research communications
Structural characterization and Hirshfeld surface analysis of 2-iodo-4-(pentafluoro-λ6-sulfanyl)benzonitrile
aDepartment of Chemistry, University of Puerto Rico-Rio Piedras Campus, PO Box 23346, San Juan, 00931-3346, Puerto Rico, and bDepartment of Chemistry and the Molecular Sciences Research Center, University of Puerto Rico-Rio Piedras Campus, PO Box 23346, San Juan, 00931-3346, Puerto Rico
*Correspondence e-mail: dalice.pinero@upr.edu
The title compound, C7H3F5INS, a pentafluorosulfanyl (SF5) containing arene, was synthesized from 4-(pentafluorosulfanyl)benzonitrile and lithium tetramethylpiperidide following a variation to the standard approach, which features simple and mild conditions that allow direct access to tri-substituted SF5 intermediates that have not been demonstrated using previous methods. The molecule displays a planar geometry with the benzene ring in the same plane as its three substituents. It lies on a mirror plane perpendicular to [010] with the iodo, cyano, and the sulfur and axial fluorine atoms of the pentafluorosulfanyl substituent in the plane of the molecule. The equatorial F atoms have symmetry-related counterparts generated by the mirror plane. The pentafluorosulfanyl group exhibits a staggered fashion relative to the ring and the two hydrogen atoms ortho to the substituent. S—F bond lengths of the pentafluorosulfanyl group are unequal: the equatorial bond facing the iodo moiety has a longer distance [1.572 (3) Å] and wider angle compared to that facing the side of the molecules with two hydrogen atoms [1.561 (4) Å]. As expected, the axial S—F bond is the longest [1.582 (5) Å]. In the crystal, in-plane C—H⋯F and N⋯I interactions as well as out-of-plane F⋯C interactions are observed. According to the Hirshfeld analysis, the principal intermolecular contacts for the title compound are F⋯H (29.4%), F⋯I (15.8%), F⋯N (11.4%), F⋯F (6.0%), N⋯I (5.6%) and F⋯C (4.5%).
Keywords: substituted arenes; pentafluorothio; functionalized aromatic rings; organometallic synthesis; crystal structure.
CCDC reference: 1943767
1. Chemical context
Organic compounds containing the trifluoromethyl (CF3) or pentafluorothio (or pentafluoro-λ6-sulfanyl, SF5) groups play an important role in organofluorine chemistry because of their special properties including low surface energy, hydrophobicity, high chemical resistance, high thermal stability and high (Kirsch et al., 1999, 2014; Iida et al., 2015; Beier et al., 2011). SF5, coined as the `super-trifluoromethyl' group, is often preferred to CF3 as it is more electronegative, lipophilic and chemically stable, and possesses a higher (Bowden et al., 2000). The current interest in the field of drug discovery of fluorinated substituents is based on the possibility of improving both the metabolic stability and bioavailability of receptor binders upon the incorporation of susbtituents with one or more fluorine atoms (Altomonte et al., 2014; Savoie & Welch, 2015; Sowaileh et al., 2017). In fact, several blockbuster drugs include such a group, demonstrating the prominent role of the trifluoromethyl group in the area of drug discovery (O'Hagan, 2010; Müller et al., 2007; Purser et al., 2008). New molecules incorporating the SF5 group are thus potential alternatives to already existing biologically active molecules containing the CF3 substitution. Additionally, the chemical robustness of SF5 has been explored in other areas such as polymer chemistry (Zhou et al., 2016). Despite the popularity of the title compound, an important precursor in organofluorine chemistry, its crystallographic characterization, which is an important milestone in the synthesis of next-generation materials containing this motif, has not been reported. Herein, we describe a variation to the synthetic approach and give details of its simple crystallization through slow evaporation methods, yielding X-ray diffraction-quality single crystals.
The title compound was obtained as part of our studies toward the synthesis of functionalized 5 moiety. Its synthesis involves a one-pot reaction in which the interaction of the cyano group in 4-(pentafluorosulfanyl)benzonitrile to the Lewis acidic lithium cation in lithium tetramethylpiperidide (LiTMP) allows deprotonation from the nearest ortho-H atom on the arene. The SF5-containing organolithium species is then quenched with iodine to yield the title compound. This reaction pathway was proposed by Iida et al. (2015) for the synthesis of SF5-substituted zinc phthalocyanines. We modified the synthesis by adding tetramethylethylenediamine (TMEDA), an amine additive that serves to break up the lithiated base aggregates, allowing for accelerated reactivity because of the increased basicity. This variation improves the total yield of the title compound by 8%.
containing the SF2. Structural commentary
Fig. 1 shows the molecular structure of the title compound, which crystallizes in the Pnma. Its comprises a single molecule lying on a mirror plane perpendicular to [010] with the iodo, cyano, and the sulfur and axial fluorine atoms of the pentafluorosulfanyl substituent in the plane of the molecule. The fluorine atoms of the pentafluorosulfanyl group in the equatorial positions lie above and below the plane in a staggered fashion relative to the two hydrogen atoms ortho to the substituent; of those, two of the four fluorine atoms are generated symmetrically by the mirror plane. The S1—F(eq) bond distances differ from each other depending on which side of the molecule the bond is located (Table 1). The S1—F2(eq) bond and its symmetry equivalent S1—F2 i(eq) [symmetry code: (i) x, −y + , z] are on the same side as the iodine atom and exhibit a longer bond distance of 1.572 (3) Å in comparison to S1—F1(eq) and S1—F1i(eq), which are further away from the iodine and have a shorter bond length distance of 1.561 (4) Å. The S1—F3(ax) bond length of 1.582 (5) Å is the longest and is consistent with those in similar structures [1.588 (2) and 1.573 (3) Å; Du et al., 2016].
3. Supramolecular features
The packing of the title compound is consolidated through a series of intermolecular interactions, which can be classified as being in-plane and out-of-plane (Table 2). Each molecule acts as a C—H donor through the meta- and para-hydrogen atoms of the phenyl ring counter to the iodine atom. Two C–H⋯F hydrogen bonds, C5—H5⋯F3 and C6—H6⋯F3 with H⋯F distances of 2.5 and 2.6 Å, respectively, create an in-plane network (Table 2 and Fig. 2). Both the H5 and H6 atoms are highly acidic because of the electron-withdrawing effects of the –SF5 and –CN substituents. Additionally, significant in-plane halogen-bonding interactions [N1⋯I1( + x, − y, − z) = 3.408 (10) Å] are observed (Metrangolo et al., 2005). Out-of-plane intermolecular interactions arise primarily from F⋯π ring interactions at one of the `corners' of the ring (Fig. 3) with an F2⋯C3(2 − x, − + y, 1 − z) distance of 3.124 (5) Å.
4. Hirshfeld surface analysis
The Hirshfeld surface (Spackman & Jayatilaka, 2009) for the title compound mapped over dnorm is shown in Fig. 4 while Fig. 5 shows the associated two-dimensional fingerprint plots (McKinnon et al., 2007), both generated with CrystalExplorer17 (Turner et al., 2017). Red spots on the Hirshfeld surface mapped over dnorm in the colour range −0.4869 to 1.4157 arbitrary units confirm the previously mentioned main intermolecular contacts. The fingerprint plots are given for all contacts and those delineated into F⋯H/H ⋯F (29.4%; Fig. 5b), F⋯I/I⋯F (15.8%; Fig. 5c), F⋯N/N⋯F (11.4%; Fig. 5d), H⋯N/N⋯H (6.3%; Fig. 5e), I⋯N/N⋯I (5.6%; Fig. 5f), C⋯F/F⋯C (4.5%; Fig. 5g), C⋯H/H⋯C (4.5%; Fig. 5h), I⋯H/H⋯I (3.3%; Fig. 5i), C⋯N/N⋯C (1.6%; Fig. 5j), C⋯C (9.5%; Fig. 5k), F⋯F (6.0%; Fig. 5l) and I⋯I (2.2%; Fig. 5m) interactions. Thus, the Hirshfeld surface analysis indicates that the most significant contributions arise from F⋯H and F⋯I contacts.
5. Database survey
A search of the Cambridge Structural Database (Version 5.39, updated May 2017; Groom et al., 2016) revealed no matching compounds with the title compound and the three substituents. However, a search for SF5 aryl compounds fragment revealed about 85 hits: 77 of these structures were reported in the last 10 years, which shows the increasing interest in the SF5 group. Most of these compounds are used as reagents in the synthesis and modification of pharmaceuticals, such as the antimalarial agent mefloquine (Wipf et al., 2009) and the anti-obesity drug fenfluramine (Welch et al., 2007).
6. Synthesis and crystallization
All solvents and reagents were purified prior to being used. 4-(Pentafluorosulfanyl)benzonitrile was obtained commercially and used without further purification. A solution of 2.5 M n-butyl lithium in hexanes was used. Column chromatography was carried out on a column packed with silica gel 70–230 mesh.
The synthesis of the title compound was performed through the regioselective ortho-lithiation of 4-(pentafluorosulfanyl)benzonitrile with lithium tetramethylpiperidide (LiTMP) in THF as solvent, favouring the formation of the ortho product (1,2,4-substituted arene) over the meta product (1,3,4-substituted arene). The ortho-metalated product was subsequently quenched with I2 to afford the iodinated trisubstituted arene. A dry 50 mL Schlenk tube was charged with 4 mL of dry THF and 300 µL of 2,2,6,6-tetramethyl piperidine (1.75 mmol, 2 eq.) and 262 µL of N,N,N,N-tetramethylethylendiamine (1.75 mmol) were added under an inert atmosphere. The solution was cooled to 273 K and 700 µL of 2.5 M n-butyl lithium in hexane (1.75 mmol, 2 eq.) were added slowly. The reaction mixture was stirred at 273 K for 30 minutes and then cooled to 195 K. A solution containing 200 mg of 4-(pentafluorosulfanyl)benzonitrile (0.872 mmol, 1 eq.) in 4 mL THF was added dropwise: the solution changed from pale yellow to dark brown upon formation of the metalated intermediary. After stirring for 1 h at 195 K, a solution of 244 mg I2 (0.960 mmol, 1.2 eq.) in 4 mL THF was added dropwise and stirred for 2 h. The mixture was then warmed to room temperature and stirred for 1 h.
The reaction was quenched with water and THF was removed under reduced pressure, followed by extraction with diethyl ether. The combined organic phase was washed with aqueous 0.1 M HCl, 0.1 M Na2S2O3 and brine, then dried over MgSO4. The crude product was purified by (9:1, hexane:ethyl acetate) to yield 71 mg (46%) of the pure arene product as a yellow solid (m.p. 367–369 K). Block-like yellow crystals suitable for X-ray diffraction were obtained by slow evaporation of a saturated CH2Cl2 solution of the 2-iodo-4-(pentafluoro-λ6-sulfanyl)benzonitrile at room temperature over a period of four days. NMR analyses were performed on a Bruker AV-500 spectrometer using chloroform-d as solvent (CDCl3). The solvent signals at 7.26 and 77.00 ppm were used as internal standards for proton and carbon, respectively. 1H NMR (500 MHz, Chloroform-d) δ 8.31 (d, J = 2.1 Hz, 1H), 7.89 (dd, J = 8.6, 2.1 Hz, 1H), 7.75 (d, J = 8.6 Hz, 1H). 13C NMR (125 MHz, CDCl3) δ, 98.22, 117.83, 124.10, 126.16, 134.39, 136.82, 156.15.
7. Refinement
Data collection, crystal data and structure . H atoms were included in geometrically calculated positions and refined as riding atoms with C—H = 0.93 Å and Uiso(H) = 1.2Ueq(C).
parameters are summarized in Table 3Supporting information
CCDC reference: 1943767
https://doi.org/10.1107/S2056989020000365/dx2019sup1.cif
contains datablock I. DOI:Supporting information file. DOI: https://doi.org/10.1107/S2056989020000365/dx2019Isup3.cml
Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020000365/dx2019Isup4.hkl
Data collection: CrysAlis PRO (Rigaku OD, 2018); cell
CrysAlis PRO (Rigaku OD, 2018); data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: ShelXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).C7H3F5INS | Dx = 2.308 Mg m−3 |
Mr = 355.06 | Cu Kα radiation, λ = 1.54184 Å |
Orthorhombic, Pnma | Cell parameters from 6922 reflections |
a = 8.0634 (1) Å | θ = 2.7–68.4° |
b = 7.7088 (1) Å | µ = 26.99 mm−1 |
c = 16.4410 (3) Å | T = 300 K |
V = 1021.96 (3) Å3 | Irregular, clear light yellow |
Z = 4 | 0.26 × 0.17 × 0.12 mm |
F(000) = 664 |
SuperNova, Single source at offset/far, HyPix3000 diffractometer | 953 reflections with I > 2σ(I) |
ω scans | Rint = 0.082 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018) | θmax = 68.8°, θmin = 5.4° |
Tmin = 0.287, Tmax = 1.000 | h = −9→9 |
9403 measured reflections | k = −9→9 |
1020 independent reflections | l = −19→19 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.042 | H-atom parameters constrained |
wR(F2) = 0.111 | w = 1/[σ2(Fo2) + (0.071P)2 + 1.8371P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
1020 reflections | Δρmax = 0.74 e Å−3 |
85 parameters | Δρmin = −1.77 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
Refinement. ShelXL |
x | y | z | Uiso*/Ueq | ||
I1 | 0.67725 (6) | 0.750000 | 0.31142 (3) | 0.0540 (3) | |
S1 | 0.97572 (19) | 0.750000 | 0.62917 (9) | 0.0398 (4) | |
F3 | 1.1407 (6) | 0.750000 | 0.6812 (3) | 0.0641 (14) | |
F2 | 1.0576 (4) | 0.6065 (5) | 0.5743 (2) | 0.0641 (9) | |
F1 | 0.9063 (5) | 0.8925 (6) | 0.68738 (19) | 0.0819 (13) | |
C4 | 0.7869 (8) | 0.750000 | 0.5682 (4) | 0.0356 (13) | |
C3 | 0.8020 (7) | 0.750000 | 0.4841 (4) | 0.0335 (13) | |
H3 | 0.905856 | 0.750000 | 0.459508 | 0.040* | |
C2 | 0.6572 (8) | 0.750000 | 0.4373 (4) | 0.0352 (13) | |
C1 | 0.5034 (8) | 0.750000 | 0.4752 (4) | 0.0467 (16) | |
C7 | 0.3514 (9) | 0.750000 | 0.4290 (5) | 0.056 (2) | |
C5 | 0.6348 (10) | 0.750000 | 0.6059 (5) | 0.065 (3) | |
H5 | 0.628167 | 0.750000 | 0.662401 | 0.078* | |
N1 | 0.2295 (10) | 0.750000 | 0.3943 (6) | 0.080 (2) | |
C6 | 0.4948 (10) | 0.750000 | 0.5606 (5) | 0.072 (3) | |
H6 | 0.391926 | 0.750000 | 0.586180 | 0.087* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.0575 (4) | 0.0786 (4) | 0.0259 (3) | 0.000 | −0.00566 (16) | 0.000 |
S1 | 0.0409 (8) | 0.0534 (9) | 0.0250 (8) | 0.000 | −0.0044 (6) | 0.000 |
F3 | 0.055 (3) | 0.097 (4) | 0.040 (3) | 0.000 | −0.020 (2) | 0.000 |
F2 | 0.0622 (18) | 0.0697 (19) | 0.0605 (18) | 0.0256 (16) | −0.0188 (15) | −0.0192 (17) |
F1 | 0.081 (3) | 0.110 (3) | 0.055 (2) | 0.022 (2) | −0.0146 (16) | −0.044 (2) |
C4 | 0.038 (3) | 0.045 (3) | 0.024 (3) | 0.000 | −0.002 (3) | 0.000 |
C3 | 0.037 (3) | 0.038 (3) | 0.026 (3) | 0.000 | 0.000 (2) | 0.000 |
C2 | 0.047 (4) | 0.033 (3) | 0.025 (3) | 0.000 | −0.003 (2) | 0.000 |
C1 | 0.038 (3) | 0.066 (4) | 0.036 (4) | 0.000 | −0.003 (3) | 0.000 |
C7 | 0.046 (4) | 0.081 (6) | 0.042 (5) | 0.000 | −0.004 (3) | 0.000 |
C5 | 0.047 (4) | 0.121 (8) | 0.027 (4) | 0.000 | 0.002 (3) | 0.000 |
N1 | 0.049 (4) | 0.121 (7) | 0.071 (5) | 0.000 | −0.016 (4) | 0.000 |
C6 | 0.036 (4) | 0.139 (9) | 0.042 (4) | 0.000 | 0.014 (3) | 0.000 |
I1—C2 | 2.076 (6) | C3—H3 | 0.9300 |
S1—F3 | 1.582 (5) | C3—C2 | 1.399 (8) |
S1—F2 | 1.572 (3) | C2—C1 | 1.388 (9) |
S1—F2i | 1.572 (3) | C1—C7 | 1.442 (10) |
S1—F1i | 1.561 (4) | C1—C6 | 1.406 (11) |
S1—F1 | 1.561 (4) | C7—N1 | 1.136 (10) |
S1—C4 | 1.823 (7) | C5—H5 | 0.9300 |
C4—C3 | 1.388 (9) | C5—C6 | 1.353 (11) |
C4—C5 | 1.374 (10) | C6—H6 | 0.9300 |
F3—S1—C4 | 179.4 (3) | C5—C4—C3 | 121.8 (6) |
F2i—S1—F3 | 87.52 (18) | C4—C3—H3 | 120.8 |
F2—S1—F3 | 87.52 (18) | C4—C3—C2 | 118.4 (6) |
F2i—S1—F2 | 89.4 (3) | C2—C3—H3 | 120.8 |
F2—S1—C4 | 92.04 (19) | C3—C2—I1 | 118.9 (5) |
F2i—S1—C4 | 92.04 (19) | C1—C2—I1 | 121.2 (5) |
F1i—S1—F3 | 88.3 (2) | C1—C2—C3 | 119.9 (6) |
F1—S1—F3 | 88.3 (2) | C2—C1—C7 | 121.6 (6) |
F1—S1—F2i | 90.4 (2) | C2—C1—C6 | 119.5 (6) |
F1—S1—F2 | 175.8 (2) | C6—C1—C7 | 118.9 (7) |
F1i—S1—F2 | 90.4 (2) | N1—C7—C1 | 178.4 (9) |
F1i—S1—F2i | 175.8 (2) | C4—C5—H5 | 120.1 |
F1i—S1—F1 | 89.5 (4) | C6—C5—C4 | 119.8 (7) |
F1i—S1—C4 | 92.2 (2) | C6—C5—H5 | 120.1 |
F1—S1—C4 | 92.2 (2) | C1—C6—H6 | 119.7 |
C3—C4—S1 | 118.3 (5) | C5—C6—C1 | 120.6 (7) |
C5—C4—S1 | 119.8 (5) | C5—C6—H6 | 119.7 |
I1—C2—C1—C7 | 0.000 (2) | F1i—S1—C4—C5 | 44.79 (18) |
I1—C2—C1—C6 | 180.000 (2) | C4—C3—C2—I1 | 180.000 (1) |
S1—C4—C3—C2 | 180.000 (2) | C4—C3—C2—C1 | 0.000 (2) |
S1—C4—C5—C6 | 180.000 (2) | C4—C5—C6—C1 | 0.000 (3) |
F2—S1—C4—C3 | −44.74 (15) | C3—C4—C5—C6 | 0.000 (3) |
F2i—S1—C4—C3 | 44.74 (15) | C3—C2—C1—C7 | 180.000 (2) |
F2i—S1—C4—C5 | −135.26 (15) | C3—C2—C1—C6 | 0.000 (2) |
F2—S1—C4—C5 | 135.26 (15) | C2—C1—C6—C5 | 0.000 (3) |
F1i—S1—C4—C3 | −135.21 (18) | C7—C1—C6—C5 | 180.000 (2) |
F1—S1—C4—C3 | 135.21 (18) | C5—C4—C3—C2 | 0.000 (2) |
F1—S1—C4—C5 | −44.79 (18) |
Symmetry code: (i) x, −y+3/2, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H5···F3ii | 0.93 | 2.57 | 3.501 (1) | 174 |
C6—H6···F3iii | 0.93 | 2.56 | 3.476 (1) | 169 |
Symmetry codes: (ii) x−1/2, −y+3/2, −z+3/2; (iii) x−1, −y+3/2, z. |
S1—F1(eq) and S1—–F1i(eq) | 1.561 (4) |
S1—F2(eq) and S1—F2i(eq) | 1.572 (3) |
S1—F3(ax) | 1.582 (5) |
C4—S1—F2(eq) | 92.0 (2) |
C4—S1—F1(eq) | 92.2 (2) |
Symmetry code: (i) x, -y + 3/2, z. |
D—H···A/D···A | D—H | H···A | D···A | D—H···A |
C5—H5···F3 | 0.93 | 2.57 | 3.501 (1) | 174 |
F2···C3 | – | – | 3.123 (1) | – |
C6—H6···F3 | 0.93 | 2.56 | 3.476 (1) | 169 |
N1···I1 | – | – | 3.408 (1) | - |
Contact | % contribution | Contact | % contribution |
F···H/H···F | 29.4 | C···C | 9.5 |
F···I/I···F | 15.8 | F···F | 6.0 |
F···N/N···F | 11.4 | I···I | 2.2 |
H···N/N···H | 6.3 | ||
I···N/N···I | 5.6 | ||
C···F/F···C | 4.5 | ||
C···H/H···C | 4.5 | ||
I···H/H···I | 3.3 | ||
C···N/N···C | 1.6 |
Funding information
The authors acknowledge financial support by the NSF–CREST Center for Innovation, Research and Education in Environmental Nanotechnology (CIRE2N) grant No. HRD-1736093. The single crystal x-ray diffractometer was acquired through the support of the National Science Foundation under the Major Research Instrumentation Award No. CHE-1626103.
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