Im looking for a tool to help design the structure of a website to be built. I want to be able to clearly communicate what will be contained in the site when it is finished with the use of diagrams.
I am not too sure what you mean, if you mean the actual design implementation you could use something like dreamweaver. If you mean actually designing your website, prototypes are generally done one paper since they are easiest and you can test it easily with users. However I believe there is prototyping software available, google will be your friend here.