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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

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Abstract

The title compound, C6H4N4S2·C3H7NO, 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.

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Acknowledgments

Thanks are due to “Plan de Apoyo a la Investigación, al Desarrollo Tecnológico y a la Innovación” of the University of Jaén (project RFC/PP2008/UJA-08-16-08) and Junta de Andalucía (FQM-273) for financial support. Also, the “Centro Informático Científico de Andalucía” (CICA) is acknowledged for computational facilities.

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Authors and Affiliations

  1. Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071, Jaén, Spain

    Nuria A. Illán-Cabeza & Miguel N. Moreno-Carretero

  2. Departamento de Química Física y Analítica, Universidad de Jaén, 23071, Jaén, Spain

    Tomás Peña-Ruiz

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  1. Nuria A. Illán-Cabeza
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  2. Tomás Peña-Ruiz
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  3. Miguel N. Moreno-Carretero
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Correspondence to Miguel N. Moreno-Carretero.

Electronic supplementary material

CCDC-756140 contains the full crystal data for the reported XRD structure. These data can be obtained free of charge at the Cambridge Crystallographic Data Centre CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK (fax: +44-1233-336-033; e-mail: deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.ac.uk/conts/retrieving.html).

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Illán-Cabeza, N.A., Peña-Ruiz, T. & Moreno-Carretero, M.N. 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. J Mol Model 18, 815–824 (2012). https://doi.org/10.1007/s00894-011-1109-1

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  • DOI: https://doi.org/10.1007/s00894-011-1109-1

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