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Article

Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts

by
Luka Fotović
and
Vladimir Stilinović
*
Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10002 Zagreb, Croatia
*
Author to whom correspondence should be addressed.
Crystals 2021, 11(10), 1240; https://doi.org/10.3390/cryst11101240
Submission received: 29 September 2021 / Revised: 11 October 2021 / Accepted: 12 October 2021 / Published: 14 October 2021
(This article belongs to the Special Issue Advanced Research in Halogen Bonding)
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Abstract

:
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.

Graphical Abstract

1. Introduction

A halogen bond [1,2,3,4,5], an attractive σ-hole [6,7,8] interaction between a halogen atom (Lewis acid) and a Lewis base, is a well-established tool of crystal engineering and supramolecular chemistry [9,10,11,12]. To date, various Lewis bases (neutral molecules or charged species) have been employed as halogen bond acceptors in constructing halogen-bonded supramolecular assemblies. These have most commonly been organic [13,14] and metal-organic [15] molecules containing electron-rich nitrogen [16,17,18,19,20,21,22,23,24,25,26] and oxygen atoms [27,28,29,30,31,32,33,34,35,36,37,38,39,40,41], as well as inorganic anions such as halogenides [42,43,44,45,46,47,48,49,50,51,52,53,54]. The most commonly used halogen bond donors have traditionally been neutral organic molecules where a halogen atom is bonded to electron-withdrawing molecular residues. Fluorine atoms [55,56,57,58,59,60], nitro and cyano groups [61,62,63,64,65], or C–C triple bond [16,66,67,68], exhibit an electron withdrawing effect on the halogen atom and consequently increase the positive electrostatic potential (ESP) of the σ-hole of the halogen atom. The same effect can be archived if the halogen atom is bonded to a more electronegative heteroatom such as nitrogen in N-halogenoimides [69,70,71,72,73,74,75,76] or oxygen in organic hypoiodites [77].
There is an alternative approach to making a reliable halogen bond donor by placing a halogen atom on a positively charged species. To date, a number of halogenoimidazolium and halogenopyridinum cations employed as halogen bond donors in salts with organic [78,79] and inorganic [13,25,44,45,46,47,48,49,50,51,52,53,54,80,81,82,83,84,85,86,87,88,89,90,91] counterions have been published. Halogenopyridinium cations have been studied as anion receptors [92,93,94,95,96], catalysts in halogenide abstraction [97], colour tuning [98,99] and as counterions for tuning conductivity and magnetic properties in supramolecular conductors [100,101,102,103].
Generally, N-methylation of halogenopyridines (iodopyridines in particular) greatly increases the ESP of the σ-hole of the halogen atom, rendering them formidable halogen bond donors. This is also evident from the structural data, which show that iodopyridinium cations tend to form quite short halogen bonds with both neutral and anionic halogen bond acceptors, such as halogenide anions [104].
Herein, we report a structural study of a series of halogenides of N-alkylated 3-halogenopyridinium cations with N-substituents other than methyl group. In the first place, we prepared a series of s of N-ethyl-3-halopyridinium (chloro, bromo and iodo) iodides, in order to compare them with the N-methyl-3-halopyridinium analogues to examine whether the increased N-substituent has any observable effect on the halogen bonding capability of the cations. In addition, we have attempted preparation of dications comprising a pair of 3-iodopyridinium rings separated by an aliphatic linker, which might act as ditopic cationic halogen bond donors (Scheme 1).

2. Materials and Methods

All the solvents used (ethanol, acetone, dichloromethane) were procured from Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany. Ethyl iodide (EtI) and 3-chloropyridine (3-ClPy) were procured from Acros Organics, Fisher Scientific UK Ltd., Leicestershire, United Kingdom. 3-bromopyridine (3-BrPy), 3-iodopyridine (3-IPy), 4-iodopyridine (4-IPy), 1,3-diiodopropane (PropI2) and 1,4-dibromobuta-2-ene (BuenBr2) were procured from Apollo Scientific Ltd., Cheshire, United Kingdom. All reagents, as well as the organic solvents, were used without additional purification.

2.1. Solution and Single Crystal Synthesis of Cocrystals

N-ethyl-3-chloropyridinium iodide [N-Et-3-ClPy]I and was obtained by dissolving halogenopyridine (1 mmol) in hot acetone and adding ethyl iodide in excess (ca 1.2 mmol) whereupon the solutions were left to cool and evaporate. Yellow crystals suitable for single-crystal X-ray diffraction experiments appeared in one day. Yield: 213 mg (79%).
N-ethyl-3-bromopyridinium iodide [N-Et-3-BrPy]I was obtained by dissolving halogenopyridine (1 mmol) in hot dichloromethane and adding ethyl iodide in excess (ca 1.2 mmol) whereupon the solution was left to cool and evaporate. Brown crystals suitable for single-crystal X-ray diffraction experiments appeared in three days. Yield: 183 mg (58%).
N-ethyl-3-iodopyridinium iodide [N-Et-3-IPy]I was obtained by dissolving halogenopyridine (1 mmol) in hot dichloromethane and adding ethyl iodide in excess (ca 1.2 mmol) whereupon the solution was left to cool and evaporate. Yellow crystals suitable for single-crystal X-ray diffraction experiments appeared in three days. Yield: 297 mg (82%).
N-(2-oxopropyl)-3-bromopyridinium iodide ([N-Ace-3-BrPy]I) was obtained by dissolving 3-bromopyridine (1 mmol) in hot acetone and adding ethyl iodide in excess (ca 1.2 mmol) whereupon the solution was left to cool and evaporate. Mixture of brown crystals ([N-Et-3-BrPy]I and [N-Ace-3-BrPy]I) appeared in 12 h.
4-iodopyridinium hemihydroiodide ([4-Ipy]2HI) was obtained by dissolving 4-iodopyridine (1 mmol) in mixture of hot acetone and dichloromethane (1:1; volume ratio) and adding ethyl iodide in excess (ca 1.2 mmol) whereupon the solution was left to cool and evaporate. Blue crystals suitable for single-crystal X-ray diffraction experiments appeared in one day.
N-(3-iodopropanyl)-3-iodopyridinium iodide ([N-IProp-3-IPy]I) was obtained by dissolving 3-iodopyridine (2 mmol) in hot acetone and adding 1,3-diiodopropane (1 mmol) whereupon the solution was left to cool and evaporate. Yellow powder appeared in three days, while yellow crystals suitable for single-crystal X-ray diffraction experiments appeared in ten days. Yield: 144 mg (29%).
(2E)-1,4-bis(pyridin-1-ium-1-yl)but-2-en dibromide ([N,N′-Buen-(3-IPy)2]Br2) was obtained by dissolving 3-iodopyridine (2 mmol) in mixture of hot acetone and ethanol (1:1; volume ratio) and adding (E)-1,4-dibromobuta-2-ene (1 mmol) whereupon the solution was left to cool and evaporate. White microcrystalline product appeared in one day. Yield: 494 mg (79%).
N-((2E)-4-iodobuta-2-enyl)-3-iodopyridinium iodide ([N-IBuen-3-IPy]I) was obtained by dissolving [N,N′-Buen-(3-IPy)2]Br2 (1mmol) in deionized water (20 mL) and passing the solution through an anion exchange column. The ion-exchange resin (Dowex 21K chloride form, 16-30 mesh, Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany) was regenerated with 50 mL aqueous solution of sodium hydroxide (c = 1 mol L−1). Hydroiodic acid (c = 1 mol L−1) was added dropwise in the obtained solution until neutralization. Yellow crystals suitable for single-crystal X-ray diffraction experiments appeared in three days. Yield: 57 mg (9%).
Single crystals (suitable for single crystal X-ray diffraction experiment) of [3-ClPyMe]I, [3-BrPyMe]I, [3-IPyMe]I, ([N-Ace-3-BrPy]I, [4Ipy]2HI, [N-IProp-3-IPy]I and [N-IBuen-3-IPy]I were obtained from the synthetic procedure, while single crystals of ([N,N′-Buen-(3-IPy)2]Br2) were prepared by crystalizing the initially obtained microcrystalline salt from mixture of ethanol and water (3:1; volume ratio).
FT-IR (ATR) spectra of prepared compounds are shown in Figures S21–S26 in Supplementary Materials.

2.2. Powder X-ray Diffraction Measurements

Powder X-ray diffraction experiments on the samples were performed on an Aeris X-ray diffractometer (Malvern Panalytical, Malvern Worcestershire, UK) with CuKα1 (λ = 1.54056 Å) radiation. The scattered intensities were measured with a PIXcel-1D-Medipix3 detector. The angular range was from 5° to 40° (2θ) with a continuous step size of 0.02° and measuring a time of 0.5 s per step.
Data collection methods were created using the program package START XRDMP CREATOR (Malvern Panalytical, Malvern Worcestershire, UK) while the data were analysed using X’Pert HighScore Plus (Version 2.2, Malvern Panalytical, Malvern Worcestershire, UK) [105]. Comparison of measured and calculated PXRD patterns of the prepared compounds are shown in Figures S9–S14 in Supplementary Materials.

2.3. Single Crystal X-ray Diffraction Measurements

Single crystal X-ray diffraction experiments were performed using an Oxford Diffraction Xcalibur Kappa CCD X-ray diffractometer (Oxford Diffraction Ltd., Abingdon, UK) with graphite-monochromated MoKα (λ = 0.71073 Å) radiation. The data sets were collected using the ω-scan mode over the 2θ—range up to 54°. Programs CrysAlis PRO CCD and CrysAlis PRO RED were employed for data collection, cell refinement, and data reduction [106,107]. The structures were solved and refined using SHELXS (Version 2013, Göttingen, Germany), SHELXL programs (Version 2013, Göttingen, Germany), SHELXT programs (Version 2013, Göttingen, Germany), respectively [108,109]. The structural refinement was performed on F2 using all data. The hydrogen atoms were placed in calculated positions and treated as riding on their parent atoms (C–H = 0.93 Å and Uiso(H) = 1.2 Ueq(C) for aromatic and methine hydrogen atoms; C–H = 0.96 Å and Uiso(H) = 1.5 Ueq(C) for methyl hydrogen atoms, C–H = 0.97 Å and Uiso(H) = 1.2 Ueq(C) for methylene hydrogen atoms). The position of the proton in [4-IPy···H···4-IPy]+ cation could not be reliably located from the electron difference map, and it was modelled as disordered over two positions on the nitrogen atoms of both 4-IPy molecules with 0.5 occupancy. All calculations were performed using the WinGX or Olex2 1.3-ac4 crystallographic suite of programs [110,111]. The figures were prepared using Mercury 2020.2.0 (CCDC, Cambridge, UK) [112]. Crystallographic data of the prepared compounds are shown in Table S2 in Supplementary Materials. ORTEP plots of the obtained compounds are shown in Figures S1–S8 in Supplementary Materials. CCDC No. 2109490-2109497, contain crystallographic data for this paper.

2.4. Thermal Analysis

Differential scanning calorimetry (DSC) and thermogravimetric (TG) measurements were performed simultaneously on a Mettler-Toledo TGA/DSC 3+ module (Mettler Toledo, Greifensee, Switzerland). Samples were placed in alumina crucibles (40 µL) and heated 25 to 300 °C, at a heating rate of 10 °C min−1 under nitrogen flow of 150 mL min−1.
Data collection and analysis were performed using the program package STARe Software (Version 15.00, Mettler Toledo, Greifensee, Switzerland) [113]. TG and DSC thermograms of the prepared compounds are shown in Figures S15–S20 in the Supplementary Materials.

2.5. Calculations

All calculations were performed using CrystalExplorer software package [114]. Hirshfeld surfaces were generated with high resolution. Molecular electrostatic potentials were calculated at B3LYP-DGDZVP level of theory [115,116,117,118].

3. Results and Discussion

All three meta-halogenopyridines (chloro, bromo and iodo) were successfully N-ethylated using EtI, producing corresponding iodide salts. The crystal structure of [N-Et-3-ClPy]I comprises centrosymmetric cyclical [N-Et-3-ClPy]2I2 tetramers in which [N-Et-3-ClPy]+ cations and iodide anions are interconnected through C−H⋯I− hydrogen bonds (d(C3⋯I1) = 3.901(6) Å, d(C4⋯I1) = 3.876(6) Å) (Figure 1a). C−H⋯I− hydrogen bonds and anion-π interactions, d(C5⋯I1) = 3.729(7) Å). The tetramers are connected into a layer via C−H⋯I− hydrogen bonds (d(C1⋯I1) = 3.866(6) Å), and the layers are then stacked on top of each other. Chlorine atoms do not participate in any significant supramolecular interactions. Analysing the electrostatic potential plotted on the Hirshfeld surface (Figure 1b), it has been found that ESP on the Hirshfeld surface in the σ-hole area (0.112 a.u.) is less positive than the mean ESP of chloropyridinium cation (0.148 a.u.). On the other hand, ESP on Hirshfeld surface near hydrogen atoms, which participate in supramolecular interactions, corresponds to the most positive regions of the [N-Et-3-ClPy]+ cation (0.229 au).
Substitution of chlorine on the pyridine ring with bromine leads to a significant difference in the structural arrangement of the cations and anions. The main difference is the presence of a C−Br⋯I− halogen bond shorter by ca. 6% than the sum of the corresponding van der Waals radii (d(Br1⋯I1) = 3.611(7) Å, ∠ (C2–Br1∙∙∙ I1) = 169.2(2)°). A methylene hydrogen atom of the ethyl group participates in a C−H⋯I− hydrogen bond with the iodide anion (d(C6⋯I1) = 4.013(6) Å). This combination of halogen and hydrogen bonds connects bromopyridinium cations and iodide anions in helical chains extending along the crystallographic b axis. The iodide anions also participate in anion-π contacts (d(C1⋯I1) = 3.575(5) Å) with cations from the neighbouring chains, which leads to formation of layers perpendicular to the c axis in the structure of [N-Et-3-BrPy]I (Figure 2).
In the structure of [N-Et-3-Ipy]I the cations and the anions are also connected in chains (along the crystallographic b axis) with combinations of C−I⋯I− halogen bonds (d(I1⋯I2) = 3.473(3) Å, ∠ (C2–I1∙∙∙ I2) = 178.25(7)°) shorter by ca. 12% than the sum of the corresponding van der Waals radii, and C−H⋯I− hydrogen bonds (d(C1⋯I2) = 3.778(3) Å), but here the hydrogen bond is formed by an aromatic hydrogen atom in ortho position to the pyridine nitrogen. The chains are connected into layers via C−H⋯I− hydrogen bonds (d(C7⋯I2) = 4.094(3) Å) with a methyl hydrogen atom (Figure 3).
The halogen bond strengths also reflect the thermal stability of the iodide salts of the N-ethylated 3-halogenopyridines. The inspection of the results of the thermal analysis (see DSC and TG thermograms in the ESI) revealed that all three compounds exhibit well-defined melting points, which are then followed by simultaneous decomposition and evaporation. Melting point temperatures increase from 110 °C for [N-Et-3-ClPy]I to 116 °C for [N-Et-3-BrPy]I and finally 127 °C for [N-Et-3-IPy]I showing a clear increase in the melting point temperature with the size of halogen bond donor atom and, therefore, the strength of the C−X⋯I− halogen bond.
If one is to compare halogen bonding in N-ethylated 3-halogenopyridinium iodides to those in N-methylated 3-halogenopyridinium iodides, one can see that in both series cations derived from 3-bromopyridine and 3-iodopyridine participate in C−X⋯I− halogen bonds. Conversely, in N-ethyl-3-chloropyridinium iodide, cations do not participate in halogen bonding, while in N-methyl-3-chloropyridinium iodide some of symmetrically independent cations participate in the C−Cl⋯I− halogen bonds with iodide anion, but these halogen bonds are longer than the sum of the corresponding van der Waals radii. When comparing the lengths of the halogen bonds in the two series of iodides, both the C−Br⋯I− and the C−I⋯I− halogen bonds are shorter in the N-ethylated salts than in the N-methylated salts (Table 1). The ESP values plotted on the Hirshfeld surface of cations are similar in 3-bromopyridinium cations while in case of 3-iodopyridinium cations N-methylated one have somewhat smaller ESP value than the N-ethylated one. All in all, there is no significant difference in halogen bonding between the N-ethylated and the N-methylated halogenopyridinium cations with iodide anions.
Interestingly, while the reaction of iodoethane with 3-chloropyridine and 3-iodopyridine in acetone yielded only the expected N-ethyl-3-pyridinium iodides, 3-bromopyridine yielded a mixture of the expected [N-Et-3-Brpy]I and N-(2-oxopropyl)-3-bromopyridinium iodide ([N-Ace-3Brpy]I, Figure 4a). This by-product was formed by reaction of an acetone molecule with 3-bromopyridine, presumably through the formation of an intermediate iodoacetone in situ. When dichloromethane was used as the solvent, only pure [N-Et-3-Brpy]I was obtained.
In the structure of [N-Ace-3-Brpy]I, the bromine atom again forms a halogen bond with the iodide anion (d(Br1⋯I1) = 3.694(7) Å, ∠ (C2–Br1∙∙∙ I1) = 166.4(1)°). Iodide anion also binds [N-Ace-3-Brpy]+ cation through C−H⋯I− hydrogen bonds (d(C1⋯I1) = 3.754(4) Å) with an aromatic hydrogen atom in ortho position to the pyridine nitrogen which lead to the formation of helical chains extending along the crystallographic b axis (Figure 4b). A different set of C−H⋯I− hydrogen bonds (d(C3⋯I1) = 3.847(5) Å) leads to the formation of the 2D structure (Figure 4c).
In order to expand the series of N-ethylated iodopyridinium salts, we have attempted to synthesize N-ethyl-4-iodopyridinium iodide from 4-iodopyridine and ethyl iodide. However, despite numerous attempts of synthesis, we were not able to isolate the desired product. Instead, when the reaction was performed in a mixture of hot acetone and dichloromethane, a minute amount (two single crystals) of solid product was obtained, which was identified as 4-iodopyridinium hemihydroiodide ((4-IPy)2HI). It was presumably formed by a reaction of 4-IPy and the traces of hydroiodic acid produced by hydrolysis of ethyl iodide with water absorbed from the atmosphere over time. Although in the structure of (4-IPy)2HI the position of the HI hydrogen atom could not be ascertained from the electron difference map, it is evident that it is placed between the nitrogen atoms of a pair of molecules, interconnecting them by a charge assisted [119] (probably symmetrical) N⋯H⋯N hydrogen bond (d(N⋯N) = 3.202(8) Å) into a [(4-IPy)2H]+ complex. The iodide anion participates in two C−I⋯I− halogen bonds (d(I1⋯I3) = 3.502(7) Å, ∠ (C3–I1∙∙∙I3) = 173.8(2)°; d(I2⋯I3) = 3.533(7) Å, ∠ (C8–I2∙∙∙I3) = 172.7(2)°), with two neighbouring [(4-IPy)2H]+ hydrogen-bonded complexes. This combination of hydrogen and halogen bonds forms supramolecular chains which are further connected into double chains through C−H⋯I− hydrogen bonds (d(C6⋯I1) = 4.028(7) Å) (Figure 5). It is interesting to note that this structure presents an excellent illustration of the HSAB principle in supramolecular chemistry[120,121]—the iodine atom of the [(4-IPy)2H]+ complex is the softer Lewis acid and therefore preferentially binds to the softer Lewis base, i.e., iodide. In contrast, the proton is the hardest Lewis acid and preferentially bind to the harder Lewis base, i.e., pyridine nitrogen.
As shown above, the hydrogen bonded [(4-IPy)2H]+ complex acts in the crystal structure of (4-IPy)2HI as a linear ditopic cationic halogen bond donor. This observation inspired us to attempt deliberate synthesis of ditopic cationic halogen bond donors by linking a pair of iodinated pyridine rings with different hydrocarbon linkers. For this purpose, we selected 3-IPy (which has shown to be a more reliable substrate for N-alkylation) as the iodopyridine, and propylene and (E)-buta-2-enylene chains as linkers. These linkers were selected as the latter was expected to result in a linear ditopic donor (due to the constricted rotation about the double bond), while the former would result in a bent molecule (the linker being an odd-numbered hydrocarbon chain).
The reaction of 3-IPy with 1,3-diiodopropane in 2:1 ratio, which was expected to produce the bent dication did not yield the desired product. Instead, we obtained N-(3-iodopropane)-3-iodopyridinium iodide ([N-IProp-3-IPy]I). [N-IProp-3-IPy]I crystalized in centrosymmetric P21/c space group with two crystallographically independent ion pairs in the asymmetric unit. This structure comprised chains of alternating cations and anions connected by C−I⋯I− halogen bonds (Figure 6). In spite of the fact that only one iodine atom of the reactant 1,3-diiodopropane was substituted by 3-IPy, the cations acted as ditopic halogen bond donors. Both cations bind two iodide anions, one through C−I⋯I− halogen bonds (d(I1⋯I5) = 3.487(7) Å, ∠ (C2–I1∙∙∙I5) = 174.3(2)°; d(I3⋯I6) = 3.558(7) Å, ∠ (C10–I3∙∙∙I6) = 174.4(2)°) with the iodine bonded to pyridine ring, and the other through C−I⋯I− halogen bonds (d(I4⋯I5) = 3.870(8) Å, ∠ (C8–I4∙∙∙I5) = 176.0(2)°; d(I2⋯I6) = 4.044(8) Å, ∠ (C16–I2∙∙∙I6) = 152.4(2)°) with the iodine atom bonded to alkyl chain. Halogen bonds involving the pyridine iodine atom as halogen bond donor are ca. 10% and 12% shorter than the sum of the corresponding van der Waals radii. On the other hand, one of the two halogen bonds involving an alkyl iodine atom as a halogen bond donor is ca. 2% shorter, while the other one is ca. 2% longer than the sum of the corresponding van der Waals radii. The neighbouring chains are further interconnected by a network of C−H⋯I− and C−H⋯I contacts in a 3D structure (Figure 6).
Unlike 1,3-diiodopropane, (E)-1,4-dibromobuta-2-ene reacted with 3-IPy in the expected 1:2 ratio, yielding a bromide salt of a [N,N`-Buen-(3-IPy)2]2+ cation (Figure 7a). This salt crystalized in the centrosymmetric space group P 21/c with the cation placed on an inversion centre. The cation binds two bromide anions via C−I⋯Br− halogen bonds (d(11⋯Br1) = 3.240(6) Å, ∠ (C2–I1∙∙∙Br1) = 174.5(1)°). In addition to this halogen bond, the bromide anion participates only in C−H⋯Br− hydrogen bonds with aromatic and methine hydrogen atoms of four neighbouring cations (Figure 7b) leading to formation of a 3D structure.
In order to be able to better compare the [N,N′-Buen-(3-IPy)2]2+ cation to other halogen bond donors covered by this study (all obtained as iodide salts), we attempted to obtain its iodide salt by ion exchange. Unfortunately, the cation was decomposed by the process: instead of the expected product, we obtained [N-IBuen-(3-IPy)]I, an iodide salt of a monocation equivalent to the [N-IProp-3-IPy]+ cation described above. In contrast to [N-IProp-3-IPy]I, in [N-IBuen-(3-IPy)]I, the cation does not act as a ditopic donor. Only the pyridyl iodine atoms participate in halogen bonding with iodide anions. The C−I⋯I− halogen bonds are ca. 14% and 10% shorter than the sum of the corresponding van der Waals radii (d(I1⋯I3) = 3.395(1) Å, ∠ (C2–I1∙∙∙I5) = 176.1(4)°; d(I4⋯I6) = 3.569(1) Å, ∠ (C11–I4∙∙∙I6) = 177.2(4)°). Those two halogen-bonded ion pairs (independent by symmetry) are connected in tetramers through C−H⋯I− hydrogen bonds with methylene and aromatic hydrogen atoms (orhto to the pyridine nitrogen) (d(C1⋯I6) = 3.841(1) Å, d(C6⋯I6) = 3.874(2) Å; d(C10⋯I3) = 3.852(1) Å, d(C15⋯I3) = 3.987(1) Å). Tetramers are linked into chains through C−H⋯I− hydrogen bonds with hydrogen atoms in meta position to the pyridine nitrogen atom (d(C4⋯I6) = 3.961(2) Å, d(C13⋯I3) = 3.918(2) Å) (Figure 8).
The failure of the alkyl iodine atom of [N-IBuen-(3-IPy)]+ to act as a donor of a halogen bond can be rationalised by an examination of the ESP values plotted on the Hirshfeld surfaces of the cations (Figure 9a). Generally, it can be seen that the positive charge is mainly located around pyridine nitrogen atom and neighbouring atoms (carbon and hydrogen) and spread on the pyridine ring rather than on the alkyl chain. As a result, the ESP in the region of the σ-hole of the aliphatic iodine atom on the aliphatic chain is considerably lower than that of the iodine on the pyridine ring. Consequently, the aliphatic iodine atom is a weaker halogen bond donor. This can also be seen from the comparison of the lengths of the C−I⋯I− halogen bond involving pyridine iodine atom and aliphatic iodine atom as halogen bond donor in [N-IProp-3-IPy]I. Halogen bonds involving iodine atoms bonded to pyridine ring (ESP of 0.227 a.u. and 0.203 a.u.) are ca. 10–14% shorter than the sum of the corresponding van der Waals radii, while those involving iodine bonded to the aliphatic chain are in one case (ESP of 0.118 a.u.) slightly shorter, and in the other (ESP of 0.100 a.u.) even longer, than the sum of the corresponding van der Waals radii (Figure 9a).
If we compare the Cpy−I⋯I− halogen bonds in [N-IProp-3-IPy]I and [N-IBuen-(3-IPy)]I, we can see that [N-IBuen-(3-IPy)]+ forms somewhat shorter halogen bond with iodide anion than [N-IProp-(3-IPy)]+ cation. Furthermore although the Cpy−I⋯I− halogen bonds in [N-IProp-3-IPy]I are somewhat longer than the one in [N-Et-3-Ipy]I, there appears to be a trend of longer chains as N-substituents generally leading to shorter Cpy−I⋯I− halogen bonds in N-alkyl-3-iodopyridinium iodides (Figure 10a). The values of ESP corresponding to the σ-hole of the iodine on the pyridinium ring (plotted on the Hirshfeld surfaces of these four cations in the crystal structures of the corresponding iodides) also follow the same trend, with the σ-hole of the iodine being the most positive in [N-IBuen-(3-IPy)]+, and least positive in [N-Me-3-Ipy]+ (Figure 10b).

4. Conclusions

Introducing various (aliphatic) N-substituents on the pyridine ring of 3-bromo- and 3-iodopyridine appears to be a viable method for preparation of an entire class of cationic halogen bond donors. Using aliphatic dihalogenides to produce bis-(halogenopyridinium) dications capable of acting as ditopic halogen bond donors has proven to be somewhat less successful—of the two attempted target cations, only one was isolated, and it decomposed during an attempted ion exchange. However, this opened the possibility of the synthesis of potentially ditopic asymmetric aliphatic–aromatic monocationic halogen bond donors, with two halogens which greatly differ in ESP values corresponding to the halogen σ-hole, and therefore in halogen bonding potential.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/cryst11101240/s1, Figure S1. Molecular structure of [N-Et-3-ClPy]I showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S2. Molecular structure of [N-Et-3-BrPy]I showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S3. Molecular structure of [N-Et-3-IPy]I showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S4. Molecular structure of [N-Ace-3-ClPy]I showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S5. Molecular structure of [4-IPy]2HI showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S6. Molecular structure of [N-PropI-3-IPy]I showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S7. Molecular structure of [N,N`-Buen-(3-IPy)2]Br2 showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S8. Molecular structure of [N-BuenI-3-IPy]I showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, and H atoms are shown as small spheres of arbitrary radius; Figure S9. Measured (black) and calculated (blue) PXRD patterns of [N-Et-3-ClPy]I; Figure S10. Measured (black) and calculated (blue) PXRD patterns of [N-Et-3-BrPy]I; Figure S11. Measured (black) and calculated (blue) PXRD patterns of [N-Et-3-IPy]I; Figure S12. Measured (black) and calculated (blue) PXRD patterns of [N-PropI-3-IPy]Br; Figure S13. Measured (black) and calculated (blue) PXRD patterns of [N,N`-Buen-(3-IPy)2]Br2; Figure S14. Measured (black) and calculated (blue) PXRD patterns of [N-BuenI-3-IPy]I; Figure S15. TG (black) and DSC (red) thermograms of [N-Et-3-ClPy]I; Figure S16. TG (black) and DSC (red) thermograms of [N-Et-3-BrPy]I; Figure S17. TG (black) and DSC (red) thermograms of [N-Et-3-IPy]I; Figure S18. TG (black) and DSC (red) thermograms of [N-PropI-3-IPy]I; Figure S19. TG (black) and DSC (red) thermograms of [N,N`-Buen-(3-IPy)2]Br2; Figure S20. TG (black) and DSC (red) thermograms of [N-BuenI-3-IPy]I; Figure S21. IR spectrum (ATR) of [N-Et-3-ClPy]I; Figure S22. IR spectrum (ATR) of [N-Et-3-BrPy]I; Figure S23. IR spectrum (ATR) of [N-Et-3-IPy]I; Figure S24. IR spectrum (ATR) of [N-PropI-3-IPy]I; Figure S25. IR spectrum (ATR) of [N,N`-Buen-(3-IPy)2]Br2; Figure S26. IR spectrum (ATR) of [N-BuenI-3-IPy]I; Table S1. An overview and crystallographic data of the prepared compounds. CCDC 2109490-2109497 contain crystallographic data for this paper. These data can be obtained free of charge from the Director, CCDC, 12 Union Road, Cambridge, CBZ 1EZ, UK (Fax: +44-1223-336033; email: deposit@ccdc.cam.ac.uk or www: http://www.ccdc.cam.ac.uk accessed on 25 August 2021).

Author Contributions

Conceptualization, L.F. and V.S.; methodology, L.F. and V.S.; formal analysis, L.F.; investigation, L.F.; data curation, L.F.; writing—original draft preparation, L.F.; writing—review and editing, L.F. and V.S.; visualization, L.F. and V.S.; supervision, V.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Croatian Science Foundation under the project IP-2019-04-1868.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Acknowledgments

We acknowledge the support of project CIuK co-financed by the Croatian Government and the European Union through the European Regional Development Fund-Competitiveness and Cohesion Operational Programme (Grant KK.01.1.1.02.0016.).

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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Crystals 11 01240 sch001 550
Scheme 1. Cationic halogen bond donors examined in this study.
Scheme 1. Cationic halogen bond donors examined in this study.
Crystals 11 01240 sch001
Crystals 11 01240 g001 550
Figure 1. (a) Layers of [N-Et-3-ClPy]+ cations and iodide anions connected through C−H⋯I− hydrogen bonds in the structure of [N-Et-3-ClPy]I; (b) Hirshfeld surface with mapped ESP (computed on B3LYP-DGDZVP level of theory) of the [N-Et-3-ClPy]+ cation and the contact iodide anions in [N-Et-3-ClPy]I.
Figure 1. (a) Layers of [N-Et-3-ClPy]+ cations and iodide anions connected through C−H⋯I− hydrogen bonds in the structure of [N-Et-3-ClPy]I; (b) Hirshfeld surface with mapped ESP (computed on B3LYP-DGDZVP level of theory) of the [N-Et-3-ClPy]+ cation and the contact iodide anions in [N-Et-3-ClPy]I.
Crystals 11 01240 g001
Crystals 11 01240 g002 550
Figure 2. [N-Et-3-BrPy]+ cations and iodide anions connected into layers through C−Br⋯I− halogen bonds, C−H⋯I− hydrogen bonds and anion-π contacts in the structure of [N-Et-3-BrPy]I.
Figure 2. [N-Et-3-BrPy]+ cations and iodide anions connected into layers through C−Br⋯I− halogen bonds, C−H⋯I− hydrogen bonds and anion-π contacts in the structure of [N-Et-3-BrPy]I.
Crystals 11 01240 g002
Crystals 11 01240 g003 550
Figure 3. [N-Et-3-IPy]+ cations and iodide anions connected into layers through C−I⋯I− halogen bonds and C−H⋯I− hydrogen bonds in the structure of [N-Et-3-IPy]I.
Figure 3. [N-Et-3-IPy]+ cations and iodide anions connected into layers through C−I⋯I− halogen bonds and C−H⋯I− hydrogen bonds in the structure of [N-Et-3-IPy]I.
Crystals 11 01240 g003
Crystals 11 01240 g004 550
Figure 4. (a) [N-Ace-3-BrPy]+ cation; (b) [N-Ace-3-BrPy]+ cations and iodide anions connected through C−Br⋯I− halogen bonds and C−H⋯I− hydrogen bonds into chains in the structure of [N-Ace-3-BrPy]I; (c) View along crystallographic b axis—chains connected into layer through C−H⋯I− hydrogen bonds.
Figure 4. (a) [N-Ace-3-BrPy]+ cation; (b) [N-Ace-3-BrPy]+ cations and iodide anions connected through C−Br⋯I− halogen bonds and C−H⋯I− hydrogen bonds into chains in the structure of [N-Ace-3-BrPy]I; (c) View along crystallographic b axis—chains connected into layer through C−H⋯I− hydrogen bonds.
Crystals 11 01240 g004
Crystals 11 01240 g005 550
Figure 5. [(4-IPy)2H]+ hydrogen bonded complexes and iodide anions connected through C−I⋯I− halogen bonds and C−H⋯I− hydrogen bonds into double chains in the structure of [(4-IPy)2H]I.
Figure 5. [(4-IPy)2H]+ hydrogen bonded complexes and iodide anions connected through C−I⋯I− halogen bonds and C−H⋯I− hydrogen bonds into double chains in the structure of [(4-IPy)2H]I.
Crystals 11 01240 g005
Crystals 11 01240 g006 550
Figure 6. (a) [N-IProp-3-IPy]+ cations and iodide anions connected through C−I⋯I− halogen bonds in chains in the structure of [N-Et-3-IPy]I; (b) Neighbouring chains are further interconnected by a network of C−H⋯I− and C−H⋯I contacts into a 3D structure.
Figure 6. (a) [N-IProp-3-IPy]+ cations and iodide anions connected through C−I⋯I− halogen bonds in chains in the structure of [N-Et-3-IPy]I; (b) Neighbouring chains are further interconnected by a network of C−H⋯I− and C−H⋯I contacts into a 3D structure.
Crystals 11 01240 g006
Crystals 11 01240 g007 550
Figure 7. (a) One [N,N′-Buen-(3-IPy)2]2+ cation binds two bromide anions by C−I⋯Br− halogen bonds in the structure of [N,N′-Buen-(3-IPy)2]Br2; (b) Bromide anion binds four neighbouring cations through C−H⋯Br− and one cation through C−I⋯Br− halogen bonds leading to formation of a 3D structure.
Figure 7. (a) One [N,N′-Buen-(3-IPy)2]2+ cation binds two bromide anions by C−I⋯Br− halogen bonds in the structure of [N,N′-Buen-(3-IPy)2]Br2; (b) Bromide anion binds four neighbouring cations through C−H⋯Br− and one cation through C−I⋯Br− halogen bonds leading to formation of a 3D structure.
Crystals 11 01240 g007
Crystals 11 01240 g008 550
Figure 8. [N-IBuen-(3-IPy)]+ cations and iodide anions connected through C−I⋯I− halogen and C−H⋯I− hydrogen bonds in cyclical [N-IBuen-(3-IPy)]2I2 tetramers linked via C−H⋯I− hydrogen bonds into chains the structure of [N-IBuen-(3-IPy)]I.
Figure 8. [N-IBuen-(3-IPy)]+ cations and iodide anions connected through C−I⋯I− halogen and C−H⋯I− hydrogen bonds in cyclical [N-IBuen-(3-IPy)]2I2 tetramers linked via C−H⋯I− hydrogen bonds into chains the structure of [N-IBuen-(3-IPy)]I.
Crystals 11 01240 g008
Crystals 11 01240 g009 550
Figure 9. Hirshfeld surface with mapped ESP (computed on B3LYP-DGDZVP level of theory) for: (a) [N-IBuen-(3-IPy)]+ cation and (b) [N-IProp-(3-IPy)]+ cation.
Figure 9. Hirshfeld surface with mapped ESP (computed on B3LYP-DGDZVP level of theory) for: (a) [N-IBuen-(3-IPy)]+ cation and (b) [N-IProp-(3-IPy)]+ cation.
Crystals 11 01240 g009
Crystals 11 01240 g010 550
Figure 10. (a) Correlation of the number of carbon atoms in N-substituent chain of N-alkyl-3-iodipyridinium cations with C−I⋯I− halogen bonds lengths; (b) plot of the values of ESP corresponding to the σ-hole of the halogen atom. vs. C−X⋯I− halogen bonds lengths.
Figure 10. (a) Correlation of the number of carbon atoms in N-substituent chain of N-alkyl-3-iodipyridinium cations with C−I⋯I− halogen bonds lengths; (b) plot of the values of ESP corresponding to the σ-hole of the halogen atom. vs. C−X⋯I− halogen bonds lengths.
Crystals 11 01240 g010
Table
Table 1. An overview of the C−X⋯I− halogen bonds and ESP values in σ-hole area in the N-ethylated and N-methylated 3-halogenopyridines [104].
Table 1. An overview of the C−X⋯I− halogen bonds and ESP values in σ-hole area in the N-ethylated and N-methylated 3-halogenopyridines [104].
N-ethylatedN-methylated
d(XB)/ÅR.S. (XB)/%ESP (X)/kJ mol−1 e−1d(XB)/ÅR.S. (XB)ESP (X)/kJ mol−1 e−1
3ClPy//2943.776–1.2381
3BrPy3.6115.74493.6375.0452
3IPy3.47312.35703.53810.7554
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Fotović, L.; Stilinović, V. Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts. Crystals 2021, 11, 1240. https://doi.org/10.3390/cryst11101240

AMA Style

Fotović L, Stilinović V. Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts. Crystals. 2021; 11(10):1240. https://doi.org/10.3390/cryst11101240

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Fotović, Luka, and Vladimir Stilinović. 2021. "Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts" Crystals 11, no. 10: 1240. https://doi.org/10.3390/cryst11101240

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