Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons.

Nicholas J Thornton,Tanja Van Mourik

doi:10.3390/ijms21186571

Nicholas J Thornton, Tanja Van Mourik

Open Access

https://doi.org/10.3390/ijms21186571

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Abstract

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).

Highlights

The last two decades have seen a huge upsurge in studies on halogen bonding, with overview articles and reviews appearing in the literature [1,2,3,4,5,6,7]
The study relates to scanning tunnelling microscopy (STM) experiments where guanine molecules were shown to form tetramer ring structures on a gold surface; these ring structures rearranged into ribbon-like structures when heated up [25]
The halogenated G-quartets display a range of halogen bond patterns

Summary

Introduction

The last two decades have seen a huge upsurge in studies on halogen bonding, with overview articles and reviews appearing in the literature [1,2,3,4,5,6,7]. A halogen bond is a type of σ-hole interaction, where a nucleophile interacts with the positively charged region (dubbed the σ-hole) at the extent of the R–X bond, where X is the halogen and R is typically C but can be another atom. Halogen bonding plays important roles in many aspects of chemistry and biology, including material science [9], molecular crystals [10], biological molecules [11], and molecular recognition [12] In 2020, a coupled experimental and computational approach identified a 1:1 adduct of Bu3POAtI as the strongest astatine-mediated halogen bond found so far [36]

Method Comparison

Ribbons R-I

Ribbons R-II

G-Quartets

Conclusions