This has to do with two things: the elements in a compound, and the way they are arranged, and the way the sensors in our nose perceive the molecules and the signals that they send to our brain!
There are certain elements, which, if present in a compound, greatly raise the chances that the substance will smell: for example, sulfur (which is what gives rotten eggs and sewage their lovely smell) and selenium. There are also certain arrangements of a combination of elements in chemicals that can smell bad: a lot of acid chlorides, ammonia and other amines, and a lot of anhydrides.
The other part of this is how our brain perceives smell, which as a lot to do with instincts we’ve evolved. For example, no one really likes the smell of rotting meat: this is because our ancestors discovered way back when that if you eat rotting meat, it will make you ill, and so the smell became associated with bad things and danger. The smell of rotten meat is also a sulfurous smell, therefore things that smell like sulfur now smell ‘bad’ to us as humans, but I imagine that if rotten meat was something we could eat, our brains would have developed so that it smelled ‘good’ to us.
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