I've been trying to construct a smooth diffeomorphism between non-smooth manifolds. Unfortunately I don't think I know enough manifolds well enough to find an example of this.
Mostly I've been looking at potential diffeomorphisms between $(\mathbb{R},A_1)$ and $(\mathbb{R},A_2)$, with $A_1$ and $A_2$ non-smooth atlases for $\mathbb{R}$. Is it possible to construct this? Or can it be proven that if two manifolds are smooth-diffeomorphic, then the manifolds themselves must be smooth?
The word "(smooth) diffeomorphism" is meaningless unless you're talking about smooth manifolds. If all you have is a pair of topological manifolds $M$ and $N$, it is not meaningful to say a map $f:M\to N$ is a diffeomorphism. To say $f$ is a diffeomorphism, you need to be able to say that $f$ and $f^{-1}$ are smooth, but you can't define this without a smooth structure on $M$ and $N$. It's like trying to define a ring-homomorphism between two groups.