It say's something if I have to do "research" on Gwen, when I couldn't be satisfied with what I saw on Torchwood. But I'll give it a shot.

The term "chemistry" can be viewed in different way's. With Jack and Martha, their chemistry is related to getting close "emotionally" during "The Year That Never Was". That and feeling second best to Rose in the eye's of the Tenth Doctor.

I wouldn't expect them to go as far as sleeping together. Jack got all coy when Martha kissed him. He probably had an imagine of Ten saying:"Don't!", in his head.

Jack also had a nickname for Martha, which is usually what someone doe's to express affection towards the one they care about.