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Question is simple but tricky, for example my chemistry teacher says that preservatives on food for example Nitrate N3 are not good in excess for your body (like everything else), but if Nitrogen is in the air, and we breath it what is the real difference in this case between Nitrate and Nitrogen.

Lets formulate the final question:

Is there any difference between taking 3 Nitrates (9 Nitrogen atoms) and taking 9 Nitrogen atoms?

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First I will clear up a few misconceptions you have:

  • Nitrate is actually the ion $\ce{NO3-}$, not $\ce{N3}$. Three nitrogens exist in the ion $\ce{N3-}$ which is called an azide ion. Nitrates are indeed used as food preservatives, e.g. sodium nitrate $\ce{NaNO3}$.
  • Nitrogen in the air is in a diatomic form, i.e. $\ce{N2}$. Nitrogen is more stable this way because it can share electrons between the two atoms in the form of a triple bond. This gives each nitrogen a full 8 electrons in its valence shell, making it more stable than free nitrogens which have only have 5.

Since nitrogens are so stable being diatomic, if any two come into contact they will likely react to form $\ce{N2}$, so it is hard to have free nitrogen atoms by themselves. $\ce{N3-}$ is a negatively charged ion so it will usually be ionically bonded to a positive ion e.g. $\ce{Na+}$ in sodium azide $\ce{NaN3}$, which is very toxic but now isn't purely nitrogen. So I think as a better example to answer your question, I will compare $\ce{O2}$ (oxygen in the air) with $\ce{O3}$ (ozone). Is there a difference between inhaling 3 $\ce{O2}$ and 2 $\ce{O3}$ if it means you're taking 6 oxygens in both cases?

For the same reasons as nitrogen, oxygen is very stable as $\ce{O2}$. Since it's so stable, it is unlikely to react with anything unless given a lot of energy, i.e. it is inert. Therefore we can breathe in oxygen safely, and it can safely be carried around the body until it reaches places where it can be given enough energy to react in processes that keep us alive.

Now with ozone, this molecule is less stable than $\ce{O2}$. The electrons in the bonds need to be shared amongst 3 nucleuses, while trying to have a full octet. This gives something called a resonance structure which stabilises the ozone, but it is still less stable than $\ce{O2}$. This means it is more reactive! And if it's more reactive, it means it can react much quicker than $\ce{O2}$ and with molecules in our body that we don't want it to react with. It can also decompose to the $\ce{O2}$ and an oxygen free radical $\ce{O.}$, which is a free oxygen atom with a single unpaired electron, making it extremely reactive. Breathing in ozone can cause throat irritation and chest discomfort among other symptoms, caused by ozone reacting with molecules in the lungs.

So the way the atoms are bonded matter. Their bonding gives them different reactivities and other properties like boiling point and solubility, which make molecules behave differently to free atoms or other molecules made of the same atom.

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