We report here on the solvothermal synthesis and crystal structure of the hybrid organic-inorganic framework material Al(2)[O(3)PC(3)H(6)PO(3)](H(2)O)(2)F(2).H(2)O (orthorhombic, Pmmn, a = 12.0591(2) A, b = 19.1647(5) A, c = 4.91142(7) A, Z = 4), the second member of the Al(2)[O(3)PC(n)H(2n)PO(3)](H(2)O)(2)F(2).H(2)O series. The structure consists of corrugated chains of corner-sharing AlO(4)F(2) octahedra in which alternating AlO(4)F(2) octahedra contain two fluorine atoms in a trans or a cis configuration. The diphosphonate groups link the chains together through Al-O-P-O-Al bridges and through the propylene groups to form a three-dimensional framework structure containing a one-dimensional channel system. The linkage of the corrugated inorganic Al-O-P layers within the structure results in the formation of two types of channel that differ in size, shape and composition. The smaller channel is unoccupied; the larger channel is more elongated and contains two extra-framework water molecules per unit cell. A computational investigation into the driving force that controls the stacking arrangement of the Al-O-P inorganic layers within this series of compounds reveals that the stacking is found to be controlled by thermodynamic factors, arising chiefly from the conformation of the organic linker molecule used to connect the inorganic sheets. It is found that the registration of the inorganic layers can be engineered by selecting an appropriate, simple organic spacer or linker alkyl chain, where an even number of carbon atoms in the alkyl chain directs formation of aligned, stacked, inorganic sheets (AAAAAA), and an odd number directs formation of unaligned, stacked sheets (ABABAB) and the formation of one or two channel types in the resultant structure, respectively. This combination of alkyl-chain linkers in conjunction with corrugated inorganic layers is an effective tool to rationally design the pore system of hybrid framework materials.