discuss them in increasing order of exoticism...

Chirality
In Chemistry, any assymetric molecules are considered Chiral. DNA is asymetric, and therefore has a chirality whose mirror image is not compatible with it. When you think of organic compounds, creatures of the reverse chirality would have trouble consuming food or other compounds of the reverse chirality (this is discussed in the Mass Effect series, where Turians, Quarians and (I think) Krogan have the opposite chirality to us, and therefore need different food.

Species that are carbon based oxygen breathers but different chirality may well interact with species like us, and can more or less live on the same planets as us, but they can't consume the same food as us and probably would be immune to a lot of our sicknesses (either that or our bacteria could make them VERY sick). In general, they're going to see out other carbon-based planets that already have life with their own chirality if possible.

Valency
Why are we called 'carbon-based' life? It's because carbon makes organic compounds possible through an attribute called Valency, or the count of other elements it can connect to in the creation of a molecule. Carbon has a high valency at 4, which makes all CHNO (Carbon, Hydrogen, Nitrogen, Oxygen) compounds, which we typically call organic compounds, possible.

Some other elements also have high valency. Chromium and Silicone in certain circumstances can have valencies up as high as 6, making them contenders for exotic element based life because of the flexibility in compounding that is afforded by that element.

Such forms of life however will have very little in common with us, and what they call an organic compound and what we call an organic compound will be very different. Such life will have very little reason to interact with us because they can't use our natural resources and we can't use theirs.

Oxidisation
You are correct when you talk about chlorine and fluorine as potential organic oxidisers, but as your reading may have already told you, these oxidisers don't play nicely in the sandpit together. Chlorine and Fluorine are both highly toxic to us in any amounts, and some compounds that contain these elements, particularly when combined with oxygen, are very highly dangerous as both combustibles and toxins.

As such, fluorine breathers are likely to find our oxygen rich environments highly toxic, and vice versa. They simply won't come anywhere near planets that we find comfortable and we won't go near theirs. There's no possibility of conflict over strategically placed planets between such species because strategic placement is all about connecting locations of value, and we wouldn't find such toxicity valuable.

Probability of Incidence
There's a very good reason why we're carbon-based oxygen breathers; generally speaking (and this is not perfectly accurate) the lower the atomic number of the element, the more abundant it is in the universe. That means that the planets where oxygen doesn't exist but fluorine does are going to be very exotic, and very rare. Same with chromium over carbon when discussing valency. That means that there's a very good probability that if we ever come across extra-terrestrial life, it'll be carbon based and oxygen breathing. While more exotic life is possible it's much less probable than even our existence is, and therefore the chance of it forming into an interstellar travel capable intelligent species is even lower again.

While your exotic life may well exist in your galaxy, it's going to be the exception, and their organic needs in terms of expansion are going to be so different from ours that it's far more likely that both species would leave each other perfectly alone. The only possible trade item that they could share would be information; there's a planet in our space we don't need that might suit you, do you have any oxygen rich planets in your areas? That kind of thing. Other than that, there would be no need to interact beyond academic curiosity.

Conclusion
Bottom line is that the more exotic you make life by comparison to ours, the less likely it is to exist at all, and if it does, it's even less likely to have survived to intelligence. Even if it does, it will have less capacity and reason to interact with us the more exotic it becomes due to the fact that there will be less resources we might consume that would be common between us.

To that end, I'd focus on species having different chiralities and the challenges of working together despite this difference. The other species just won't have any reason to interact and wouldn't even respond to each other's distress signals in space because seriously, what are a bunch of fluorine breathers going to even do for oxygen breathers in space? There would be no way to help even if they wanted to.

Species with reversed chirality on the other hand who are carbon based oxygen breathers have a far better chance of working together with us to a common goal (like saving people in space) without competing with us for ALL the same resources, like food.