research communications
Crystal and molecular structure of 4-fluoro-1H-pyrazole at 150 K
aWestern Michigan University, Department of Chemistry, 1903 W. Michigan Ave., Kalamazoo, MI 49008, USA, and bPurdue University, Department of Chemistry, 101 Wetherill Hall (WTHR), 560 Oval Drive, West Lafayette, IN 47907, USA
*Correspondence e-mail: gellert.mezei@wmich.edu
Only two 4-halo-1H-pyrazole crystal structures are known to date (chloro and bromo, the structure of 4-iodo-1H-pyrazole has not been reported yet). The triclinic structure of 4-fluoro-1H-pyrazole, C3H3FN2 (P), reported here is not isomorphous with those of the chloro and bromo analogues (which are isomorphous, orthorhombic Pnma). To avoid during the measurement, diffraction data were collected at 150 K. Two crystallographically unique 4-fluoro-1H-pyrazole moieties linked by an N—H⋯N hydrogen bond are found in the Unlike the trimeric supramolecular motifs found in the structures of the chloro and bromo analogues, 4-fluoro-1H-pyrazole forms one-dimensional chains by intermolecular hydrogen bonding in the crystal.
Keywords: pyrazole; crystal structure; low temperature; hydrogen-bonding motifs.
CCDC reference: 2253642
1. Chemical context
1H-Pyrazole (pzH) is both a hydrogen-bond donor and acceptor molecule, owing to its NH and N centers. Consequently, pyrazole moieties of the parent compound or C-substituted analogues form hydrogen bonds to each other in the corresponding crystal structures, and similarly to imidazole, have higher melting and boiling points than other five-membered cyclic aromatic molecules lacking either the hydrogen-bond acceptor (pyrrole), the hydrogen-bond donor (N-methyl derivatives, furan, isoxazole, oxazole, thiophene, isothiazole, thiazole) or both centers (cyclopentadiene) (Fig. 1). The proximity of the hydrogen-bond donor and acceptor centers in pz allows for the formation of either discreet hydrogen-bonded motifs, such as dimers, trimers, tetramers and hexamers, or polymeric catemers depending on the substituents (Bertolasi et al., 1999; Foces-Foces et al., 2000; Claramunt et al., 2006; Alkorta et al., 2006), whereas imidazole only forms catemers (Cammers & Parkin, 2004).
2. Structural commentary
As shown in Fig. 2, the contains two symmetry-independent 4-fluoro-1H-pyrazole moieties (Z′ = 2; P) , similarly to 1H-pyrazole (Z′ = 2; P21cn/Pna21; La Cour & Rasmussen, 1973; Sikora & Katrusiak, 2013) but unlike the chloro and bromo analogues (Z′ = 1.5; Pnma) (Rue & Raptis, 2021; Foces-Foces et al., 1999). Structures with Z′ >1 result when two or more intermolecular interactions, such as optimal shape packing, optimization of hydrogen bonds and aromatic interactions, are in conflict (Steed & Steed, 2015). Therefore, the Z′ value larger than 1 observed in these pyrazole structures emphasizes the importance of hydrogen bonding in their solid-state structures.
The two crystallographically independent 4-Fpz moieties, which are identical within experimental error, are planar with deviations from the C3FN2 mean-plane of less than 0.004 and 0.008 Å, respectively. Table 1 presents a comparison of bond lengths determined by X-ray diffraction for the parent pzH at 150 K (Sikora & Katrusiak, 2013), 4-FpzH at 150 K, 4-ClpzH at 150 K (Rue & Raptis, 2021) and 4-BrpzH at room temperature (Foces-Foces et al., 1999). All structures contain two symmetry-independent moieties. In the case of pzH and 4-FpzH, the NH and N centers of the pz rings are distinct, unlike in the case of 4-Cl/BrpzH. Therefore, in the former case two distinct sets of C—N and C—C bond distances are observed. Similarly to pzH, in 4-FpzH the C—N bond adjacent to N is shorter than the one adjacent to NH [by 0.008 (1)/0.010 (1) Å], whereas the C—C bond adjacent to N is longer than the one adjacent to NH [by 0.019 (1)/0.018 (1) Å]. In general, the N—N, C—N and C—C bond distances in 4-RpH are consistent across the R = H, F, Cl and Br series.
3. Supramolecular features
The pz N—H proton donates an N—H⋯N hydrogen bond to a neighbouring pz unit on one side, while the pz N atom accepts an N—H⋯N hydrogen bond from another pz unit on the opposite side (Table 2, Fig. 3). Thus, pz units in the resulting 4-FpzH catemer form dihedral angles of 59.74 (3)° with each other, with centroid–centroid distances of 4.9487 (5) Å. Adjacent catemers interact with each other by π–π stacking [distance between pz mean-planes = 3.4911 (8) Å; dihedral angle between pz mean planes = 0°, crystallographically imposed; centroid–centroid distance = 3.7034 (6) Å] and C—H⋯π interactions [dihedral angle between pz mean planes = 59.74 (3)°; centroid–centroid distance = 4.3794 (5)/4.4791 (5) Å, H⋯centroid distance = 2.8030 (3)/2.9007 (4) Å], on alternate sides (Fig. 4). As a result, the pz units are arranged in a herringbone pattern within the crystal (Fig. 5).
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4. Database survey
Although the parent pyrazole (pzH) also forms a hydrogen-bonded catemer in the crystal packing, its structure is quite different from the one formed by 4-FpzH. As illustrated in Fig. 6, pairs of pz units are found in two different geometries in the catemer of pzH: one in which they form dihedral angles of 5.45 (9)° with centroid–centroid distances of 5.1659 (15) Å, and another with dihedral angles of 74.64 (9)° and centroid–centroid distances of 5.0504 (15) Å. In contrast, pz units in 4-Cl/BrpzH form discreet hydrogen-bonded trimers. While the presence/nature of the 4-halo substituent leads to very different outcomes in terms of the overall packing and hydrogen-bonded motifs in 4-RpzH (R = H, F, Cl/Br), it has little effect on the corresponding hydrogen bonding parameters (Table 2). Interestingly, the structure of the catemer in 4-FpzH is essentially identical to the one found in the lattice of 4-acetyl-1H-pyrazole (monoclinic P21/n; Frey et al., 2014), with dihedral angles of 57.28 (7)° and centroid–centroid distances of 4.9501 (13) Å between adjacent pz units. The structure of the different catemer of pzH is also found in the crystal lattices of 4-phenyl-1H-pyrazole (orthorhombic, Pbcn; Reger et al., 2003) and 4-adamantyl-1H-pyrazole (triclinic, P; Cabildo et al., 1994), despite the large substituents. 4-Methyl-1H-pyrazole (orthorhombic, Pca21; Goddard et al., 1999) and 4-nitro-1H-pyrazole (triclinic, P; Llamas-Saiz et al., 1994), on the other hand, form trimers, similarly to 4-Cl/BrpzH.
5. Synthesis and crystallization
4-Fluoro-1H-pyrazole was synthesized according to a published procedure, from sodium fluoroacetate (WARNING: highly toxic!) by reaction with oxalyl chloride and dimethylformamide, followed by treatment with base and then hydrazine (England et al., 2010). Single crystals were obtained from the powder by slow isothermal inside a sealed vial under ambient conditions.
6. Refinement
Crystal data, data collection and structure . C—H bond distances were constrained to 0.95 Å and these H atoms were refined as riding. Positions of N-bound H atoms were freely refined. Uiso(H) values were set to 1.2 times Ueq(C/N) for all H atoms.
details are summarized in Table 3
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Supporting information
CCDC reference: 2253642
https://doi.org/10.1107/S2056989023003055/vm2280sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023003055/vm2280Isup2.hkl
Data collection: APEX4 v2022.1-1 (Bruker, 2022); cell
SAINT V8.40B (Bruker, 2022); data reduction: SAINT V8.40B (Bruker, 2022); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b), ShelXle Rev1460 (Hübschle et al., 2011).C3H3FN2 | Z = 4 |
Mr = 86.07 | F(000) = 176 |
Triclinic, P1 | Dx = 1.522 Mg m−3 |
a = 5.6045 (2) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 7.4315 (3) Å | Cell parameters from 9943 reflections |
c = 9.5396 (4) Å | θ = 2.3–33.1° |
α = 71.689 (2)° | µ = 0.14 mm−1 |
β = 87.731 (2)° | T = 150 K |
γ = 84.968 (2)° | Block, colourless |
V = 375.72 (3) Å3 | 0.45 × 0.43 × 0.38 mm |
Bruker AXS D8 Quest diffractometer | 2875 independent reflections |
Radiation source: fine focus sealed tube X-ray source | 2635 reflections with I > 2σ(I) |
Triumph curved graphite crystal monochromator | Rint = 0.024 |
Detector resolution: 7.4074 pixels mm-1 | θmax = 33.2°, θmin = 2.3° |
ω and phi scans | h = −8→8 |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | k = −11→11 |
Tmin = 0.678, Tmax = 0.747 | l = −14→14 |
15049 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.036 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.108 | w = 1/[σ2(Fo2) + (0.0579P)2 + 0.0788P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
2875 reflections | Δρmax = 0.47 e Å−3 |
116 parameters | Δρmin = −0.26 e Å−3 |
0 restraints | Extinction correction: SHELXL2018/3 (Sheldrick 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: dual | Extinction coefficient: 0.040 (10) |
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. |
x | y | z | Uiso*/Ueq | ||
F1_1 | 0.51610 (12) | 0.62514 (11) | 0.13759 (7) | 0.03931 (17) | |
N1_1 | 0.64380 (12) | 0.73038 (10) | 0.45438 (7) | 0.02162 (13) | |
H1N_1 | 0.721 (3) | 0.7343 (19) | 0.5331 (15) | 0.032* | |
N2_1 | 0.42422 (12) | 0.82300 (10) | 0.42828 (7) | 0.02262 (14) | |
C1_1 | 0.71303 (14) | 0.64372 (11) | 0.35314 (9) | 0.02302 (15) | |
H1_1 | 0.859931 | 0.571209 | 0.349074 | 0.028* | |
C2_1 | 0.52537 (14) | 0.68285 (11) | 0.25714 (8) | 0.02251 (15) | |
C3_1 | 0.34891 (13) | 0.79346 (11) | 0.30642 (8) | 0.02192 (15) | |
H3_1 | 0.198692 | 0.840571 | 0.260776 | 0.026* | |
F1_2 | 0.00161 (11) | 0.77865 (9) | 1.05091 (6) | 0.03386 (15) | |
N1_2 | 0.13614 (12) | 0.82593 (10) | 0.68400 (7) | 0.02239 (14) | |
H1N_2 | 0.217 (3) | 0.845 (2) | 0.6004 (16) | 0.034* | |
N2_2 | −0.06438 (12) | 0.73275 (10) | 0.69835 (7) | 0.02286 (14) | |
C1_2 | 0.19488 (14) | 0.85549 (11) | 0.81020 (8) | 0.02229 (15) | |
H1_2 | 0.328762 | 0.916175 | 0.826384 | 0.027* | |
C2_2 | 0.01926 (14) | 0.77888 (11) | 0.91040 (8) | 0.02065 (14) | |
C3_2 | −0.13824 (14) | 0.70401 (11) | 0.83817 (8) | 0.02168 (14) | |
H3_2 | −0.276718 | 0.642113 | 0.881490 | 0.026* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1_1 | 0.0372 (3) | 0.0597 (4) | 0.0370 (3) | −0.0145 (3) | 0.0046 (2) | −0.0357 (3) |
N1_1 | 0.0213 (3) | 0.0267 (3) | 0.0166 (3) | −0.0024 (2) | −0.0017 (2) | −0.0061 (2) |
N2_1 | 0.0220 (3) | 0.0284 (3) | 0.0182 (3) | −0.0005 (2) | 0.0008 (2) | −0.0090 (2) |
C1_1 | 0.0207 (3) | 0.0237 (3) | 0.0261 (3) | −0.0022 (2) | 0.0014 (2) | −0.0098 (3) |
C2_1 | 0.0232 (3) | 0.0278 (3) | 0.0213 (3) | −0.0083 (3) | 0.0027 (2) | −0.0131 (3) |
C3_1 | 0.0197 (3) | 0.0276 (3) | 0.0190 (3) | −0.0036 (2) | −0.0007 (2) | −0.0075 (2) |
F1_2 | 0.0395 (3) | 0.0492 (3) | 0.0174 (2) | −0.0117 (2) | 0.00202 (19) | −0.0149 (2) |
N1_2 | 0.0231 (3) | 0.0266 (3) | 0.0183 (3) | −0.0023 (2) | 0.0033 (2) | −0.0085 (2) |
N2_2 | 0.0236 (3) | 0.0275 (3) | 0.0196 (3) | −0.0021 (2) | −0.0016 (2) | −0.0102 (2) |
C1_2 | 0.0210 (3) | 0.0261 (3) | 0.0216 (3) | −0.0044 (2) | 0.0006 (2) | −0.0094 (3) |
C2_2 | 0.0228 (3) | 0.0248 (3) | 0.0156 (3) | −0.0029 (2) | −0.0004 (2) | −0.0078 (2) |
C3_2 | 0.0208 (3) | 0.0256 (3) | 0.0200 (3) | −0.0044 (2) | 0.0002 (2) | −0.0082 (2) |
F1_1—C2_1 | 1.3428 (8) | F1_2—C2_2 | 1.3396 (8) |
N1_1—C1_1 | 1.3473 (10) | N1_2—C1_2 | 1.3476 (10) |
N1_1—N2_1 | 1.3484 (9) | N1_2—N2_2 | 1.3513 (10) |
N1_1—H1N_1 | 0.892 (14) | N1_2—H1N_2 | 0.878 (14) |
N2_1—C3_1 | 1.3391 (10) | N2_2—C3_2 | 1.3375 (10) |
C1_1—C2_1 | 1.3729 (11) | C1_2—C2_2 | 1.3742 (10) |
C1_1—H1_1 | 0.9500 | C1_2—H1_2 | 0.9500 |
C2_1—C3_1 | 1.3922 (11) | C2_2—C3_2 | 1.3924 (10) |
C3_1—H3_1 | 0.9500 | C3_2—H3_2 | 0.9500 |
C1_1—N1_1—N2_1 | 112.75 (6) | C1_2—N1_2—N2_2 | 112.72 (6) |
C1_1—N1_1—H1N_1 | 129.5 (9) | C1_2—N1_2—H1N_2 | 129.9 (9) |
N2_1—N1_1—H1N_1 | 117.7 (9) | N2_2—N1_2—H1N_2 | 116.9 (9) |
C3_1—N2_1—N1_1 | 105.50 (6) | C3_2—N2_2—N1_2 | 105.43 (6) |
N1_1—C1_1—C2_1 | 105.09 (7) | N1_2—C1_2—C2_2 | 105.10 (7) |
N1_1—C1_1—H1_1 | 127.5 | N1_2—C1_2—H1_2 | 127.5 |
C2_1—C1_1—H1_1 | 127.5 | C2_2—C1_2—H1_2 | 127.5 |
F1_1—C2_1—C1_1 | 125.91 (7) | F1_2—C2_2—C1_2 | 126.25 (7) |
F1_1—C2_1—C3_1 | 126.73 (7) | F1_2—C2_2—C3_2 | 126.46 (7) |
C1_1—C2_1—C3_1 | 107.36 (7) | C1_2—C2_2—C3_2 | 107.29 (6) |
N2_1—C3_1—C2_1 | 109.29 (7) | N2_2—C3_2—C2_2 | 109.46 (7) |
N2_1—C3_1—H3_1 | 125.4 | N2_2—C3_2—H3_2 | 125.3 |
C2_1—C3_1—H3_1 | 125.4 | C2_2—C3_2—H3_2 | 125.3 |
C1_1—N1_1—N2_1—C3_1 | 0.49 (9) | C1_2—N1_2—N2_2—C3_2 | 0.85 (9) |
N2_1—N1_1—C1_1—C2_1 | −0.31 (9) | N2_2—N1_2—C1_2—C2_2 | −0.88 (9) |
N1_1—C1_1—C2_1—F1_1 | 179.71 (7) | N1_2—C1_2—C2_2—F1_2 | −178.67 (7) |
N1_1—C1_1—C2_1—C3_1 | 0.01 (9) | N1_2—C1_2—C2_2—C3_2 | 0.55 (9) |
N1_1—N2_1—C3_1—C2_1 | −0.46 (9) | N1_2—N2_2—C3_2—C2_2 | −0.46 (9) |
F1_1—C2_1—C3_1—N2_1 | −179.41 (7) | F1_2—C2_2—C3_2—N2_2 | 179.16 (7) |
C1_1—C2_1—C3_1—N2_1 | 0.29 (9) | C1_2—C2_2—C3_2—N2_2 | −0.06 (9) |
Numbers marked with an asterisk indicate average values in the case of pyrazoles with disordered NH/N centers. |
N—N | C—N (NH) | C—N (N) | C—C (NH) | C—C (N) | |
pzHa | 1.354 (2) | 1.337 (3) | 1.330 (3) | 1.368 (3) | 1.389 (3) |
1.351 (2) | 1.344 (3) | 1.326 (3) | 1.366 (3) | 1.389 (3) | |
4-FpzHb | 1.3484 (9) | 1.3473 (10) | 1.3391 (10) | 1.3729 (11) | 1.3922 (11) |
1.3513 (10) | 1.3476 (10) | 1.3375 (10) | 1.3742 (10) | 1.3924 (10) | |
4-ClpzHc | 1.346 (2) | 1.335 (2)* | 1.334 (2)* | 1.380 (2)* | 1.374 (2)* |
1.345 (3) | 1.334 (2)* | 1.334 (2)* | 1.377 (2)* | 1.377 (2)* | |
4-BrpzHd | 1.335 (9) | 1.327 (10)* | 1.331 (10)* | 1.391 (11)* | 1.338 (10)* |
1.335 (9) | 1.343 (10)* | 1.343 (10)* | 1.371 (9)* | 1.371 (9)* |
Notes: (a) Sikora & Katrusiak (2013); (b) this work; (c) Rue & Raptis (2021); (d) Foces-Foces et al. (1999). |
D—H···A | D—H | H···A | D···A | D–H···A |
pzH | ||||
N1—H1···N3 | 0.860 (2) | 2.038 (2) | 2.885 (3) | 167.73 (10) |
N4—H5···N2i | 0.861 (2) | 2.083 (2) | 2.881 (3) | 153.87 (13) |
4-FpzH | ||||
N1_2—H1N_2···N2_1 | 0.878 (14) | 2.014 (16) | 2.8764 (10) | 166.6 (13) |
N1_1—H1N_1···N2_2ii | 0.892 (14) | 2.017 (16) | 2.9024 (10) | 172.4 (15) |
4-ClpzH | ||||
N1—H1A···N1iii | 0.88 | 2.03 | 2.885 (3) | 165 |
N2—H2···N3iv | 0.88 | 1.99 | 2.8582 (19) | 169 |
N3—H3A···N2iv | 0.88 | 1.99 | 2.8582 (19) | 169 |
4-BrpzH | ||||
N12—H12···N21 | 1.02 | 1.87 | 2.871 (9) | 169 |
N21—H21···N12 | 1.01 | 1.87 | 2.871 (9) | 171 |
N22—H22···N22v | 1.02 | 1.93 | 2.922 (9) | 164 |
Symmetry codes: (i) x + 1/2, -y + 3/2, z; (ii) x + 1, y, z; (iii) x, -y + 3/2, z; (iv) -x + 1, -y + 1, -z; (v) x, -y+1/2, z. |
Funding information
Funding for this research was provided by: National Science Foundation (grant No. CHE-1808554 to Western Michigan University for Gellert Mezei; grant No. CHE-1625543 to Purdue University for the single-crystal X-ray diffractometer).
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