This is kind of more on the mathematics side of quantum chemistry, but I can't quite figure out why the Lowdin Orthogonalization is called a basis set change. I get how it works from the perspective of matrices, and that it creates an orthonormal set as long as you have linearly independent input, but I don't get why it works as a change of basis.
Typically to change the basis set of a matrix $M$ you use a non-singular linear transformation $A$, which need not be unitary, as such: $$M'=A^{-1}MA.$$ Quantum mechanics, we are dealing with Hilbert Spaces, which produce an isometry between the Hilbert space and the dual (I think?), and then for post HF methods most methods often use unitary transformations, so that $A^\dagger=A^{-1}$, and so it becomes trivial.
The Lowdin transformation between nonorthogonal AO $|\phi\rangle$ and orthogonal AO $|\phi\rangle_\perp$ involves the overlap matrix $S$ as: $$ |\phi \rangle_\perp = S^{-\frac{1}{2}}|\phi\rangle $$ Then, the corresponding bra just has the adjoint, which is also $S^{\frac{-1}{2}}$ because the matrix is self-adjoint: $$ \langle \phi|_\perp = \langle \phi|(S^{-\frac{1}{2}})^\dagger = \langle \phi|S^{-\frac{1}{2}}$$
But, considering the matrix analog, why don't we use the inverse?
For instance, we have the identity: $$ D^{AO} = C D^{MO}C^T $$ where $D$ is the 1-electron reduced density matrix. In my thinking this has to be a transformation from the MO to the AO on the right of $D^{MO}$, and from the AO to the MO on the left, which gives you $D^{AO}$. However, $C$ is not unitary obviously, because it comes from the Lowdin procedure, and so while $C$ on the left is from the AO to the MO, $C^{-1}$ is not equivalent to $C^T$.
Furthermore to get $D^{MO}$ matrix in terms of the $D^{AO}$ you DO have to apply the inverse relationship with $C^{-1}$. $$D^{MO} = C^{-1}D^{AO}(C^T)^{-1},$$ because $C^{-1}$ and $C$ and related non-trivially through $S$.
Hopefully this is appropriate to ask here. I think the answer involves Hilbert spaces but I can't find a lot on non-orthogonal transformations. Thanks!