Structural flexibility is a unique property of some metal-organic frameworks (MOFs) that clearly distinguishes them from other inorganic porous materials, such as zeolite and porous silica. A MIL-53(Al), the most well-known flexible metal-organic framework (MOF), leads to dynamic changes as closed pore transitions to open pore, also called ‘breathing’ phenomenon. During the flexible and reversible transition, the pore apertures are continuously adjusted, thus providing the tremendous opportunity to separate mixtures of hydrogen isotope that require precise pore tuning. Recently, we have observed a perculiar 2nd breathing mode only under specific condition in MIL-53, thus here we propose to perform a neutron diffraction study on E9 to investigate exact adsorption sites of hydrogen isotopes at different pressures and find out a possible structural origin of the second breathing mode.