Synthesis,crystal structure and DFT calculations of a new Hg (II) metal-organic polymer

2.1 Materials and experimental techniques

All reagents for the synthesis and analysis were commercially available and used as received. Microanalyses were carried out using a Heraeus CHN-O-Rapid analyzer. Melting points were measured on an Electro thermal 9100 apparatus and are uncorrected.IR spectra were recorded using Perkin-Elmer 597 and Nicolet 510P spectrophotometers.

2.2 Synthesis

2.3 X-ray crystallography

Single crystal X-ray diffraction data were obtained with a Gemini four circle diffractometer manufactured by Oxford Diffraction equipped with an Atlas CCD detector, using graphite a monochromator and Mo Ka radiation (λ= 0.71073 A°). Standard data collection strategy of CrysAlis [30] was used for data collection; the same program was used for integration of CCD images and absorption correction. The crystal structure was solved by direct methods with program SIR2002 [31] and refined with Jana2006 [32] by full-matrix least-squares technique on F². Crystallographic data and details of the data collection and structure refinement are listed in Table 1. The calculated structure factors and full lists of bond distances, bond angles and torsion angles are given in the supplementary data. X-ray crystal structure is shown in Fig. 1.

2.4 Computational details

The geometry of 1 has been optimized using the B3LYP density functional model. In these calculations the 3–21G* basis set was used for C and H atoms, while the 6–31G* basis set was used for N and O, atoms. For the Hg and I atoms, the LanL2DZ valence and effective core potential functions were used. All DFT calculations were performed using the Gaussian 98 R-A.9 package [33–37]. X-ray structures were used as input geometries when available.

3.1 Infrared spectra

The IR spectra display characteristic absorption bands for compound. For 1, the absorption band at 3084.51 (cm^–1) are due to the C–H modes involving the aromatic ring hydrogen atoms [38]. The C–H modes involving the aliphatic hydrogen atoms of ligand L in compound 1 reveal around 2923.36 (cm^–1) [39]. The absorption bands with variable intensity in the frequency range 1449.47–1502.22 (cm^–1) correspond to ring vibrations of the pyridine moiety of the ligand [40–48].

3.2 Crystal structure

Single crystals of 1 were obtained by the reactions of mercury (II) iodide with the ligand L under thermal gradient conditions using the branch-tube method. After 3 days, X-ray quality crystals of {2[Hg(L)I₂](HgI₂)}n (1) were obtained. Structural analysis by single crystal X-ray diffraction revealed that 1 crystallizes in the monoclinic system with space group P 1 21/n1(Fig. 1) and showed that the compound in the solid state, consist of two distinct linear one dimensional polymer chains, which will be denoted as parts A and B. In part A with formula 2[Hg(I)₂]_n, the Hg (II) centers is chelated by two iodide atoms with distances of Hg₁ ...  I₁(2.636 Å) and two iodide atoms with distances of Hg₁ ...  I₁(3.368 Å). Coordination number for Hg₁ centers is four with a HgI₄ chromophore and the Hg (II) ions are in a distorted square planar geometry. Each ring of (HgI₂)_n polymeric chain is lozenge symmetry form (Fig. 2) and the two I₁-Hg₁-I’₁ angles have opened up to 90.92°, respectively and the two Hg₁-I₁- Hg₁ angles have reduced to 89.08° indicating a little distortion from a regular square planar but the sum of angels around the metal center is 360.0° that shows geometry is quite planar (Fig. 1).

In part B with formula 2[Hg(L)I₂]_n, single crystal analysis revealed a Hg (II) polynuclear complex forming linear one dimensional polymeric chain along a axis (Fig. 2) with Hg ...  Hg separation 4.243  Å. In this structure only one of the pyridine, but not the imines nitrogen atoms of the ligand L with distance of Hg₂ ...  N₄ (2.371 Å) is linked to each mercury atom, one iodide atom is terminally coordinated to the mercury atoms with distance of Hg₂ ...  I₃ (2.624 Å) and are not bridging and two iodide atoms with distances of Hg₂ ...  I₂ (2.641 Å) and (3.364 Å) are as a bridge to form a one-dimensional polymeric chain along to the a direction (Fig. 2). Coordination number for Hg₂ centers is four (one pyridyl nitrogen atom and three iodide atoms) with the distorted tetrahedral geometry. The angles around the Hg₂ center deviate significantly from 109.4° that indicating distortion from regular tetrahedral (for more information about the bonds distances and angles see Table.3). Thus we find both form of coordination number of four square planar and tetrahedral in this polymeric compound. The Hg ...  Hg separation in part A and B is 4.243 Å. The individual 1D chains are parallel to each other and further linked by O₁ ...  H hydrogen bonds with bonds distances of O₁ ...  H_8b of 2.686 Å, O₁ ...  H_8c of 2.299Å and O₁ ...  H₂N₂ of 2.188 Å (Fig. 3). Compound 1 also exhibits weak CH ...  I₁ hydrogen bonds with bonds distances of C₁H₁ ...  I₁ of 3.129 Å and C₅H₅ ...  I₁ of 3.110 Å and intermolecular interaction between nitrogen from pyridine ring with Hg₁ atoms with bond distance of N₁ ...  Hg₁ of 2.870 Å Fig. 4. The details about the hydrogen bonds are summarized in Table 2. Whereas O₁ ...  H_8b, O₁ ...  H_8c and O₁ ...  H₂N₂ interconnect only crystallographic equivalent parts of type B, the remaining hydrogen bonds (C₁H₁ ...  I₁ and C₅H₅ ...  I₁) are interaction involving between parts A and B. A search was made for π... π stacking interactions in the complex, revealed that in the crystal packing of complex, the interplanar distance between L rings is 4.243 Å, The Parallel arrays of the planes of the aromatic moieties in the complex indicate that these interactions are of the slipped face-to-face stacking types. Also there is a strong C–H ... π stacking interaction named C₈–H_8a ... π, with a separation of 3.404 Å between the hydrogen atoms of the methyl with the pyridyl ring of the adjacent unit (Fig. 5). Thus compound 1 expands the 1D polymeric chains into 3D coordination compound via these intermolecular interactions. Consequently, the strong Hg–N, hydrogen bonding, π–π and C–H ... π stacking interactions may control the coordination sphere of mercury (II) ion in this complex.

3.3 DFT calculations

The calculated structural parameters are listed in Table 3. It should be noted that the experimental data belong to the solid phase, whereas the calculated data correspond to the isolated molecule in gas-phase. However, the experimental and computational data in Table 3 clearly show that both data only slightly differ from each other. For example, the largest difference between experimental and calculated Hg2-N4 length is about 0.027. As a result, the calculated geometrical parameters represent a good approximation. The computed IR frequencies are listed in Table 4 together with the experimentally determined frequencies. The assignment of the experimental ν(Hg–I) vibration is based on the theoretically calculated frequencies. Both calculated and experimental frequencies are found to be in agreement. The NBO charges of Hg(II) and the coordinated atoms were also calculated. The positive charge of the Hg(II) ions was 0.897 and 0637. The charges of the aliphatic N and O atoms of the ligands were –0.377, –0.305 and –0.607. The charges of aromatic N atoms of ligands were 0.585 and –0.510 while the iodide anions have charges between –0.320 ––0.509. The calculations indicate that complex 1 has 102 occupied molecular orbitals (MOs) for the per unit. The value of the energy separation between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) was calculated. Figure 6 shows the HOMO and LUMO for the Hg(II) complex. As will be seen in Fig. 1, the HOMO is principally localized among two aromatic carbon of ligand, whereas the LUMO is delocalized approximately on another aromatic carbon and nitrogen atoms of the ligand. The calculated HOMO–LUMO gap is 0.093 a.u.