With the disclaimer that I'm neither a tech writer or tech editor:
Scientific and academic books are generally organized by function. Unlike a narrative book where the chapters are broken down by feel or by narrative rhythm, a scientific or academic book has a certain amount of material to cover, and it makes logical sense to divide the book according to those functional guidelines. In this case you have two functional areas: Isolation of natural products, and biological function of natural products.
However, I understand your hesitation. Having only two chapters does feel a little strange.
Will those two chapters subdivide in any way? Is there any structure within these two chapters? If so, perhaps you can divide the book into two parts instead, and subdivide the parts into chapters. Just take care not to have insanely short "chapters" or you risk making the book seem fragmented.
I'd also check MLA or APA (or whatever style guide you're using) for advice about chapterization. I know that the Chicago Manual of Style addresses these issues, perhaps these academically-oriented style manuals do as well.