As part of our program in understanding hydrogen bonding systems, exploiting crystal engineering in our synthesis of complexes containing desired HB motifs, we investigate hydrogen bonded base-pairing of nucleic acid bases and pseudo-base-pairing with related planar moieties, currently focusing on investigating the effect of fluorination on the HB geometry. The 1:1 molecular complex 5-fluorocytosine: 3,5-dinitrobenzoic acid exhibits base pairing between cytosine molecules, but unusually, the cytosine molecule is only half protonated. The 3,5-DNBA is also half protonated and forms a dimer. Both hydrogen bonded systems could be described by a single minimum centred H atom or by a disordered double minimum hydrogen bond, but X-ray diffraction does not resolve this subtlety. Neutron diffraction is thus required to resolve fully the subtle behaviour of these H bonded systems.