On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective

Abstract

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.

Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations

“…Chalcogen bonds have been defined as the attractive NCIs between an electrophilic region related to a covalent-bonded group VI atom (O, S, Se, Te) and a nucleophilic region within the same or another molecular entity [ 29 ]. In recent years, ChBs have garnered considerable attention from theoreticians and experimentalists owing to their important contributions to crystal engineering [ 30 , 31 ], molecular recognition [ 17 , 32 ], organocatalysis [ 33 , 34 ], drug design [ 6 , 35 ], materials science [ 36 , 37 ], and biological systems [ 13 , 38 , 39 ]. ChBs belong not only to a subclass of σ–hole interactions but also to a subclass of π–hole interactions [ 40 , 41 ].…”

Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te)

“…Gleiter and colleagues [42,43] theoretically studied the binary complexes of CH 3 YCH 3 and CH 3 YZ (Y = S, Se, Te; Z = CH 3 , CN), and symmetry-adapted perturbation theory (SAPT) analysis demonstrated that dispersion and induction forces are responsible for the formation of chalcogen•••chalcogen interactions. Additionally, statistical analyses of crystal structure surveys have also shown that there is a great number of chalcogen•••chalcogen interactions in small molecules, nucleic acids, proteins, and protein-ligand complexes [33,35,36,[44][45][46][47], further suggesting the importance of such chalcogen•••chalcogen interactions.…”

“…Currently, the vast majority of investigations concerning ChBs focus on the divalent chalcogen atoms as the ChB donors [18,[27][28][29][30][31][32][33][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50]. However, the chalcogen atoms can also frequently participate in hypervalent bonding such as tetravalent bonding [21,[51][52][53].…”