Home Crystal structure of bis(3,5-dimethyl-1H-pyrazol-4-ammonium) tetrafluoroterephthate, 2[C5H10N3][C8F4O4]
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Crystal structure of bis(3,5-dimethyl-1H-pyrazol-4-ammonium) tetrafluoroterephthate, 2[C5H10N3][C8F4O4]

  • Kiyoshi Fujisawa ORCID logo EMAIL logo , Seigo Harakuni , Keigo Ageishi and Edward R. T. Tiekink ORCID logo EMAIL logo
Published/Copyright: August 21, 2023

Abstract

2[C5H10N3][C8F4O4], monoclinic, P21/n (no. 14), a = 6.1490(2) Å, b = 11.0063(3) Å, c = 14.0214(3) Å, β = 94.386(5), V = 946.16(5) Å3, Z = 2, R gt (F) = 0.0371, wR ref (F2) = 0.1127, T = 178 K.

CCDC no.: 2285587

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.16 × 0.14 × 0.10 mm
Wavelength: MoKα radiation (0.71073 Å)
μ: 0.14 mm−1
Diffractometer, scan mode: Rigaku XtaLAB P200, ω
θmax, completeness: 29.6°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 6985, 2414, 0.021
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 2259
N(param)refined: 159
Programs: CrysAlisPRO [1], IL MILIONE [2], SHELX [3], WinGX/ORTEP [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z Uiso*/Ueq
N1 0.36750 (15) 0.33299 (9) −0.08110 (7) 0.0178 (2)
H1N 0.291 (2) 0.3370 (14) −0.1373 (8) 0.021*
N2 0.26894 (15) 0.36280 (9) −0.00029 (7) 0.0182 (2)
N3 0.83825 (14) 0.32853 (9) 0.08590 (6) 0.0156 (2)
H2N 0.841 (3) 0.2570 (10) 0.1197 (10) 0.023*
H3N 0.853 (3) 0.3915 (12) 0.1283 (10) 0.023*
H4N 0.955 (2) 0.3320 (15) 0.0496 (11) 0.023*
C1 0.72698 (19) 0.28321 (12) −0.14236 (8) 0.0230 (2)
H1A 0.733071 0.194500 −0.147514 0.034*
H1B 0.874302 0.315120 −0.127015 0.034*
H1C 0.667020 0.317498 −0.203310 0.034*
C2 0.58520 (17) 0.31739 (10) −0.06537 (7) 0.0155 (2)
C3 0.62920 (16) 0.33752 (9) 0.03093 (7) 0.0139 (2)
C4 0.43077 (17) 0.36511 (9) 0.06909 (7) 0.0155 (2)
C5 0.39585 (18) 0.39193 (11) 0.17112 (8) 0.0211 (2)
H5A 0.239157 0.398388 0.178724 0.032*
H5B 0.467426 0.468767 0.189879 0.032*
H5C 0.458021 0.326241 0.211774 0.032*
F1 −0.27376 (11) 0.38486 (7) −0.38662 (5) 0.02198 (18)
F2 0.40163 (11) 0.57251 (7) −0.42807 (5) 0.02257 (18)
O1 0.25345 (15) 0.35392 (8) −0.28398 (6) 0.0240 (2)
O2 0.08167 (14) 0.52050 (9) −0.23902 (6) 0.0265 (2)
C6 0.14165 (17) 0.44777 (10) −0.29906 (7) 0.0157 (2)
C7 0.06848 (17) 0.47559 (9) −0.40327 (7) 0.0145 (2)
C8 −0.13667 (17) 0.44180 (9) −0.44222 (7) 0.0152 (2)
C9 0.20297 (17) 0.53508 (9) −0.46292 (7) 0.0153 (2)

1 Source of material

Under an argon atmosphere, the reaction of 4-amino-3,5-dimethyl-1-pyrazole (0.050 g, 0.45 mmol) with tetrafluoroterephthalic acid (0.049 g, 0.21 mmol) in anhydrous methanol (10 mL) was conducted at room temperature overnight. The solvent was removed in vacuo. The colourless crystals of (I), suitable for X-ray analysis, were obtained by slow evaporation at room temperature from an anhydrous methanol and toluene solution (7:3 v/v) (0.042 g, 0.091 mmol, 43 % yield). Anal. Calcd. for C18H20F4N6O4: C 46.96, H 4.38, N 18.25 %. Found: C 46.85, H 4.41, N 18.27 %. 1H NMR (CD3OD, 500 MHz): δ 2.17 (s, 12H, CH3); N–H protons were not observed. IR (KBr, cm−1): 3197 s ν(N–H), 2894 s ν(C–H), 1639 s ν(C=O), 1607 s ν(C=O), 1466 s, 1382 s, 978 s, 728 s.

2 Experimental details

The C-bound H atoms were geometrically placed (C–H = 0.98 Å) and refined as riding with Uiso(H) = 1.5Ueq(C). The N-bound H atoms were located in a difference Fourier map and refined with pyrazolyl–N–H = 0.88 ± 0.01 Å and ammonium–N–H = 0.91 ± 0.01 Å with Uiso(H) = 1.2 and 1.5Ueq(N), respectively.

3 Comment

Recently, covalent organic frameworks (COFs) became recognised as a new class of materials featuring linkages supported by strong covalent bonds to form two-or three-dimensional, porous and stable crystalline materials [5]. In COFs the covalent links can arise from, for example, B–O, imine–C=N and amide–C–N bond formation [6]. The title salt (I, systematic name: bis(3,5-dimethyl-1H-pyrazol-4-aminium) 2,3,5,6-tetrafluorobenzene-1,4-dicarboxylate) was generated in an on-going study into imine–C=N bond formation, employing an aliphatic or aromatic amine reacting with an aldehyde followed by dehydration. Previously, the structure of the result of C=N bond formation by the direct reaction of 4-amino-3,5-diisopropyl-1-pyrazole (L1HpzNH2) [7] with terephthalaldehyde (benzene-1,4-dicarboxaldehyde) was described [8]. Moreover, the structure obtained by the reaction of the less hindered methyl-substituted pyrazole viz. 4-amino-3,5-dimethyl-1-pyrazole (L0HpzNH2) with terephthalaldehyde in anhydrous methanol solution has also been described recently [9]. In this article, the results of the exploration of amide bond formation by the reaction of L0HpzNH2 with a carboxylic acid, i.e. tetrafluoroterephthalic acid, are outlined. While initially terephthalic acid was employed as the carboxylic acid source, this acid has very poor solubility in normal organic solvents such as methanol, ethanol and chloroform. Therefore, tetrafluoroterephthalic acid was evaluated as the carboxylic acid precursor, since the presence of fluoride improves the solubility in regular solvents due to the polarized Cδ+ and Fδ atoms [10, 11]. In the IR spectrum, salt (I) has a characteristic absorption band at 3197 cm−1, which is assigned to N–H stretching. It is also noted that the sharp N–H2 stretching band evident at 3345 cm−1 in the IR spectrum of L0HpzNH2 disappeared. In addition, new characteristic C=O stretching bands, split at 1639 and 1607 cm−1, which are clearly shifted from those of the other starting material, tetrafluoroterephthalic acid (1700 cm−1).

The molecular structures of the constituents of salt (I) are shown in the upper view of the figure (70 % displacement ellipsoids, dashed lines indicate N–H⋯O hydrogen bonds and unlabelled atoms are related by the symmetry operation – x, 1 – y, 1 – z). The asymmetric-unit comprises a 3,5-dimethyl-1H-pyrazol-4-ammonium cation, in a general position, and half a 2,3,5,6-tetrafluorobenzene-1,4-dicarboxylate dianion, being situated about a centre of inversion. The confirmation of proton transfer during co-crystallisation is evident in the near equivalence of the C6–O1,O2 bond lengths [1.2498(13) & 1.2381(13) Å] and the wider angle at the N1 atom [C2–N1–N2 = 113.09(9)] compared with that at the N2 atom [C4–N2–N1 = 104.80(9)].

The pyrazolyl ring is planar to ±0.002(1) Å and an evaluation of the bond lengths within the five-membered ring is consistent with the delocalisation of π-electron density over the constituent atoms. Thus, the formally double-bonded C4–N2 [1.3376(14) Å] and C2–C3 [1.3745(13) Å] bonds are elongated and the formally single-bonded N1–N2 [1.3653(13) Å], C2–N1 [1.3509(14) Å] and C3–C4 [1.4026(14) Å] bonds are shortened; the exocyclic C3–N3 bond length is 1.4508(13) Å. The dianion is not planar with the carboxylate residues being close to orthogonal to the phenyl ring to which they are connected to, with the dihedral angle between the respective least-squares planes being 83.14(6). The dihedral angle between the carboxylate residue and the hydrogen bonded pyrazolyl ring is 41.84(8).

The crystal structure of the neutral 3,5-dimethyl-4-aminopyrazole molecule has been described [12]. There is a high degree of concordance in the geometric parameters in the pyrazolyl rings although the N1–N2 bond length of 1.353(2)° is shorter than that in (I) [1.3653(13) Å]. Further, two molecules of 3,5-dimethyl-4-aminopyrazole coordinate the cobalt(II) atom of CoCl2 via the imine–N atoms to generate a tetrahedral complex [13]. Finally, a cation of 3,5-dimethyl-4-aminopyrazole with a 3,4-dicarboxy-3-hydroxybutanoate counter-anion, as a monohydrate, has been reported [14]. Here, protonation has occurred at the ring rather than at the amino–N atom in (I).

As anticipated from the compositon of (I), extensive hydrogen-bonding is evident in the crystal; all specified hydrogen bonds are charge-assisted. The connection between the pyrazolyl–N–H and the carboxylate–O1 atoms [N1–H1n⋯O1: H1n⋯O1 = 2.060(11) Å, N1⋯O1 = 2.8865(13) Å with angle at H1n = 154.5(11)] is highlighted as blue-dashed bonds in the unit-cell diagram shown in the lower view of the figure. When viewed down the a-axis direction, the crystal comprises columns of cations and anions such that each column comprising cations is surrounded by six columns of alternatively charged species, whereas each column of anions is surrounded by six columns of cations. Hydrogen bonds linking cations within a column are of the type ammonium–N–H⋯N(pyrazolyl) [N3–H4n⋯N2 i : H4n⋯N2 i  = 2.130(13) Å, N3⋯N2 i  = 3.0176(13) Å with angle at H4n = 164.1(13) for symmetry operation (i) 1 + xy, z]. The remaining ammonium–N–H⋯O(carboxylate) hydrogen bonds involve two different carboxylate residues within the same column [N3–H2n⋯O1 ii : H2n⋯O1 ii  = 1.928(14) Å, N3⋯O1 ii  = 2.7890(13) Å with angle at H2n = 155.4(15) and N3–H3n⋯O2 iii  = H3n⋯O2 iii  = 1.848(14) Å, N3⋯O2 iii  = 2.7297(13) Å with angle at H3n = 161.7(13) for (ii) – x, 1 – y, – z and (iii) 1 – x, 1 – y, – z]. All specified contacts occur within a three-dimensional assembly. Complementing the hydrogen-bonding interactions are close methyl–C–H⋯O(carboxylate) [C5–H5a⋯O2 iv : H5a⋯O2 iv  = 2.38 Å, C5⋯O2 iv  = 3.2992(14) Å with angle at H5a = 156° for (iv) 1/2 + x, 1/2 – y, 1/2 + z] interactions, shown as bright-green dashed bonds in the unit-cell diagram, and π(pyrazolyl)⋯π(pyrazolyl) [Cg(pyrazolyl)⋯Cg(pyrazolyl) iii  = 3.5008(7) Å] contacts between centrosymmetrically related molecules occupying different columns (purple dashed lines). Longer [3.7880(6) Å] π(pyrazolyl)⋯π(phenyl) contacts are also noted.

This analysis was augmented by the calculation of the Hirshfeld surfaces and of the full and delineated two-dimensional fingerprint plots with the aid of Crystal Explorer 21 [15] and standard protocols [16]. The calculations were based on the three-molecule aggregate shown in the upper view of the figure, and highlight the prominent role hydrogen plays in the molecular packing by participating in 86.0 % of all surface contacts. While H⋯H contacts contribute 23.5 % to the calculated surface, the greatest contribution comes from O⋯H/H⋯O contacts, reflecting, in part, the prominent role of hydrogen-bonding involving oxygen. After these, the next most dominant contacts involve fluoride with F⋯H/H⋯F contacts contributing 19.8 % to the surface but at separations greater than the van der Waals criterion. At 9.2 and 7.7 %, significant contributions are made by N⋯H/H⋯N and C⋯H/H⋯C contacts, respectively. Smaller contributions are made by F⋯F [3.8 %], C⋯C [3.7 %], N⋯C/C⋯N [3.6 %] and F⋯C. C⋯F [2.1 %] surface contacts. Naturally, when the individual ions were evaluated for their specific surface contacts, vastly different distributions of surface contacts are apparent. Thus, for the cation, the most signficant contributions to the surface about this species were H⋯H [35.0 %], H⋯O [21.3 %], H⋯N/N⋯H [13.9 %], H⋯F [13.5 %] and H⋯C/C⋯H [6.2 %]. For the di-anion, O⋯H [42.6 %], F⋯H [26.3 %], F⋯F [9.3 %] and C⋯H [8.8 %] surface contacts predominate.


Corresponding authors: Kiyoshi Fujisawa, Department of Chemistry, Ibaraki University, Mito, Ibaraki 310–8512, Japan, E-mail: ; and Edward R. T. Tiekink, Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia, E-mail:

Acknowledgments

KF is grateful for support from the joint usage/research programme “Artificial Photosynthesis” based at Osaka City University.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This study was financially supported by the Joint Usage/Research Center for Catalysis (Proposals 22DS0143 and 23DS0198).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2023-07-18
Accepted: 2023-07-31
Published Online: 2023-08-21
Published in Print: 2023-10-26

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  34. The structure of RUB-1, (C8H16N)6[B6Si48O108], a boron containing levyne-type zeolite, occluding N-methyl-quinuclidinium in the cage-like pores
  35. The crystal structure of diaqua-(naphthalene-4,5-dicarboxylate-1,8-dicarboxylic anhydride1O)-(4′-(4-(1H-benzimidazolyl-1-yl)phenyl)-2,2′:6′,2″-terpyridine-κ3N,N′,N″)–manganese(II) dihydrate, C42H27MnN5O9·2H2O
  36. Crystal structure of 6,6′-((1E,1′E)-hydrazine-1,2-diylidenebis(methanylylidene))bis (3-(3-bromopropoxy)phenol), C20H22Br2N2O4
  37. The crystal structure of 3-(2-hydroxyphenyl)-4-phenyl-6-(p-tolyl)-2H-pyran-2-one, C24H18O3
  38. Crystal structure of bis(μ2-2-(1,5-dimethyl–3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)imino)methyl)phenolato-κ4O:O,N,O′)-(nitrato-κ2O,O′)dicobalt(II), C36H32Co2N8O4
  39. Synthesis and crystal structure of (3E,5S,10S,13S,14S,17Z)-17-ethylidene-10,13-dimethylhexadecahydro-3H-cyclopenta[α] phenanthren-3-one O-(4-fluorobenzoyl) oxime, C28H36FNO2
  40. The crystal structure of 4-aminiumbiphenyl benzenesulfonate, C18H17NO3S
  41. Synthesis and crystal structure of 1-(7-hydroxy-3-(4-hydroxy-3-nitrophenyl)-4-oxo-4H-chromen-8-yl)-N,N-dimethylmethanaminiumnitrate, C18H17N3O9
  42. Crystal structure of N-(Ar)-N′-(Ar′)-formamidine, C14H12Br2N2O
  43. The crystal structure of 4-(2,4-dichlorophenyl)-2-(4-fluorophenyl)-5-methyl-1H-imidazole, C16H11Cl2FN2
  44. Crystal structure of 1-(4–chlorophenyl)-4-benzoyl-3-methyl-1H-pyrazol-5-ol, C17H13ClN2O2
  45. The crystal structure of 5-amino-1-methyl-4-nitroimidazole, C4H6O2N4
  46. Crystal structure of 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene-N,N′-bis(1,3-bis(2,6-diisopropylphenyl)-1,3-dihydro-2H-1,3,2-diazaborol-2-yl)-l2-germenediamine, C63H94B2GeN8
  47. The crystal structure of (bromido, chlorido)-tricarbonyl-(5,5′-dimethyl-2,2′-bipyridine)-rhenium(I), C15H12Br0.2Cl0.8N2O3Re1
  48. Crystal structure of [N(E),N′(E)]-N,N′-(1,4-phenylenedimethylidyne)bis-3,5-bis(propan-2-yl)-1H-pyrazol-4-amine, C26H36N6
  49. The crystal structure of poly[2-(4-carboxypyridin-3-yl)terephthalpoly[diaqua-(μ4-2-(6-carboxylatopyridin-3-yl)terephthalato-κ5O,N:O′:O″,O‴)]) cadmium(II)] dihydrate, C28H20Cd3N2O16
  50. Crystal structure of [tetraaqua-bis((3-carboxy-5-(pyridin-4-yl)benzoate-κ1N)cobalt(II)] tetrahydrate, C26H32CoN2O16
  51. Crystal structure of bis(μ2-azido-κ2N:N)-tetrakis(azido-κ1N)-tetrakis(1,10-phenanthroline-κ2N,N′)dibismuth(III), C48H32N26Bi2
  52. Crystal structure of (Z)-N-(4-(4-(4-((4,5,6-trimethoxy-3-oxobenzofuran-2(3H)-ylidene)methyl)phenoxy)butoxy)phenyl)acetamide, C30H31NO8
  53. Crystal structure of poly[diaqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2N:N′)-bis(μ2-5-carboxybenzene-1,3-dicarboxylato-O,O′:O″)-aqua-di-zinc dihydrate solvate], C27H28N4O16Zn2
  54. Crystal structure of 2-(3,5,5-trimethylcyclohex-2-en-1-ylidene)malononitrile, C12H14N2
  55. Crystal structure of chlorido-(5-nitro-2-phenylpyridine-κ2N,C)-[(methylsulfinyl)methane-κ1S]platinum(II), C13H13ClN2O3PtS
  56. The crystal structure of the co-crystal 1,4-dioxane–4,6-bis(nitroimino)-1,3,5-triazinan-2-one(2/1), C11H19N7O9
  57. Crystal structure of [N(E),N′(E)]-N,N′-(1,4-phenylenedimethylidyne)bis-3,5-dimethyl-1H-pyrazol-4-amine di-methanol solvate, C18H20N6·2(CH3OH)
  58. Crystal structure of catena-poly[bis(μ2-azido-k2N:N′)-(nitrato-K2N:N′)-bis(1,10-phenanthroline-K2N:N′)samarium(III)], C24H16N11O3Sm
  59. Crystal structure of (Z)-2-(4-((5-bromopentyl)oxy)benzylidene)-4,5,6-trimethoxybenzofuran-3(2H)-one, C23H25BrO6
  60. Crystal structure of bis(3,5-dimethyl-1H-pyrazol-4-ammonium) tetrafluoroterephthate, 2[C5H10N3][C8F4O4]
  61. Crystal structure of 2-amino-4-(2-fluoro-4-(trifluoromethyl)phenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-3-ium chloride, C20H18ClF4N3O
  62. Crystal structure of 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine-sebacic acid (2/1), C13H17N6O2
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