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Dark matter clouds the synapses
that once allowed you to love me.
I used to sit on the rim of your glasses
as we drank constellation wine,
connecting dots in our minds and I
would sprinkle nebula glitter on my breast,
you'd take my krypton fingers and we'd
dance across the galaxy, comets at our feet,
it was a nova just beginning.

When we were both molecules,
still young and foolish, you'd whisper
soundtracks about how family 11 would
inhabit my fingers, you'd shower me in
antimony compliments that'd never
brush the veneer of my noble soul.
Here, we were ignored the threats of a
thousand white dwarfs, dark stars,
and black holes that sulk in the shadows
of the subways.

The night of the blue moon,
you told me you were atomic 109.
You're only nuclear fusion, artificial,
bound to break apart.

That was the night I learned not
to confuse science with the stars.

Hmm. No, chemistry does not equal astronomy.
While this was well-constructed and unique, I felt that it was cluttered up with too many scientific references to flow as nicely as it might have. It was a little overbaked or oversalted, perhaps.

I used to sit on the rim of your glasses
as we drank constellation wine

I like this line the best, especially when it's followed up by that bit about connecting dots.
The first stanza makes me think of the narrator and subject as humans, or at least a little more tangible than molecules, while the second stanza begins, "When we were both molecules..." Are you in fact making the narrator and subject out to be elements or is it figurative? If you intended the latter, I think it was taken a bit too far.

The third stanza is cute and bubbling with the chem references. I'm not sure about that one...
The fourth stanza? The statement sounds rather trite. I'm not really sure. Cut it out first, then find something to replace it with.

Here, we were ignored the threats of a
thousand white dwarfs, dark stars,

I'm a little confused about the phrasing here. "We were ignored the threats..." You ignored the threats? The way it is right now, sounds like it should be "We were denied the threats" which doesn't make any sense, but that's the way it's phrased, like someone had forced something upon the narrator and subject, like it wasn't their choice.

Here's an example of being overcrowded with references and chemistry/astronomy metaphors:

would sprinkle nebula glitter on my breast,
you'd take my krypton fingers and we'd
dance across the galaxy, comets at our feet,
it was a nova just beginning.

Nebula. Krypton. Galaxy. Comets. Nova. These phrases are all fascinating alone, but piled together, they're just a bit too much to swallow. It's like a traffic jam. I'd say you could cut out 75% of the allusions in this poem and it would still be perfectly understandable, decent poetry.

Nice stuff!
Colleen