”poison” and ”toxic” are sort of blanket terms, like ”death” or ”dying”: there's a zillion different ways a poison or toxin can screw with your system.

for instance, opiates (drugs derived directly from poppy plants) aren't exactly toxic, but they might be considered a poison... if someone overdoses, they stop breathing, and die because they stopped breathing. if you were to put them on a ventilator, when the opiates were metabolized by their body, they'd be fine... minus the trauma of sticking a tube into their lungs for the ventilator.

digitalis screws with the balance of sodium and potassium... mainly around your heart. roughly, sodium causes a muscle to contract, potassium causes it to relax. those two, plus calcium, also work in the mitochondria to produce atp. a little bit of digitalis was one of the first heart medications for atrial fibrillation (the top part of the heart spasming)... too much really screws with the sodium/potassium balance in the entire body... and you die.

arsenic is a bit more of a full-body thing from the start... it disrupts atp production in the cells, killing your cells directly. this tends to destroy everything that gets access to the arsenic, which is usually your organs first. interestingly, arsenic was also used as a medicine quite a while back, and in small doses is a stimulant.

cyanide (a whole category of molecules) kills by binding to the iron in your body, disrupting your ability to transport oxygen... one of the reasons for its name (cyan is a blue-ish color): you turn blue when poisoned with it, similar to asphyxiation... except you can breathe, you just can't do anything useful with the oxygen.

hell, if you dive underwater (scuba), pure oxygen itself becomes toxic well before you get 33' (10m) deep. really deep prolonged divers breath a mix of gases, going sometimes as low as 0.8% oxygen. i don't exactly remember the mechanism that kills you here.

some things, like tylanol (acetaminophen, apap), aren't toxic directly, but as your liver depletes the stuff it uses to break the drug down, it starts using a secondary reaction to get rid of the excess... this secondary reaction produces a toxic substance that kills your liver... aaannnddd you die.

think of the body as a miraculous balancing act: there are hundreds (possibly thousands) of balances between two or sometimes lots more than two things. to an extent it trys to maintain a balance... but swing something too far in one direction and the whole thing collapses. because it's balanced in so many different ways, there's a lot of different ways you can screw with that balance.

edit/add: some of the most potent things are very similar to the signals your body uses to signal that one or more of those balances are off... or to signal your body to correct one of those balances somehow. a metaphor here would be tossing a bit of sand in the eye watching a crane do its work: a tiny bit of sand can lead to something catastrophic if the person running the crane is doing something delicate. same with your body: screw with the wrong signaling mechanism and your body will destroy itself trying to correct a problem that doesn't exist anywhere except the alert system telling your body something is wrong.

keep in mind, those signaling and sensing mechanisms in your body are also in balance.

some we call ”medicine”... some we call toxins or poisons... the difference is usually the dose and intent, not the substance.

there's a thing called a ”therapeutic index”, which is a measure of how big the difference between ”medicine” and ”poison” is. some things, like a lot of over the counter medicine, has a very high therapeutic index. other things, like digitalis, has a very low therapeutic index...

so therefore at a molecular level, there's nothing that i know that can kill you, a human, from having a few molecules of it in your body... unless you consider a prion a molecule, in which case a few of those in the wrong place can cause a horrible death in a number of years... or rna/dna, like in a virus... but those are generally considered disease vectors and not directly toxic.

in short, a few molecules of something won't kill you because you are made of a shitload of molecules. it can get a bit dicey, though, when you start getting into micrograms of things that are very finely balanced. keep in mind there are a lot of molecules in a microgram.

anyhoo, apologies for the braindump, (writing this on my mobile off the top of my head) and not having a simpler answer for you :(