An X-ray crystallographic study of the structure of some metal coordination compounds

PART. 1: The crystals of Ni(histidine)₂.H₂0 are composed of two kinds of complex: Ni(D histidine)₂ and Ni(L histidine)₂ related to each other by glide planes. Each histidine ligand is tridentate, and is co-ordinated to the nickel atom by the imidazole nitrogen(N₂) the "peptide" nitrogen (N₁) and a carboxyl oxygen(O₁). The bonds to Ni do not differ significantly in length, and agree with those quoted in literature. The co- ordination of Ni is very nearly regular octahedral. The two histidine ligands attached to Ni, are related by a two -fold axis passing through Ni, the two bulky imidazole rings being trans to one another, with O₁ and O'₁ cis and also N₁ and N'₁ cis. Comparison with the structures of the two histidine complexes [3,4] and histidine hydrochloride [14] shows a significant difference in histidine conformation, brought about by rotation about the C₃ -C₄ bond. Also the conformation along the N₁ -C₂ bond is not staggered as in other determinations, and this is probably due to the stronger binding of O₁ and the fewer degrees of freedom in the nickel complex. The "peptide group" is not planar, the nitrogen deviating by about .3 °A from the plane of the other atoms, as has been found elsewhere [4,14].The crystal, which is very stable, is held together by an intricate system of hydrogen bonds, with Van der Waals' contact between parallel imidazole rings. The single water molecule does not hydrogen-bond in such a way as to help in binding molecules together, but seems to fill a vacant space in the crystal.PART.2: DETERMINATION of the STRUCTURE of BIS(DIMETHYLDITHIOCARBAMATO) PYRIDINE ZINC. The doubt about the light atom positions in the Fourier refinement of the b -axis projection, showed that the data was not good enough to be able to locate them with sufficient accuracy. The analysis could have been carried into three dimensions, but there would still be inaccuracies in the light atom parameters due to the weakness or absence of the high order reflections. So attempts were made to recrystallise the complex. It was noticed at once that on recrystallising from a large excess of benzene, fine needles were obtained that gave good X -Ray photographs. The analysis of the b -axis projection was therefore abandoned.Few conclusions of any interest can be drawn from this analysis itself. However comparison with the projection down the molecular two -fold axis of the complex (see Fig. 18) reveals some interesting points: -(i) The b -axis Patterson and Fourier (Figs. 9 and 10) show quite a good agreement with the final structure, as determined in the crystals with benzene of crystallisation. The heavy atom positions agree well, but some of the light atom peaks, especially C7 and C8, are slightly off their expected positions. But there can be no doubt that in these crystals the molecular two -fold axis lies parallel or very nearly parallel to the b -axis. There is only one significant difference - the orientation of the pyridine ring. Both the Patterson and the Fourier indicate that the pyridine plane passes between Si and S2, an orientation about 90° from that in the crystals with benzene of crystallisation.(ii) The final analysis shows that the complex can probably possess exact two -fold symmetry in solution, although it does not in the crystals with benzene of crystallisation. It is very likely therefore that it will crystallise on a crystallographic two -fold axis whenever possible. This isstrong evidence for C2 /c as opposed to Cc. However it does not constitute proof. There is still the possibility, however unlikely, that the true space group is Cc. The two space groups are closely related. If objects of two -fold symmetry are placed in space group Cc with their axes parallel to b, the symmetry is transformed to that of C2 /c. It is clear that if the objects are not exactly symmetric, the symmetry cannot be exactly C 2 /c, although it must closely resemble it. Undoubtedly the symmetry of these crystals is very near to C 2 /c, but this cannot be taken as proof that the complex possesses an accurate two-fold axis.There does not seem to be any method capable of distinguishing the two space groups in a case like this. The statistical test of intensities would certainly indicate a centrosymmetric structure.(iii) Packing. The structure consists of sheets of molecules perpendicular to the c -axis. One sheet is related to the next by the c glide, but due to lack of knowledge of the y co- ordinates, the interactions of one sheet with the next cannot be described in detail. However it can be said that their methyl groups are in contact, and one sheet "lies" on the methyl groups of its neighbour.The packing within a sheet is of course face centred. The distance from C3 of pyridine to Zn along y is 4.1 5, and the pyridines therefore fit into the "pocket" of sulphur atoms of the molecule next along the y axis. Each pyridine probably has two contacts with methyl groups of C face -centred neighbours, one on either side. There are no pyridine -pyridine contacts as in the crystals with the benzene of crystallisation. This packing arrangement is consistent with the orientation of the pyridine ring.PART3: DETERMINATION OF THE STRUCTURE OF BIS(DIMETHYLDITHIOCARBAMATO) PYRIpINE ZINC WITH BENZENE OF CRYSTALLISATION The complex (PZDC) is a 5- coordinate zinc complex with a distorted trigonal bipyramidal configuration. The two axial Zn -S bonds average 2.60 °A, with the two equatorial Zn -S bonds, 2.33 °A and Zn -N₁ 2.08 °A The equatorial bonds are of normal length, but the two axial bonds are considerably longer than usual. This is probably due to a combination of electron pair repulsions, and a weakening of the axial Zn -S bonds due to the coordination of pyridine. The mean N-C bond length in the dithiocarbamate groups is 1.338 °A , which is very similar to the lengths found in all other dithiocarbamate complexes, and indicates about 84% double bond character. This agrees with the experiments of Chatt et al [69] and is further evidence against the theories of Kerk et al [68]. Both the Zn -S and the N-C bond lengths show that the electron shift scheme for amine coordination proposed by Higgins and Saville, must be revised. The coordination of an amine appears to affect only two of the four Zn -S bonds, and has no effect on the N -C bond.In agreement with other determinations, the dimethyldithiocarbamate groups are both planar and the bond lengths and angles are all normal. Zn, however, lies slightly out of the plane of both ligands, and its position is different relative to each. The Me N Me angle is slightly less than 120° as has been found also by Vaciago et al [63]. This is probably due to repulsion of the methyl groups by the sulphurs.There is an approximate two-fold axis through Zn, N₁ and C₃, but the axis of the pyridine ring deviates by 4° from the axis of the rest of the molecule. This is caused by Van der Waal's contacts in the crystal. The difference in the deviations of Zn from the dithiocarbamate planes may be connected with this. It is very probable that the complex can assume accurate two -fold symmetry in solution. The orientation of pyridine is obviously largely dependent on intermolecular forces, since it is different in the crystals without benzene of crystallisation.The crystals with benzene of crystallisation, consist of two types of complex, D and L. The packing is rather irregular, and there are some large empty spaces especially between benzene molecules along the y-axis