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In my story there has been an event which made the air toxic. Just a few breaths guarantees death.
What event could create such an atmosphere in an unfixable way?
The time is just before WW1. I was thinking some sort of large scale government experiments going wrong, but not sure what.
An idea I had was chlorine gas, but i'm not sure if that would be permanent.
In general, nothing.
As I mentioned the previous few times a question like this has come up, toxic gasses are toxic because they react readily. This means they tend to break down on short timescales: sulfur dioxide, for example, has an atmospheric half-life of around 24 hours, and even long-lived stuff like nitrogen oxides don't last more than a month or two.
In order to get a permanently poisonous atmosphere, you need to release so much of your chosen poison that everything it can react with, it has reacted with. This happened once in Earth's history: the Great Oxygenation Event, and took somewhere between 2000 and several hundred million years. For more exotic poisons such as chlorine, there may not be enough of it in the entire world to do the job.
This idea is the topic of Arthur Conan Doyle's novel The Poison Belt. In this story, the poisoning is caused by the passage of the Earth through a poisonous volume of the luminiferous aether. Sadly, this is probably no longer an option for you, since the aether has been shown not to exist. Alternative options might be the earth passing through a dense cloud of interstellar hydrogen cyanide, or fast growing bacteria producing toxic gas as in the Great Oxygenation Event.
Another example from literature is in Zodiac by Neal Stephenson, in which a genetically engineered bacteria which has the potential to liberate all the chlorine held in the world's saltwater oceans is released into the wild.
Nanotechnology.
Quasi-living self reproducing machines the size of cells. They are essentially a synthetic fungi meant to produce enzymes to mine old landfills and trash.
By mutation or accident they produce a disassembler sub-unit that becomes airborn. It happens to be extremely toxic, as it affects some critical system in the body.
The pseudo-fungi have escaped and gotten into the soil and is spreading all over the world. Everywhere you have compost or topsoil or garbage, it grows and releases this deadly gas as a side effect.
Let's get some rough numbers on this. Earth's atmosphere has a mass of about 5x10^18 kg. HCN seems like a good example of a gas that's deadly in low concentrations: the recommended upper limit for exposure in air is 4.7 parts per million, and the immediate danger level is 50ppm. The kind of rapid death you're looking for will happen at a higher level, let's say 100ppm, which is 1/10,000. So we need about 5x10^14 kg of HCN. That's really quite a lot.
The interstellar medium is really low-density. About 10^-13 times the density of Earth's atmosphere, but let's give it 100 times that for a freak cloud, 10^-11 of an atmosphere, and 10^-4 of an atmosphere of HCN is deadly. So the Earth needs to sweep up 10^7 times the atmosphere's volume of this molecular cloud. That would actually be possible in a few months in that cloud, since the Earth moves a distance equal to about 3.5 times the equivalent depth of the atmosphere every second.
The (fortunate) reason this won't actually work is the solar wind, which maintains a bubble of reasonably friendly conditions around the solar system. If the system moved into a dense molecular cloud, the bubble would shrink, but I'm reasonably sure the Earth would still be inside it and not exposed to the molecular cloud. It currently extends far beyond Pluto's orbit, call it a 50AU radius spheroid. If it shrinks to 5AU radius, it gets a thousand times denser, well above the density of the cloud.
A comet made of semi-pure HCN hitting the Earth could provide enough. We need about 7.5x10^8 cubic metres of frozen HCN (density about 0.7 tons per cubic metre) which is about a 2km comet. That doesn't cause a mass extinction just as an impactor, but the HCN would. It's fortunate comets don't come in high-purity grades.
How real do you want this? Real enough that it could actually happen (why? — are you hoping to do it?) or just real enough to be plausible in a work of fiction?
As you probably know, diamonds and graphite (pencil “lead”) are both pure carbon. They are distinguished by different crystal structures. They are called allotropes, and there are others.
Warning: spoilers ahead.
Polymorphs are similar to allotropes, but the term allotrope applies only to elements, while polymorph applies only to compounds. Polymorphs are most often found in minerals and organic compounds (e.g., pharmaceuticals). There are polymorphs of ice (solid $\mathrm{H_2O}$), but the ordinary ice that forms on puddles in winter (and that we make in our freezers and put into our drinks) is the only one that can exist at standard pressure. However, Kurt Vonnegut’s novel Cat’s Cradle stipulates that there are others that can exist at standard pressure. In particular, one called “ice-nine” has a melting point of $\mathrm{45.8\:°C}$ $(\mathrm{114.4\:°F})$, so it is stable at room temperature — and, indeed, on most of the Earth. It has the additional property that if any liquid (or gaseous) $\mathrm{H_2O}$ comes into contact with ice-nine, it immediately freezes and also becomes ice-nine. For most of the book, the ice-nine is kept carefully controlled and locked away. But eventually it escapes into the environment and causes all the oceans to freeze, and it’s pretty much curtains for mankind.
Oxygen has allotropes, too. The best known ones are ordinary, atmospheric oxygen $(\mathrm{O_2})$ and ozone $(\mathrm{O_3})$, but there are others, including tetraoxygen $(\mathrm{O_4})$, which is unstable (or metastable). Wikipedia notes:
Triatomic oxygen (Ozone, O3), is a very reactive allotrope of oxygen that is destructive to materials like rubber and fabrics and is also damaging to lung tissue. Traces of it can be detected as a sharp, chlorine-like smell, coming from electric motors, …
Now suppose that $\mathrm{O_5}$ is stable at standard atmospheric pressure and temperature. And suppose that, like ice-nine, it acts as a catalyst, converting $\mathrm{O_2}$ (and maybe also $\mathrm{O_3}$) into $\mathrm{O_5}$, and that this conversion is very hard to undo (think particle accelerator). It would be quite reasonable to expect $\mathrm{O_5}$ not to react chemically the way $\mathrm{O_2}$ does (remember the differences between the characteristics of diamonds and graphite). Once this stuff got into the lungs of an oxygen breather, it would convert all the ordinary oxygen (including, eventually, the stuff in hemoglobin) into $\mathrm{O_5}$, which would not give the cells what they need. You’d suffocate.
Or maybe it’s just very, very bad for you — like ozone.
I don’t know how $\mathrm{O_5}$ would be created with pre-WWI technology, but the existence of tetraoxygen $(\mathrm{O_4})$ was first predicted in 1924 as a result of experiments with liquid oxygen — so that technology existed then. You would need very little handwavium to explain how somebody cooled oxygen, past the point where it condenses into a liquid, near to its freezing temperature, and this caused $\mathrm{O_5}$ crystals to form. When allowed to thaw, they did not decompose, but rather started a Cat’s Cradle-like chain reaction that converted all the oxygen on the planet into toxic $\mathrm{O_5}$.
Global warming causes the oceans to become anoxic, leading to the production of large amounts of hydrogen sulfide. Theorized to have happened during the Permian-Triassic extinction. See e.g. http://geology.gsapubs.org/content/33/5/397.abstract Not of course universally fatal, at least the P-T version, because some species did survive.
Do not add anything, just remove oxygen. If the partial concentration of oxygen in the air drops our lungs will be unable to maintain oxygen in the blood. Indeed stepping out to low-oxygen atmosphere will result in the oxygen in our blood being rapidly lost. The effects will be the same as if the air was toxic despite the process actually working in the reverse.
Losing the oxygen itself is fairly simple, just burn something and free oxygen will be consumed. The only issue is that it can't be carbon since photosynthetic bacteria can reduce carbon dioxide, that is why we have free oxygen in the first place.
The two valid alternatives are hydrogen and iron. The two valid sources for either are from space or from terrestrial deposits. The choice matters in ways that are beyond this question as all alternatives have huge "side effects." I am not going to explain those in detail here. I mean, the question is old and it is better to ask for details in a follow up question.
For hydrogen the alternatives are a coronal mass ejection or a series of them releasing huge amounts of hydrogen which then hits Earth and huge amounts of methane or hydrogen sulphide being released by volcanism. Or just global warming.
For iron, metallic meteorites could bring it to Earth. If the individual meteorites are small enough they'll burn in the atmosphere are bind oxygen. The metal dust or rabble could be left overs from solar system formation or a result of successfully stopping an extinction level asteroid hit. Volcanism could release huge amounts of iron if everything goes "right". The iron is down there, it is just unlikely for something to bring it up.
Such deep volcanism might also bring up lots of other things that burn and bind oxygen. Silicon and aluminium for example are fairly common and bind oxygen into silicates or aluminosilicates (aka rocks) that life cannot release oxygen from.
