# Potential Energy between molecules

## Homework Statement

The two sides of the DNA double helix are connected by pairs of bases (adenine, thymine, cytosine, and guanine). Because of the geometric shape of these molecules, adenine bonds with thymine and cytosine bonds with guanine. The figure shows the thymine–adenine bond. Each charge shown is +/- e and the H-N distance is 0.110 nm.

http://imageshack.us/photo/my-images/41/236ir.jpg/

1)
Calculate the electric potential energy of the adenine–thymine bond. To keep the calculations fairly simple, yet reasonable, consider only the electric field due to the and the combinations, assuming that these two combinations are parallel to each other. Remember, however, that in the set, the exerts a force on both the and the and likewise along the set.

2)
Compare this energy with the potential energy of the proton–electron pair in the hydrogen atom. The electron in the hydrogen atom is 0.0529 from the proton.

## The Attempt at a Solution

So for part 1, U=kq1q2/r

But what do I take the potential energy of? Every combination of the 6 charges? How do I know what r is in between the OHN and NHN? I know the distances between charges for each charge in OHN, and for each charge in NHN, but not between the two.

For part 2, I have less of a clue because it requires using the answer to part 1 (answer to part 1 divided by U_hydrogen)

So for the potential energy of hydrogen, I assume I use +q and -q as the two charges, and 0.0529nm as r?

I've already done all the other HW problems because they were straightforward, but when they throw chemistry into the mix I get confused...