Dear Takeshi Shimizu thank you for this very interesting technical question. Even though the synthetic methods for preparing different but very similar MOFs may be exactly the same, they do not necessarily have the same crystal structures. The presence or absence of a polar functional group such as –OH or –NH2 can make a big difference. If you have one of these substituents present in the linker or other ligands in the MOF, there is the possibility of forming hydrogen-bonding interactions with other functional groups. This can easily lead to a different crystal structure.

For more information please see e.g. this very instructive research article entitled

Distinguishing Metal−Organic Frameworks

Article Distinguishing Metal–Organic Frameworks

Fortunately this article is freely available as public full text on ResearchGate and can be downloaded as pdf file. In this paper it is stated that "By changing a metal type or substituting the functional group of an organic linker, one can in principle systematically change the properties of a known MOF."

This is, however, not a general rule. Other MOFs can perhaps be isostructural even when different substituents are present. Thus you cannot make any predictions. In each case the crystal structures need to be determined individually. For more general information about this topic please also have a look at this rather interesting article entitled

Crystallography of metal–organic frameworks

Article Crystallography of metal–organic frameworks

This paper is also freely available as public full text on RG.

Stay safe and healthy! 😊