Molecules that are not part of life?

two points:
One:
The terrestrial biosphere goes far down into rock and surface soils. Extremophiles exist in places you might not believe - boiling mud and the outer crust of many rocks and minerals, for example. So directly or indirectly biological activity is virtually everywhere. There are bacteria in ocean water that break down petroleum from natural seeps and now ocean going vessels; bacteria that stain rocks with manganese salts (desert varnish) and so on.

Two:
As of today there are a lot of polymers that do not degrade in landfills - polymers humans made. But - as bacteria evolve take advantage of all these newly introduced polymers they eventually will degrade as part of a newly minted metabolic pathway as well. We have seen it happen with the plastic used for laundry bleach bottles. So, in that sense, there are complex molecules created by life that are biologically inert. For a while.

As an aside, I was in a class long ago where the nature of required elements for life was discussed. The "fact" that silicon oxides and derived molecules were biologically inert was discussed. So, silicon was not ever used by plants. Few years later I learned that scouring rushes (horsetails - Equisteum and friends) have silicon oxide based lithocysts which work very like a plants version of sandpaper, and are great for cleaning dishes. I tried it. Cool.

So duh. That means the horsetail was able to uptake and transport silicon-based molecules from the soil into plant tissues. To do that requires chemically "messing" with silicon oxides. Meaning: ignorance is not proof of a concept. Or maybe: watch out for scientists who do not know that they do not know.

So beware of any answers that dogmatically state X molecule cannot ever, ever interact with any biological entity. Some exist now - true. But give it 100 years.
Edit:
@Ygggdrasil has a better shorter answer.

 

Hmm. May I ask if you've had a chemistry class. Organic molecules (carbon) and silicones pretty much rule the complex molecule domain. Maybe Buckyballs are what you are looking for...
Se Buckminsterfullerene: https://en.wikipedia.org/wiki/Buckminsterfullerene

 

Also consider -
From wikipedia:

https://en.wikipedia.org/wiki/Miller–Urey_experiment