Smell results from a chemical reaction, more precisely a "binding reaction", between the chemical and smell receptors located in your nose. Smell receptors are cell surface molecules that cause intracellular changes in specific nerve cells. These signals are relayed to the brain, and interpreted by the brain.
All smells involve tiny amounts of chemicals rising through the air and landing on your cell receptors.
In this case, the WTC stench was more than just a smell, although there was a kind of smell to it that is unmistakeable, despite the inability to objectively identify it. The other component to the smell was tingling, even pain, in the nose and lips.
My theory is that small particles of finely powdered iron were interacting with cell surface receptors that were sending electrical signals to smell centers in the brain, which was interpreting the smell as "such and such" as it interprets every smell. That "such and such" is unforgettable. Millions of New Yorkers would recognize it if they ever saw it again, even though it doesn't now have a proper name.
The other component of the smell, the pain, was probably caused by cellular damage caused by the iron particles landing on your sensitive mucosa.