Of course, there will be chemical reactions, in terms of the response to physical senses, of the decisions that go out to the body ('close your eyes' etc) or simply thoughts. There is no conflict. What you are assuming, however, is that we are simply and only a machine. The Christian would argue that there is a soul which controls the machine - the chemical reactions are the servants, not the authors.
Of course, then the whole matter becomes impossible to prove - the existence of the soul, blah blah.
Read those. There are FAR more, and as with pretty much any verse, they can be quoted out of context - out of context of verses alongside, out of context of chapter, out of context of book. Is such a common source of mistaken belief in biblical contradiction.Interestingly, free will is not a very biblical idea, see here for a list of bible quotes about free will - two suggest we do have free will and eight suggest we don't.
ALL those misunderstandings can be solved
And as closing note - I'll read the pages of thread I missed, tomorrow - free will is shown so clearly right in Genesis. It doesn't have to be written out as formally as a scientific thesis.