A Study of π–π Stacking Interactions and Aromaticity in Polycyclic Aromatic Hydrocarbon/Nucleobase Complexes

Abstract

We analysed the interactions and aromaticity electron-density delocalisation observed in π-π complexes between the phenalenyl radical and acenaphthylene, and the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine and uracil). Interaction energies are obtained at the M06-2X/6-311++G(2df,p) computational level for gas phase and PCM-water conditions. For both the phenalenyl radical and acenaphthylene, the complexes formed with guanine are the most stable ones. Atoms in molecules and natural bond orbital results reveal weak π-π interactions between both interacting moieties, characterized by bond critical points between C⋅⋅⋅C and C⋅⋅⋅N atoms. Nucleus independent chemical shifts (NICS) indicate the retention of the aromatic character of the monomers in the outer region of the complex. The fluctuation indexes reveal a loss of electron delocalisation upon complexation for all cases except guanine complexes. Nevertheless, the interface region shows large negative NICS values, which is not associated with an increase of the aromaticity or electron-density delocalisation, but with magnetic couplings of both molecules, leading to an unrealistic description of the aromatic behaviour in that region.

Interactions between temozolomide and guanine and its S and Se-substituted analogues

“…The importance of p-p stacking has been recognized for some time [86][87][88][89][90][91][92] . As a recent example, an examination of such forces [89] included a variety of nucleobases combined with acenapthalene and phenalenyl radical that both contain extended aromatic systems. Geometries adopted were of the stacked variety, forgoing any HBs that might otherwise be formed with the latter p-systems.…”

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

“…Aromaticity indexes have described the aromatic character of nucleobases to decrease in the order of A > G ≥ C > T ≥ U . A, C , and G are described as aromatic systems, while T and U are almost nonaromatic systems; even solvent effects appear to cause negligible changes in the aromatic character of nucleobases . Umadevi and Sastry analyzed the physisorption of nucleobases onto carbon nanomaterials, computing also the its aromatic character from magnetic properties through the nucleus‐independent chemical shifts (NICS) model .…”

“…However, minor efforts have been devoted to understanding the effects of physisorption into the aromatic character of the adsorbed nucleobases, in addition to its role in the physisorption strength. Aromaticity indexes have described the aromatic character of nucleobases to decrease in the order of A > G ≥ C > T ≥ U . A, C , and G are described as aromatic systems, while T and U are almost nonaromatic systems; even solvent effects appear to cause negligible changes in the aromatic character of nucleobases .…”

“…Taking into account that the geometric/electronic structure of nucleobases is weakly affected by binding on graphene, the conclusion about the aromaticity of nucleobases on graphene could be overestimated as obtained from NICS, and it should be clarified yet. Furthermore, theoretical analyses showed that the aromaticity is badly described by NICS in π−π complexes of nucleobases with acenaphthylene and phenalyl radical, which is not associated with the increase/decrease of aromaticity . In addition, NICS is a local descriptor of aromaticity, hence, cannot describe the current density in a clear picture and does not correlate with other indices of aromaticity .…”

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

“…The hydrogen [1,2], halogen [3][4][5][6][7][8][9][10], chalcogen [11][12][13][14][15][16][17][18][19][20][21][22][23][24], pnictogen [25][26][27][28][29][30][31], tetrel [32] bonding, stacking [33][34][35][36][37], cation/anion-π [38][39][40][41][42], and metallophilic interactions [43][44][45] play key roles in many chemical, physical, and biochemical processes, due to their ability to control structures and properties of associates and supramolecular systems.…”