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The "Big Rip" is a theoretical scenario for the death of the universe. Let's assume that this scenario is true.

What can we expect to happen to chemistry and nuclear interactions in the time between t=A, when they are significantly affected by the expansion, and t=B, when each particle in the universe is isolated?

Also, how long is the span of time between A and B?

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The time interval between expansion affecting chemical bonds and the end in a Big Rip cosmology is very short. The $w=-3/2$ example model in Caldwell et al. suggests atoms dissociate at $10^{-19}$ seconds before the end, so that would be the end of chemistry. They also state that nuclei and nucleons would be dissociated shortly after that (although no doubt physical processes like pair production would complicate the picture).

They don't calculate the time when molecules will be disrupted, but assuming the same rough scaling as for other systems (disruption about a third of a rotational period before the end) that would imply that macromolecules may start disintegrating a few milliseconds before the end and water somewhere around $10^{-12}$ seconds before.

Basically, expansion of the universe does not affect systems with relaxation rates much faster than the expansion rate, so chemistry is unchanged until the last few milliseconds. The processes that are most affected are those that are fairly slow (low energy) compared to the steepening rate of the force gradients.

At that point each molecule will start feeling a force outwards proportional to the distance from the center of mass, not unlike how centrifugal force acts (except this is isotropic in all directions). As it intensifies chemical reactions would tend to be interrupted as molecular fragments that normally would have been attracted to other fragments now instead escape outwards. However, since this all happens after most matter has disintegrated into expanding clouds due to mechanical stress there is not much to react with. Long molecules will likely find it energetically favorable to unwind rather than curl up, but again they do not have that much time to do it.

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