Well...molecules are probably not what you should be thinking about. We don't even know what to call the 'thing' that MAY have pre-existed the Big Bang. General relativity says that we cannot properly think of either a time or a place before the Big Bang, because these physical constructs came into existence with the Big Bang itself. Theoreticians, however, imagine that there may have existed some 'state' that went through a 'vacuum fluctuation' and which ran away with itself to produce the Big Bang. Vacuum fluctuations occur by a process called quantum tunneling, but what this all means without reference to space or time is anyone's guess. It isn't even known how the devil a scientist is supposed to test such a prediction! What ever started the Big Bang seemed to require a process of some kind to 'tip' the right way and cause a spark of energy to flash into existence, perhaps by a quantum tunneling event from some other unknowable 'state'. This flash of energy was synonymous with the formation of the gravitational field of the universe, and from this fireball expanding and cooling, the remaining particles and fields, and even time itself, had its origin.