scholarly journals Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts

Crystals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1240
Author(s):  
Luka Fotović ◽  
Vladimir Stilinović
Keyword(s):  
Iodine Atom ◽  
Pyridine Ring ◽  
Positive Charge ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Considerable Effect ◽  
Halogen Bonds ◽  
Bond Lengths ◽  
Hirshfeld Surfaces ◽  
The One

We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.

scholarly journals Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons

2020 ◽  
Vol 21 (18) ◽  
pp. 6571
Author(s):  
Nicholas J. Thornton ◽  
Tanja van Mourik
Keyword(s):  
Base Pair ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Dna Bases ◽  
Halogen Bonds ◽  
Base Pairs ◽  
Rich Diversity ◽  
Different Types ◽  
Guanine Base ◽  
The Stability

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°).

scholarly journals Study of the Halogen Bonding between Pyridine and Perfluoroalkyl Iodide in Solution Phase Using the Combination of FTIR and 19F NMR

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Briauna Hawthorne ◽  
Haiyan Fan-Hagenstein ◽  
Elizabeth Wood ◽  
Jessica Smith ◽  
Timothy Hanks
Keyword(s):  
Halogen Bond ◽  
Equilibrium Constants ◽  
Binding Constants ◽  
Halogen Bonding ◽  
Blue Shift ◽  
Halogen Bonds ◽  
Perfluoroalkyl Iodide ◽  
Solvent Dependence ◽  
Dilution Experiments ◽  
Stretching Vibrations

Halogen bonding between pyridine and heptafluoro-2-iodopropane (iso-C3F7I)/heptafluoro-1-iodopropane (1-C3F7I) was studied using a combination of FTIR and 19F NMR. The ring breathing vibration of pyridine underwent a blue shift upon the formation of halogen bonds with both iso-C3F7I and 1-C3F7I. The magnitudes of the shifts and the equilibrium constants for the halogen-bonded complex formation were found to depend not only on the structure of the halocarbon, but also on the solvent. The halogen bond also affected the Cα-F (C-F bond on the center carbon) bending and stretching vibrations in iso-C3F7I. These spectroscopic effects show some solvent dependence, but more importantly, they suggest the possibility of intermolecular halogen bonding among iso-C3F7I molecules. The systems were also examined by 19F NMR in various solvents (cyclohexane, hexane, chloroform, acetone, and acetonitrile). NMR dilution experiments support the existence of the intermolecular self-halogen bonding in both iso-C3F7I and 1-C3F7I. The binding constants for the pyridine/perfluoroalkyl iodide halogen bonding complexes formed in various solvents were obtained through NMR titration experiments. Quantum chemical calculations were used to support the FTIR and 19F NMR observations.

scholarly journals In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1589 ◽  
Author(s):  
Yunwen Tao ◽  
Yue Qiu ◽  
Wenli Zou ◽  
Sadisha Nanayakkara ◽  
Seth Yannacone ◽  
...  
Keyword(s):  
Bond Strength ◽  
Vibrational Mode ◽  
Halogen Bond ◽  
Molecular Crystals ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
Mode Theory ◽  
Local Vibrational Mode ◽  
Intrinsic Strength

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ -hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n → σ ∗ (X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.

scholarly journals Halogen Bonding in the Complexes of Brominated Electrophiles with Chloride Anions: From a Weak Supramolecular Interaction to a Covalent Br–Cl Bond

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1075
Author(s):  
Cody Loy ◽  
Matthias Zeller ◽  
Sergiy V. Rosokha
Keyword(s):  
Bond Strength ◽  
Halogen Bond ◽  
Covalent Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
Nucleophilic Reaction ◽  
X Ray ◽  
Wide Range ◽  
Judicious Choice ◽  
Range Variation

The wide-range variation of the strength of halogen bonds (XB) not only facilitates a variety of applications of this interaction, but it also allows examining the relation (and interconversion) between supramolecular and covalent bonding. Herein, the Br…Cl halogen bonding in a series of complexes of bromosubstituted electrophiles (R-Br) with chloride anions were examined via X-ray crystallographic and computational methods. Six co-crystals showing such bonding were prepared by evaporation of solutions of R-Br and tetra-n-propylammonium chloride or using Cl− anions released in the nucleophilic reaction of 1,4-diazabicyclo[2.2.2]octane with dichloromethane in the presence of R-Br. The co-crystal comprised networks formed by 3:3 or 2:2 halogen bonding between R-Br and Cl−, with the XB lengths varying from 3.0 Å to 3.25 Å. Analysis of the crystallographic database revealed examples of associations with substantially longer and shorter Br…Cl separations. DFT computations of an extended series of R–Br…Cl− complexes confirmed that the judicious choice of brominated electrophile allows varying halogen Br…Cl bond strength and length gradually from the values common for the weak intermolecular complexes to that approaching a fully developed covalent bond. This continuity of halogen bond strength in the experimental (solid-state) and calculated associations indicates a fundamental link between the covalent and supramolecular bonding.

The15N NMR chemical shift in the characterization of weak halogen bonding in solution

2017 ◽  
Vol 203 ◽  
pp. 333-346 ◽  
Author(s):  
Sebastiaan B. Hakkert ◽  
Jürgen Gräfenstein ◽  
Mate Erdelyi
Keyword(s):  
Hydrogen Bond ◽  
Chemical Shift ◽  
Halogen Bond ◽  
Molar Fraction ◽  
Halogen Bonding ◽  
Relative Strength ◽  
Lewis Base ◽  
Halogen Bonds ◽  
Bonded Complexes

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.

scholarly journals Catalytic Activation via π –Backbonding in Halogen Bonds?

2020 ◽  
Author(s):  
Andrew Wang ◽  
Pierre Kennepohl
Keyword(s):  
Halogen Bond ◽  
Halogen Bonding ◽  
Lewis Base ◽  
Computational Studies ◽  
Halogen Bonds ◽  
Covalent Interaction ◽  
Lewis Bases ◽  
Chemical Catalysis ◽  
Catalytic Activation

The role of halogen bonding (XB) in chemical catalysis has largely involved using XB donors as Lewis acid activators to modulate the reactivity of partner Lewis bases. We explore a more uncommon scenario, where a Lewis base modulates reactivity via a spectator halogen bond interaction. Our computational studies reveal that spectator halogen bonds may play an important role in modulating the rate of S<sub>N</sub>2 reactions. Most notably, π acceptors such as PF<sub>3</sub> significantly decrease the barrier to subsitution by decreasing electron density in the very electron rich transition state. Such π-backbonding represents an example of a heretofor unexplored situation in halogen bonding: the combination of both s-donation and π-backdonation in this “non-covalent” interaction.

scholarly journals Halogen Bonding to the Azulene Pi-System: Cocrystal Design of Pleochroism

2020 ◽  
Author(s):  
Jogirdas Vainauskas ◽  
Filip Topic ◽  
Oleksandr S. Bushuyev ◽  
Christopher J. Barrett ◽  
Tomislav Friscic
Keyword(s):  
Halogen Bond ◽  
Halogen Bonding ◽  
Molecular Solids ◽  
Halogen Bonds ◽  
Rational Development ◽  
Different Types ◽  
Pi System

We describe the rational development of a design to create pleochroic molecular solids, by using C-I...pi halogen bonds to pre-organise different types of chromophores in a cocrystal. Using as a blueprint the structure of a non-dichroic cocrystal of naphthalene, we show how the systematic introduction of chromophores able to act as halogen bond donors or acceptors enables the construction of optically interesting dichroic or pleochroic solids, demonstrating the reliability of C-I...pi halogen bonds in designing new properties.<br>

scholarly journals Halogen Bonding to the Azulene Pi-System: Cocrystal Design of Pleochroism

2020 ◽  
Author(s):  
Jogirdas Vainauskas ◽  
Filip Topic ◽  
Oleksandr S. Bushuyev ◽  
Christopher J. Barrett ◽  
Tomislav Friscic
Keyword(s):  
Halogen Bond ◽  
Halogen Bonding ◽  
Molecular Solids ◽  
Halogen Bonds ◽  
Rational Development ◽  
Different Types ◽  
Pi System

We describe the rational development of a design to create pleochroic molecular solids, by using C-I...pi halogen bonds to pre-organise different types of chromophores in a cocrystal. Using as a blueprint the structure of a non-dichroic cocrystal of naphthalene, we show how the systematic introduction of chromophores able to act as halogen bond donors or acceptors enables the construction of optically interesting dichroic or pleochroic solids, demonstrating the reliability of C-I...pi halogen bonds in designing new properties.<br>

Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds

2020 ◽  
Author(s):  
Emer Foyle ◽  
Nicholas White
Keyword(s):  
Crystal Engineering ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Structural Database ◽  
Van Der Waals Radii

<div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div>

Anion Templated Crystal Engineering of Halogen Bonding Tripodal Tris(halopyridinium) Compounds

2020 ◽  
Author(s):  
Emer Foyle ◽  
Nicholas White
Keyword(s):  
Crystal Engineering ◽  
Self Assembly ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Structural Database ◽  
Van Der Waals Radii

<div>In this work four new tripodal tris(halopyridinium) receptors containing potentially halogen</div><div>bonding groups were prepared. The ability of the receptors to bind anions in competitive</div><div>CD<sub>3</sub>CN/d<sub>6</sub>-DMSO was studied using <sup>1</sup>H NMR titration experiments, which revealed that the</div><div>receptors bind chloride anions more strongly than more basic acetate or other halide ions.</div><div>The solid state self–assembly of the tripodal receptors with halide anions was investigated by</div><div>X-ray crystallography. The nature of the structures was dependent on the choice of halide</div><div>anion, as well as the crystallisation solvent. Halogen bond lengths as short as 80% of the sum</div><div>of the van der Waals radii were observed, which is shorter than any halogen bonds involving</div><div>halopyridinium receptors in the Cambridge Structural Database.</div>

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