With the advent of molecular beam and cryogenic experimental methods as well
as the ever advancing theoretical methods, HBs have been proved to exist in H 2 S as
well [74]. But things go even further. About a century later, chemists have identified a wealth of new bonding types along the periodic table. Halogen bonds
(XBs) (group 17) are frequently exploited for crystal engineering [75]. Recently,
similar bonding mechanisms have been proposed for adjacent main-group elements,
and non-covalent “chalcogen bonds” (group 16) [76] and “pnictogen bonds” (group
15) [77] have also been identified in crystal structures. Recently, even carbon
bonding (group 14) [78] has been proposed as a stabilizing interaction.
One of the most interesting features of NCI is that it is based on the density.
Thus, it is expected to be able to reveal any type of bonding. Before and beyond its
corresponding identification and characterization, the signature on the electron
density will be present. In the coming sections we briefly show some representatives of the new bonds series, highlighting the possibility to reveal interactions all
along the periodic table from just the fast analysis of NCI.
18.7.1 Halogen Bonding
Halogen bonds (XBs) occur between a halogen atom, playing the role of Lewis
acid, and a Lewis base. This non-covalent interaction is analog to hydrogen
bonding in the sense that in both cases, an atom or group of atoms with high
electron density donates charge to an acceptor which is electron poor. Similar to
HBs, XBs are also anisotropic and involved in various fields, such as
supramolecular chemistry or even materials chemistry. Moreover, halogenated
coumpounds are often encountered in medicinal chemistry [79] and drug discovery
[80]. Quantum Chemistry approaches have revealed a sigma-hole along the axis
defined by the halogen atom and the acceptor. This can be studied thanks to the
Molecular Electrostatic Potentials, showing the charge distribution as well as the
nature of the interaction as electrostatics and charge transfer driven.
We have analyzed NCI in a series of trifluoromethyl halides, CF 3 X, where
X = Cl, Br, I with dimethyl ether (DME), dimethyl sulfide (DMS), trimethyl
phosphine (TMP) and imidazolin-2-ylidene (NHC). All systems were optimized
using second-order Møller-Plesset perturbation theory with the aug-cc-pVDZ(-PP)
basis set [81]. The wavefunctions were obtained at DFT level using the B3LYP
functional and the 6-31++G** basis set except for iodine, where the pseudopotential LANL2DZ was used.
In the first four cases, the 2D plots (Fig. 18.8) clearly show a spike at very low
density, corresponding to a typical van der Waals interaction. In Fig. 18.8b, a
second spike arises, exhibiting non bonding interactions between the chlorine atom
and DMS hydrogens. They are closer to the halogen than the sulfide atom and
benefit from the high electron density at the halogen.
510
C. Narth et al.
as the ever advancing theoretical methods, HBs have been proved to exist in H 2 S as
well [74]. But things go even further. About a century later, chemists have identified a wealth of new bonding types along the periodic table. Halogen bonds
(XBs) (group 17) are frequently exploited for crystal engineering [75]. Recently,
similar bonding mechanisms have been proposed for adjacent main-group elements,
and non-covalent “chalcogen bonds” (group 16) [76] and “pnictogen bonds” (group
15) [77] have also been identified in crystal structures. Recently, even carbon
bonding (group 14) [78] has been proposed as a stabilizing interaction.
One of the most interesting features of NCI is that it is based on the density.
Thus, it is expected to be able to reveal any type of bonding. Before and beyond its
corresponding identification and characterization, the signature on the electron
density will be present. In the coming sections we briefly show some representatives of the new bonds series, highlighting the possibility to reveal interactions all
along the periodic table from just the fast analysis of NCI.
18.7.1 Halogen Bonding
Halogen bonds (XBs) occur between a halogen atom, playing the role of Lewis
acid, and a Lewis base. This non-covalent interaction is analog to hydrogen
bonding in the sense that in both cases, an atom or group of atoms with high
electron density donates charge to an acceptor which is electron poor. Similar to
HBs, XBs are also anisotropic and involved in various fields, such as
supramolecular chemistry or even materials chemistry. Moreover, halogenated
coumpounds are often encountered in medicinal chemistry [79] and drug discovery
[80]. Quantum Chemistry approaches have revealed a sigma-hole along the axis
defined by the halogen atom and the acceptor. This can be studied thanks to the
Molecular Electrostatic Potentials, showing the charge distribution as well as the
nature of the interaction as electrostatics and charge transfer driven.
We have analyzed NCI in a series of trifluoromethyl halides, CF 3 X, where
X = Cl, Br, I with dimethyl ether (DME), dimethyl sulfide (DMS), trimethyl
phosphine (TMP) and imidazolin-2-ylidene (NHC). All systems were optimized
using second-order Møller-Plesset perturbation theory with the aug-cc-pVDZ(-PP)
basis set [81]. The wavefunctions were obtained at DFT level using the B3LYP
functional and the 6-31++G** basis set except for iodine, where the pseudopotential LANL2DZ was used.
In the first four cases, the 2D plots (Fig. 18.8) clearly show a spike at very low
density, corresponding to a typical van der Waals interaction. In Fig. 18.8b, a
second spike arises, exhibiting non bonding interactions between the chlorine atom
and DMS hydrogens. They are closer to the halogen than the sulfide atom and
benefit from the high electron density at the halogen.
510
C. Narth et al.