scholarly journals Strength, character, and directionality of halogen bonds involving cationic halogen bond donors

2017 ◽  
Vol 203 ◽  
pp. 47-60 ◽  
Author(s):  
Kevin E. Riley ◽  
Khanh-An Tran

Halogen bonds involving cationic halogen bond donors and anionic halogen bond acceptors have recently been recognized as being important in stabilizing the crystal structures of many salts. Theoretical characterization of these types of interactions, most importantly in terms of their directionality, has been limited. Here we generate high-quality symmetry adapted perturbation theory potential energy curves of a H3N–CC–Br+⋯Cl− model system in order to characterize halogen bonds involving charged species, in terms of contributions from electrostatics, exchange, induction, and dispersion, with special emphasis on analyzing contributions that are most responsible for the directionality of these interactions. It is found that, as in the case of neutral halogen bonds, exchange forces are important contributors to the directionality of charged halogen bonds, however, it is also found that induction effects, which contribute little to the stability and directionality of neutral halogen bonds, play a large role in the directionality of halogen bonds involving charged species. Potential energy curves based on the ωB97X-D/def2-TZVP/C-PCM method, which includes an implicit solvation model in order to mimic the effects of the crystal medium, are produced for both the H3N–CC–Br+⋯Cl− model system and for the 4-bromoanilinium⋯Cl− dimer, which is based on the real 4-bromoanilinium chloride salt, whose crystal structure has been determined experimentally. It is found that, within a crystal-like medium, charged halogen bond are significantly weaker than in the gas phase, having optimum interaction energies up to approximately −20 kcal mol−1.

2020 ◽  
Vol 21 (18) ◽  
pp. 6571
Author(s):  
Nicholas J. Thornton ◽  
Tanja van Mourik

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°).


2017 ◽  
Vol 203 ◽  
pp. 333-346 ◽  
Author(s):  
Sebastiaan B. Hakkert ◽  
Jürgen Gräfenstein ◽  
Mate Erdelyi

We have studied the applicability of15N NMR spectroscopy in the characterization of the very weak halogen bonds of nonfluorinated halogen bond donors with a nitrogenous Lewis base in solution. The ability of the technique to detect the relative strength of iodine-, bromine- and chlorine-centered halogen bonds, as well as solvent and substituent effects was evaluated. Whereas computations on the DFT level indicate that15N NMR chemical shifts reflect the diamagnetic deshielding associated with the formation of a weak halogen bond, the experimentally observed chemical shift differences were on the edge of detectability due to the low molar fraction of halogen-bonded complexes in solution. The formation of the analogous yet stronger hydrogen bond of phenols have induced approximately ten times larger chemical shift changes, and could be detected and correlated to the electronic properties of substituents of the hydrogen bond donors. Overall,15N NMR is shown to be a suitable tool for the characterization of comparably strong secondary interactions in solution, but not sufficiently accurate for the detection of the formation of thermodynamically labile, weak halogen bonded complexes.


2018 ◽  
Vol 9 (20) ◽  
pp. 4555-4561 ◽  
Author(s):  
P. Cerreia Vioglio ◽  
P. M. J. Szell ◽  
M. R. Chierotti ◽  
R. Gobetto ◽  
D. L. Bryce

One- and two-dimensional bromine-79/81 NQR spectroscopy of halogen bond donors in a series of cocrystals shows changes in resonance frequency of up to 20 MHz and differentiates between crystallographically non-equivalent bromine sites.


2020 ◽  
Vol 48 (11) ◽  
pp. 5825-5838 ◽  
Author(s):  
Kanav Kalra ◽  
Suresh Gorle ◽  
Luigi Cavallo ◽  
Romina Oliva ◽  
Mohit Chawla

Abstract We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp–π) or the OH–π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1–3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp–π interaction as compared to the OH–π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp–π or the OH–π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.


2018 ◽  
Vol 17 (03) ◽  
pp. 285-288 ◽  
Author(s):  
Daniel Barranco ◽  
Violeta I. Simón-Porcar ◽  
Juan Arroyo

AbstractThe genusNarcissusL. (Amaryllidaceae) provides a model system to study the evolution and maintenance of sexual polymorphisms. In this study, we characterized microsatellite markers forN. dubius,N. cuatrecasasii,N. assoanusandN. rupicolafor studies of genetic diversity and paternity analyses to investigate the stability of stylar dimorphism. We proved 40 new primer pairs from a genomic library ofN. papyraceusand 12 microsatellite markers characterized also forN. papyraceusin a previous study (52 primer pairs overall). Twenty markers amplified, but their transferability and variability were different among species. Polymorphism was tested at least on 74 individuals and one population per species. The number of polymorphic loci per species ranged from four to eight. The number of alleles per locus ranged from two to 19 and the observed heterozygosity and gene diversity, from 0.107 to 0.729 and 0.103 to 0.894, respectively. These markers can be used for studies of genetic diversity and paternity analyses among individuals ofN. dubius,N. cuatrecasasii,N. assoanusandN. rupicolato study the stability of stylar dimorphism.


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