, Volume 42, Issue 3, pp 245-250,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 30 Nov 2011

Ordering of the Water Molecule in the Crystal Structure of 2-[3-Methyl-4-(2,2,2-Trifluoroethoxy)-2-Pyridinyl]Methylthio-1H-Benzimidazole Hydrate (Lansoprazole Sulphide Hydrate)


Lansoprazole sulphide (2-[3-methyl-4-(2,2,2-trifluoroethoxy)-2-pyridinyl]methylthio-1H-benzimidazole) hydrate crystallizes in the triclinic space group P-1 with two molecules in the asymmetric part of the unit cell. The molecules are almost identical, the normal probability plots show that the differences between them are of statistical nature. The crystal structure is determined mainly by the O–H···N and N–H···O hydrogen bonds; and both symmetry independent molecules create the hydrogen-bonded structures on their own. The common motif is the C 2 2 (6) chain of molecules along x (A) or y (B), but the interactions between the chains are different: chains of molecules A are joined by O–H···N(pyridine) hydrogen bonds while those of molecules B– by relatively strong O–H···S hydrogen bonds. Additionally, in both cases there are also C–H···S, C–H···π and π–π interactions between the neighbouring molecules. The different intermolecular interactions might be connected with the observed disorder of water molecules in the B-chains. At room temperature the s.o.f.’s of two alternative positions refined at 0.760(17) and 0.240(17). The less-occupied water molecule does not take part in the O–H···S hydrogen bonding. When temperature decreases the importance of this interaction grows, the occupancy of less occupied position becomes smaller and finally, around 150 K the structure becomes fully ordered.

Graphical Abstract

[One of the water molecule is disordered at room temperature, but when temperature decreases the structure becomes fully ordered around 150 K.]

Room-temperature crystal structure of this compound has been recently briefly reported: Ren G-B, Hong M-H, Zhong J-L, Yi D-X, Xu L–H (2011) Acta Cryst. E67:o270.