Pyridine-4-thiol as halo­gen-bond (HaB) acceptor: influence of the noncovalent inter­action in its reactivity

Marta E G Mosquera; Silvia Dortez; Francisco Fernández-Palacio; Pilar Gómez-Sal

doi:10.1107/S205322962300205X

. 2023 Mar 15;79(Pt 4):112–117. doi: 10.1107/S205322962300205X

Pyridine-4-thiol as halogen-bond (HaB) acceptor: influence of the noncovalent interaction in its reactivity

Marta E G Mosquera ^a,^*, Silvia Dortez ^b, Francisco Fernández-Palacio ^a, Pilar Gómez-Sal ^a

Editor: A Peuronen^c

PMCID: PMC10074038 PMID: 36919972

Pyridine-4-thiol has been explored as an acceptor for a halogen-bond (HaB) interaction. For this compound, it is the S atom instead of the pyridine group that is the moiety of choice for establishing the interactions, producing a betaine-type structure. Interestingly, when left in solution, this compound forms a methylene-bridged sulfide that implies the activation of the CH₂Cl₂ solvent. The pre-organization imposed by the HaB seems to have a clear influence on the outcome.

Keywords: halogen bond, HaB, pyridine-4-thiol, C—Cl bond activation, crystal structure, chalcogen bond

Abstract

The study of pyridine-4-thiol as a halogen-bond (HaB) acceptor has allowed the isolation of its cocrystal with the HaB donor IC₆F₄I, namely, 1,2,4,5-tetrafluoro-3,6-diiodobenzene bis(pyridin-1-ium-4-ylsulfanide), C₆F₄I₂·2C₅H₅NS (1), where the S atom is the HaB acceptor, while the pyridine position is blocked by the proton. Furthermore, the S atom acts a dual acceptor and also establishes an interaction with the pyridinium proton from an adjacent molecule. The presence of these interactions in 1 contributes to the stabilization of the zwitterionic form. This pre-organization seems to have an influence on the reactivity of the compound since when left in dichloromethane solution, an unusual activation of the C—Cl bond is observed that leads to the formation of the bis[(pyridin-1-ium-4-yl)sulfanyl]methane dication, while the Cl atoms are still present as chloride counter-ions, i.e. 4,4′-[methanediyldi(sulfanediyl)]dipyridinium dichloride, C₁₁H₁₂N₂S₂ ²⁺·2Cl⁻ (2). In the crystal structure of 2 it is observed that the S atom is now acting as the donor part of a chalcogenide bond with the chloride anions.

Introduction

Halogen bonding (HaB) is a noncovalent interaction that has attracted increasing attention during the last few decades, due to its role in crystal engineering, molecular recognition processes, as a structure-directing tool and for the modulation of some physical properties (Politzer et al., 2007 ▸; Brammer et al., 2001 ▸; Aakeröy et al., 2013 ▸; Cavallo et al., 2016 ▸). Also, its influence in reactivity and catalysis is increasingly acknowledged (Bulfield & Huber, 2016 ▸; Bamberger et al., 2019 ▸; Jónsson et al., 2022 ▸).

In our group, we have explored this interaction in metallic complexes, both for main group and transition metals, and have observed the influence of HaB in the structural arrangement and reactivity (Dortéz et al., 2020 ▸; Mosquera et al., 2016 ▸, 2017 ▸; Vidal et al., 2013 ▸). In this work, we are interested in exploring pyridine-4-thiol as a HaB acceptor since there are two possible sites able to act as such, namely, the pyridine group and the S atom. Pyridines are one of the most popular types of HaB acceptor, a search in the Cambridge Structural Database (CSD; Version 5.42, with updates to September 2021; Groom et al., 2016 ▸) for HaB interactions with C—X (X = Br or I) gives over 1000 hits. On the other hand, sulfur has two available lone pairs and can be a potent HaB acceptor since it can interact with more than one HaB donor, which can lead to interesting topologies. However, it has been less studied, although in a search in the CSD, there is a significant number of structures that display S atoms as a HaB acceptor; a search for C—X⋯S (X = Br or I) interactions in the angle range 160–180° gave 715 hits.

We have explored the interaction of pyridine-4-thiol with the iconic IC₆F₄I molecule as HaB donor. Interestingly, for this molecule, it is not the pyridine group but the S atom that acts as the HaB acceptor, which is surprising since in the related compound Py–S–Py, it is the pyridine group that acts as the HaB acceptor (Arman et al., 2010 ▸). Furthermore, the presence of C—S⋯I interactions in this cocrystal favours the stabilization of the zwitterionic form for pyridine-4-thiol (namely, pyridin-1-ium-4-ylsulfanide), which has important implications in the reactivity of the molecule, and in fact an unusual C—Cl activation of the dichloromethane solvent is observed to give the bis[(pyridin-1-ium-4-yl)sulfanyl]methane dication.

The structures of 1,2,4,5-tetrafluoro-3,6-diiodobenzene bis(pyridin-1-ium-4-ylsulfanide), 1, and 4,4′-[methanediyldi(sulfanediyl)]dipyridinium dichloride, 2, are reported.

Experimental

General considerations

All manipulations were carried out under an inert atmosphere of argon using standard Schlenk techniques. All solvents were dried prior to use following standard methods. All reagents were commercially obtained and were used without further purification.

Synthesis and crystallization

Synthesis of cocrystal 1

Pyridine-4-thiol (14 mg, 0.126 mmol) and 1,2,4,5-tetrafluoro-3,6-diiodobenzene (50 mg, 0.126 mmol) were placed in a Schlenk flask. To this mixture, CH₂Cl₂ (25 ml) and tetrahydrofuran (12 ml) were added. In order to completely dissolve the solid, a brief reflux with a heat gun was performed. The solution was filtered and left to evaporate slowly. After three weeks, yellow crystals were isolated (yield: 63%, 40 mg).

Synthesis of (HPy–CH₂–PyH)Cl₂ (2)

To pyridine-4-thiol (50 mg, 0.45 mmol) in a Schlenk flask was added CH₂Cl₂ (10 ml). To this suspension, C₆F₄I₂ (180 mg, 0.45 mmol) was added and, to dissolve the mixture completely, tetrahydrofuran (10 ml) were added. The solution was left to stir for 48 h. A clear solution was formed, to which a layer of hexane (16 ml) was added. After the solution had diffused into the hexane, brown crystals of 2 of good enough quality for analysis by X-ray diffraction were isolated (yield: 32%, 22 mg).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1 ▸. H atoms were placed geometrically and left riding on their parent atoms, except for the H atoms bonded to N1 in cocrystal 1, and C10 and N1 in salt 2, which were found in a Fourier map.

Table 1. Experimental details.

Experiments were carried out at 200 K with Mo Kα radiation using a Nonius KappaCCD diffractometer. H atoms were treated by a mixture of independent and constrained refinement.

	1	2
Crystal data
Chemical formula	C₆F₄I₂·2C₅H₅NS	C₁₁H₁₂N₂S₂ ²⁺·2Cl⁻
M _r	624.18	307.25
Crystal system, space group	Monoclinic, P2₁/c	Orthorhombic, F2d d
a, b, c (Å)	16.288 (8), 5.790 (4), 10.546 (9)	8.0815 (4), 17.2161 (5), 18.9254 (12)
α, β, γ (°)	90, 104.77 (3), 90	90, 90, 90
V (Å³)	961.7 (12)	2633.1 (2)
Z	2	8
μ (mm⁻¹)	3.53	0.79
Crystal size (mm)	0.21 × 0.18 × 0.15	0.4 × 0.3 × 0.25

Data collection
Absorption correction	Multi-scan (Blessing, 1995 ▸)	–
T _min, T _max	0.371, 0.426	–
No. of measured, independent and observed [I > 2σ(I)] reflections	3983, 2181, 1458	4579, 1386, 1177
R _int	0.040	0.069
(sin θ/λ)_max (Å⁻¹)	0.649	0.650

Refinement
R[F ² > 2σ(F ²)], wR(F ²), S	0.032, 0.069, 0.93	0.041, 0.101, 1.10
No. of reflections	2181	1386
No. of parameters	122	84
No. of restraints	0	1
Δρ_max, Δρ_min (e Å⁻³)	0.99, −1.09	0.35, −0.30
Absolute structure	–	Flack x determined using 445 quotients [(I ⁺) − (I ⁻)]/[(I ⁺) + (I ⁻)] (Parsons et al., 2013 ▸)
Absolute structure parameter	–	−0.01 (11)

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Computer programs: COLLECT (Nonius, 2004 ▸), DIRAX/LSQ (Duisenberg et al., 2003 ▸), EVALCCD (Duisenberg et al., 2003 ▸), SHELXT2018 (Sheldrick, 2015a ▸), SHELXS2013 (Sheldrick, 2008 ▸), SHELXL2014 and SHELXL2016 (Sheldrick, 2015b ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸) and WinGX (Farrugia, 2012 ▸).

Results and discussion

In order to achieve the crystallization of pyridine-4-thiol and IC₆F₄I, both compounds were dissolved in a mixture of CH₂Cl₂ and tetrahydrofuran under argon. The suspension was heated briefly to obtain a clear solution (Fig. 2 ▸). From this, orange crystals were isolated after three weeks by slow evaporation and the structure was determined by X-ray diffraction analysis.

The synthetic scheme for the preparation of cocrystal 1.

As shown in Fig. 2 ▸, a cocrystal has been formed incorporating two molecules of pyridine-4-thiol and one of IC₆F₄I. This compound crystallized in the monoclinic space group P2₁/c. In this case, it is the S atom that acts as the HaB acceptor, which stabilizes the zwitterionic form of pyridine-4-thiol and, at the same time, the pyridine group is blocked by the proton. It should be noted that pyridine-4-thiol has been used frequently as a ligand for d- and f-block metals, and in those cases most often the zwitterionic form is the one present (CSD; Groom et al., 2016 ▸).

Displacement ellipsoid plot (30% probability) of 1, showing (a) the C—I⋯S halogen bonding and (b) a view of the molecular packing *via* halogen and hydrogen bonding (dashed lines).

For the HaB established between the pyridine-4-thiol and the perfluorinated unit, the S⋯I distance is particularly short [3.158 (7) Å and C—I⋯S = 175.74 (5)°; Table 2 ▸]; considering that the van der Waals radius sum is 3.78 Å (Bondi, 1964 ▸), this interaction implies a significant reduction of 16.4%. This short distance has also been observed in other compounds and, in all cases, the S atom has a negative charge, as in ours, as evidenced by a search in the CSD. As shown in Fig. 3 ▸(b), when the S atom is neutral, the majority of the interactions appear at S⋯I distances over 3.5 Å. For shorter distances [Fig. 3 ▸(a)], the majority of the examples imply the thyocyanate anion, SCN⁻ (Zuluaga et al., 2020 ▸; Postnikov et al., 2015 ▸; Bozopoulos & Rentzeperis, 1986 ▸; Hirschberg et al., 2014 ▸).

Table 2. Selected interatomic distances (Å) and angles (°) for 1 and 2 .

1			2
I1⋯S2	3.158 (7)	C10—S1	1.800 (4)
C1—S1	1.708 (5)	C1—N1	1.344 (7)
C6—I1	2.107 (4)	C5—S1	1.743 (5)
F2⋯H3	2.583 (7)

C4—N1—C3	121.7 (4)	S1—C10—S1ⁱ	116.3 (4)
F1—C7—C6	120.1 (4)	N1—C1—C6	120.4 (5)
C7—C6—I1	121.0 (3)	C5—S1—C10	104.89 (19)

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Symmetry code: (i) x, −y + Inline graphic , −z + .

Histograms of the S⋯I distances for the S⋯I—C interaction for (a) an S atom with a −1 charge (149 hits) and (b) an S atom with no charge (339 hits). In salt 2, the S⋯I distance is 3.158 (7) Å.

Sulfur can form bifurcated interactions and in this case behaves as such; on one side it interacts with the I atom and on the other side with the pyridinium N—H proton. This behaviour as a dual acceptor for both a halogen and a H atom has been observed previously; however, there are not many examples (Ding et al., 2020 ▸).

The perfluorinated unit, p-C₆F₄I₂, interacts from both sides to give discrete units formed by the interaction of two molecules of pyridine-4-thiol. These units are linked via weaker N—H⋯I and C—H⋯F interactions to give layers. As mentioned before, for the related Py–S–Py derivative, the interaction is established between the pyridine group and the I atom to give an N_Py⋯I—C contact (N_Py⋯I = 2.838 Å and N_Py⋯I—C = 177.93°) (Arman et al., 2010 ▸). Hence, the preference for one group or the other is not very strong and may even be governed by kinetics and, if there is a competing aceptor, such is in the case of the proton, may direct the choice of the donor. In fact, for the thiocyanate, which can also act as a dual donor, the formation of both HaB interactions with the N or the S atom has also been oberved for the same donors (Soldatova et al., 2020 ▸).

When the reaction is performed on a larger scale and left stirring for 48 h, the solution changes colour to brown. It was possible to obtain crystals from this solution by diffusion into a hexane layer. The isolated brown crystals were of good enough quality to be determined by single-crystal X-ray diffraction. Interestingly, a methylene-bridged sulfide resulting from the displacement of both Cl atoms from dichloromethane by two molecules of pyridine-4-thiol, i.e. an [L ₂CH₂]²⁺ dication, is formed. The displaced Cl atoms are still present as chloride counter-ions of the dication generated. The activation of the C—Cl bond has been observed previously, most often via a radical mechanism and less frequently via a nucleophilic mechanism. In fact, in our group, we have observed a similar reactivity when a zwitterionic betaine derivative composed of a nucleophilic carbene and a carbodimide (CDI-NHC) is left stirring for a long time in a dichloromethane solution (Sánchez-Roa et al., 2018 ▸). As in this case, the activation of the C—Cl bond is promoted by the presence of zwitterionic species. As mentioned before, the zwitterionic form of pyridine-4-thiol is stabilized by the presence of the HaB interaction, which implies a pre-organization that influences the outcome of the reaction. A similar behaviour has been described previously for isocyanates (Soldatova et al., 2020 ▸).

Moreover, the evolution of pyridine-4-thiol in solution when it is left stirring in solution at 67 °C for 15 h gives the [HS–Py–Py]⁺ derivative, as has been reported previously (Ding et al., 2020 ▸). In our case, the presence of IC₆F₄I favours the competitive reaction that implies the CH₂Cl₂ activation.

Compound 2 crystallized in an orthorhombic noncentrosymmetric spatial group Fdd2. The central C atom shows an angle slightly wider [116.3 (4)°] than that typical of sp ³-hybridation, probably due to the presence of the S atoms; the value is similar to that previously reported for bis[(pyridin-4-yl)sulfanyl]methane (Carballo et al., 2007 ▸, 2008a ▸,b ▸, 2009 ▸; Lago et al., 2013 ▸, 2014 ▸). The S—CH₂—S plane forms an angle of 78.66 (8)° with the planes of the pyridine rings, which are placed in opposite directions relative to the central CH₂ unit; this arrangement is also observed in the reported derivatives where bis[(pyridin-4-yl)sulfanyl]methane behaves as a ligand (Carballo et al., 2007 ▸, 2008a ▸,b ▸, 2009 ▸; Lago et al., 2013 ▸, 2014 ▸). This arrangement is the origin of the conformational chirality shown by this compound (Fig. 4 ▸). In our case, this disposition is also influenced by the presence of a hydrogen bond involving one chloride anion and the proton bonded to atom C4 of the ring. This conformation is reinforced by a chalcogen bond established between the Cl and S atoms [S⋯Cl = 3.373 (4) Å and C—S⋯Cl = 156.94 (5)°], which is significantly shorter than the van der Waals radii radius sum (3.55 Å; Bondi, 1964 ▸). Although the S atom can present two σ-holes, in this case, only one interaction is observed with the chloride anion.

Displacement ellipsoid plot (30% probability) of 2, showing (a) a view along the bc plane, (b) a view along the a direction and (c) a view of the packing directed by hydrogen and chalcogen bonds.

As mentioned before, the formation of the cation in 2 is an unusual reaction. Although similar substitution reactions have been reported for some secondary aliphatic (Souquet et al., 1993 ▸), alicyclic (Matsumoto et al., 1984 ▸) or heteroaromatic amines (Juliá et al., 1982 ▸; Zhao et al., 2011 ▸), the process usually takes place under special conditions, such as very high pressures or in highly polar solvent mixtures. Futhermore, it should be noted that the formation of the neutral equivalent bis[(pyridin-4-yl)sulfanyl]methane from pyridine-4-thiol in the presence of CH₂Cl₂ has been described previously in basic conditions, i.e. in an alcoholic solution with an excess of NaOH, the reaction taking several days to complete (Amoedo-Portela et al., 2005 ▸). In our case, the mechanism is different, as shown in the reaction pathway displayed in Fig. 5 ▸. Taking into account our previous studies, we have detected that the first step that implies the substitution of the chloride is the rate-determining step, and it proceeds via an S_N² mechanism. This process leads to a reactive chloromethyl intermediate –CH₂Cl⁺ which evolves quickly to the final product where both Cl atoms have been displaced (Sánchez-Roa et al., 2018 ▸). Hence, in this case, the IC₆F₄I role would be as a catalyst.

The proposed mechanism for the formation of salt 2.

Conclusions

The substituted pyridine pyridine-4-thiol can behave as a HaB acceptor, having a preference for the S atom as the acceptor. In the cocrystal obtained, the concomitant presence of a HaB and a hydrogen bond contributes to the stabilization of the zwitterionic form of pyridine-4-thiol. This arrangement has an effect on the reactivity and the activation of CH₂Cl₂ is promoted to give the bis[(4-pyridin-1-ium-4-yl)sulfanyl]methane dication, where two sulfide–pyridinium units are bonded to a –CH₂ group. This moiety could only come from the activation of the dichloromethane present as a solvent. Interestingly, there are not many examples of this type of activity and the current study opens up the possibility of developing processes for the transformation of chorinated hydrocarbons.

Supplementary Material

Crystal structure: contains datablock(s) global, 1, 2. DOI: 10.1107/S205322962300205X/qz3003sup1.cif

c-79-00112-sup1.cif^{(31.1KB, cif)}

Structure factors: contains datablock(s) 1. DOI: 10.1107/S205322962300205X/qz30031sup2.hkl

c-79-00112-1sup2.hkl^{(120KB, hkl)}

Structure factors: contains datablock(s) 2. DOI: 10.1107/S205322962300205X/qz30032sup3.hkl

c-79-00112-2sup3.hkl^{(76.8KB, hkl)}

Click here for additional data file.^{(6.1KB, cml)}

Supporting information file. DOI: 10.1107/S205322962300205X/qz30031sup4.cml

Click here for additional data file.^{(4.7KB, cml)}

Supporting information file. DOI: 10.1107/S205322962300205X/qz30032sup5.cml

CCDC references: 2222766, 2222767

Acknowledgments

The authors would like to acknowledge the support of Alcalá University, Spain, and the Madrid Regional Government.

Funding Statement

Funding for this research was provided by: Universidad de Alcala (grant No. PIUAH21/CC-028); Madrid Regional Government (grant No. EPUINV/2020/001).

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