Dr. Margaret Ross Had it all. She is in charge of one of the top molecular physics labs in the world, considered the authority on atomic structure. And to top it all off her fiance of seven years had finally proposed. Then it all came crashing down with the discovery of the theta particle, a unique Micro-molecule that appeared to respond to human thought patterns.
Now she's a fugitive. Everything Margaret owns has been taken away from her, and even the one man in her life she trusted refuses her calls. Forced to trust a complete stranger, and running away from a government that wants to weaponize her discovery, and a mysterious organization that will kill to keep certain secrets hidden.
That's not a synopsis, that's a blurb.
What publishers want from a synopsis, sfaict, is a summary of the plot that indicates that it holds together all the way through and has a decent ending. In other words, don't hint at secrets, show how cool they really are. Fewer of the adjectives, more straight description.
[ Publishers have people to write blurbs. I'm not aware of any published authors who get to write their own. ]
Also, calling your theta particle a micro-molecule suggests heavy-duty handwaving and not knowing much physics; there are SF editors for whom this may well be a disadvantage.
Also also, you hop back and forth between past, present and pluperfect tense in this para; the recommendations I have had suggest doing synopses entirely in present.