The effects of cation–π and anion–π interactions on halogen bonds in the [N⋯X⋯N]+ complexes: A comprehensive theoretical study

Razmazma, Hafez; Ebrahimi, Ali

doi:10.1016/j.jmgm.2018.06.006

Cited by 14 publications

(10 citation statements)

References 50 publications

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“…3). The three-center bond of halonium ions has been computationally thoroughly assessed, 8,[12][13][14][15][16] and concluded to be dominantly of covalent and electrostatic characteristics, with a smaller contribution from dispersion forces. The origin of the covalency is charge transfer, whereas the electrostatic characteristic is the result of Coulomb attraction and polarization.…”

Section: The Nature Of Halonium Ions' Halogen Bondsmentioning

confidence: 99%

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Halogen bonds of halonium ions

2020

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Section: The Nature Of Halonium Ions' Halogen Bondsmentioning

confidence: 99%

“…The above conclusions on the substituent effect were confirmed by an independent theoretical investigation. 14,15 In an analogous study, 29 the halogen position within a [D-X-D] + bond was assessed using pyridine complexes of N-halosuccinimides and N-halosaccharins ( Fig. 10b-e).…”

Section: Bond Symmetrymentioning

confidence: 99%

Halogen bonds of halonium ions

2020

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“…The strong, three-center halogen bond of halonium ions has been repeatedly reviewed from an experimental perspective; ,, however, in contrast, its computational treatment has so far received less attention. Apart from scarce examples of entirely theoretical studies, , most investigations analyzing three-center halogen bonds used DFT predominantly to support the interpretation of experimental data, most often of NMR chemical shifts obtained in solutions. ,− ,, In the past decade, diverse computational methods (DFT functionals and basis sets) have been used, however, without giving any guidance on or evaluation of the applied methods’ accuracy regarding the computed spectroscopic parameters or the geometry and the energy of such complexes. − ,− The DFT description of three-center, four-electron halogen bonds is challenging because of the self-interaction error inherent to DFT and to the incomplete description of nondynamic electron correlations in these bonds . Unsurprisingly, discrepancies between experimental observations and computational results have been reported in some cases …”

Section: Introductionmentioning

confidence: 99%

“…The strong, three-center halogen bond of halonium ions has been repeatedly reviewed from an experimental perspective; 3,37,38 however, in contrast, its computational treatment has so far received less attention. Apart from scarce examples of entirely theoretical studies, 39,40 most investigations analyzing threecenter halogen bonds used DFT predominantly to support the interpretation of experimental data, most often of NMR chemical shifts obtained in solutions. 3,[5][6][7][8][9][10][11]15,41 In the past decade, diverse computational methods (DFT functionals and basis sets) have been used, however, without giving any guidance on or evaluation of the applied methods' accuracy regarding the computed spectroscopic parameters or the geometry and the energy of such complexes.…”

Section: Introductionmentioning

confidence: 99%

Halogen Bond of Halonium Ions: Benchmarking DFT Methods for the Description of NMR Chemical Shifts

Sethio

Raggi

Lindh

et al. 2020

J. Chem. Theory Comput.

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Because of their anisotropic electron distribution and electron deficiency, halonium ions are unusually strong halogen-bond donors that form strong and directional three-center, four-electron halogen bonds. These halogen bonds have received considerable attention owing to their applicability in supramolecular and synthetic chemistry and have been intensely studied using spectroscopic and crystallographic techniques over the past decade. Their computational treatment faces different challenges to those of conventional weak and neutral halogen bonds. Literature studies have used a variety of wave functions and DFT functionals for prediction of their geometries and NMR chemical shifts, however, without any systematic evaluation of the accuracy of these methods being available. In order to provide guidance for future studies, we present the assessment of the accuracy of 12 common DFT functionals along with the Hartree–Fock (HF) and the second-order Møller–Plesset perturbation theory (MP2) methods, selected from an initial set of 36 prescreened functionals, for the prediction of 1 H, 13 C, and 15 N NMR chemical shifts of [N–X–N] + halogen-bond complexes, where X = F, Cl, Br, and I. Using a benchmark set of 14 complexes, providing 170 high-quality experimental chemical shifts, we show that the choice of the DFT functional is more important than that of the basis set. The M06 functional in combination with the aug-cc-pVTZ basis set is demonstrated to provide the overall most accurate NMR chemical shifts, whereas LC-ωPBE, ωB97X-D, LC-TPSS, CAM-B3LYP, and B3LYP to show acceptable performance. Our results are expected to provide a guideline to facilitate future developments and applications of the [N–X–N] + halogen bond.

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“…Theoretical isoelectric points (pI) for these proteins ranged from 6.26 of Y331Stop to 8.47 of E158K_E308G. The theoretical pI represents the pH at which a particular molecule or surface carries no net electrical charge, and it could help to understand the protein charge stability [20]. The mutated FMO3 proteins of this study had GRAVY indexes ranging from −0.06 of D141V_G180V to −0.21 of Y331Stop.…”

Section: Primary Structural and Biochemical Analyses Highlighted Possible Altered Chemical-physical Features In Mutated Fmo3mentioning

confidence: 90%

Adaptive Modelling of Mutated FMO3 Enzyme Could Unveil Unexplored Scenarios Linking Variant Haplotypes to TMAU Phenotypes

et al. 2021

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Background: Trimethylaminuria (TMAU) is a rare genetic disease characterized by the accumulation of trimethylamine (TMA) and its subsequent excretion trough main body fluids, determining the characteristic fish odour in affected patients. We realized an experimental study to investigate the role of several coding variants in the causative gene FMO3, that were only considered as polymorphic or benign, even if the available literature on them did not functionally explain their ineffectiveness on the encoded enzyme. Methods: Mutational analysis of 26 TMAU patients was realized by Sanger sequencing. Detected variants were, subsequently, deeply statistically and in silico characterized to determine their possible effects on the enzyme activity. To achieve this goal, a docking prediction for TMA/FMO3 and an unbinding pathway study were performed. Finally, a TMAO/TMA urine quantification by 1H-NMR spectroscopy was performed to support modelling results. Results: The FMO3 screening of all patients highlighted the presence of 17 variants distributed in 26 different haplotypes. Both non-sense and missense considered variants might impair the enzymatic kinetics of FMO3, probably reducing the interaction time between the protein catalytic site and TMA, or losing the wild-type binding site. Conclusions: Even if further functional assays will confirm our predictive results, considering the possible role of FMO3 variants with still uncertain effects, might be a relevant step towards the detection of novel scenarios in TMAU etiopathogenesis.

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The effects of cation–π and anion–π interactions on halogen bonds in the [N⋯X⋯N]+ complexes: A comprehensive theoretical study

Cited by 14 publications

References 50 publications

Halogen bonds of halonium ions

Halogen bonds of halonium ions

Halogen Bond of Halonium Ions: Benchmarking DFT Methods for the Description of NMR Chemical Shifts

Adaptive Modelling of Mutated FMO3 Enzyme Could Unveil Unexplored Scenarios Linking Variant Haplotypes to TMAU Phenotypes

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