What are you trying to achieve with this image? It looks pretty over the top for my tastes and you've got a dark sky with very vibrant foliage and building, alongside a radioactive bridge. If you were going for a surreal look you definately achieved it, but even still I feel that the sky sets the mood and the bridge and trees run counter to the mood of the sky. Just my .02 cents.
Just wanted to chip in on why the clouds appear dark. Its because the clouds are darker than the water and this makes the lighting in the photo impossible. With the super bright highlights on the concrete pilings, there's a mismatch thats upsetting.
You're very close to getting that surreal HDR look that works, but it'll need a bit more fine tuning.