XRD and DFT-modelized structures of a pteridine-2,4(1H,3H)-dithione/N,N′-dimethylformamide H-bonded cluster (2:2). MO study of the coordination ability

Abstract

The title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molecules are packed via N-H···O and N-H···N hydrogen bonds into centrosymmetric clusters containing two molecules of each class; these are roughly planar and placed into two different sets of planes -both containing the [-1,0,2] direction- mutually angled by 77.8°. Despite the distance between two neighbor planes in each set is ca. 3.4 Å, the analysis of π,π-stacking interactions shows too large slippage distance between aromatic rings from contiguous planes. Additional σ-π interactions between S2, S4 and O1S atoms and pyrazine or pyrimidine rings from adjacent molecules are present. The structure for the cluster [DTLM-DMF](2) has been simulated by using the density functionals B1B95 (6-31 G(d) and 6-31+G(d) basis sets) and M06-2X (6-31 G(d) basis set). As a result, the M06-2X/6-31 G(d) approach provides the best agreement with the experimental XRD data. For a better evaluation of the intermolecular interactions, the superposition of two dimeric adducts [DTLM-DMF](2) has been modelized. The binding capability of DTLM ligand was simulated on systems containing two metal-binding modes to palladium (N5-S4 and N1-S2) with different chelate size. The analysis of the frontier orbitals points out that the link with the metallic centers will take place through the sulfur atoms.