Dear Sara Ahmadi,

Sometimes you cannot find covalent bonds because they are longer than single covalent (or dative) bonds but shorter than van der Waals distances. These sorts of bonds are called secondary bonds. A secondary bond is defined as intra/intermolecular interactions between the metal center and another atom (X–A⋯X′ in which A: Hg, Tl, Sn, Pb, Sb, Bi, Se, Te, etc., and X = or ≠X′).

Although the secondary bonds are normally weaker than covalent bonds, they are strong enough to play a determinant role in the structure of even simple inorganic molecules and ions. Besides, the secondary bond formation increases the coordination number and distortions of the coordination geometries. For further information about this bond please read the following references:

(a) J. L. Atwood and J. W. Steed, Encyclopaedia of Supramolecular Chemistry, CRC Press, Taylor & Francis Group, vol. I, 2004.

(b) V. Singh, A. Kumar, R. Prasad, G. Rajput, M. G. B. Drew, and N. Singh, CrystEngComm, 2011, 13, 6817–6826.

Now for your first question:

Open your structure with Mercury software and increase sum of the vdw radii in short contact menu (increase it from 0.2 to 0.5 Angestrom). Then you can see some extra interactions around Mercury (in case there is any of them). These interactions indeed are secondary bonds. Please note that they should be atoms with the ability of coordination not those with the ability of only interaction.

For your second and third questions it is better to follow this instruction:

The calculation should be based on M06-2X as a DFT-D3 dispersion corrected method with 6-311G (d, p) (for light atoms of C, H, O, N) and lanl2dz (for heavy atoms of Hg, Cl, Br, I) basis sets.

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