The crystal structure of 3,5-diisopropyl-4-nitropyrazole from X-ray powder diffraction data

Journal of Molecular Structure 562 (2001) 11±17

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The crystal structure of 3,5-diisopropyl-4-nitropyrazole from X-ray powder diffraction data L.E. Ochando a,*, J.M. Amigo a, J. Rius b, D. LoueÈr c, Ch. Fontenas d, J. Elguero d a

SeccioÂn Departamental de GeologõÂa, Facultad de QuõÂmica, Universitat de ValeÁncia, Avda Dr Moliner 50, E-46100 Burjassot, Spain b Institut de CieÁncia de Materials de Barcelona, CSIC, Campus de la UAB, E-08193 Bellaterra, Catalunya, Spain c LCSIM (CNRS UMR 6511), Universite de Rennes I, 35042 Rennes, France d Instituto de QuõÂmica MeÂdica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain Received 20 July 2000; revised 6 August 2000; accepted 6 August 2000

Abstract The crystal structure of 3,5-diisopropyl-4-nitropyrazole, 3c, has been determined by a Patterson Search method from laboratory X-ray powder diffraction data. The crystal data are: monoclinic symmetry with the unit-cell parameters a ˆ  b ˆ 100:32…1†8; space group I2/a, C9H15N3O2, Z ˆ 8, 293 K. After indexing 19:530…5†; b ˆ 6:485…1† and c ˆ 17:937…3† A; the powder pattern by two methods, the unit-cell parameters found were re®ned by a least-squares technique. A whole pattern®tting program was used to extract the integrated intensities. The structure was solved taking a related compound as a search model and the ®nal Rietveld re®nement converged to Rwp ˆ 0.1971 and Rp ˆ 0.1437. The structure presents a dimer conformation between N atoms through a hydrogen bond. q 2001 Elsevier Science B.V. All rights reserved. Keywords: X-ray powder diffraction; Patterson search method; Hydrogen bonding

1. Introduction N-Unsubstituted pyrazoles form hydrogen bond networks of great complexity. Not less than four fundamental motifs have been found so far: dimers, trimers, tetramers and chains called catemers [1,2]. There are also several types of catemers depending on the pitch [2]. The motif seems to depend on the size of substituents at positions 3 and 5 of the pyrazole ring [2]. We have already studied pyrazoles bearing at these positions methyl 1 [3±5] and tert-butyl groups 2 [6]. To further understand the crystal chemistry of this family of compounds it is of interest to know the * Corresponding author. Tel.: 134-96-386-4603; fax: 134-96386-4372. E-mail address: [email protected] (L.E. Ochando).

structure of the related phases. The present study deals with the crystal structure of one variety of 3,5diisopropylpyrazoles 3, solved ab initio from conventional monochromatic X-ray powder diffraction patterns (Scheme 1).

2. Experimental A brief schematic synthesis of 3,5-diisopropylpyrazoles, all of them previously unknown, are reported in Scheme 2. Three forms of 3,5-diisopropylpyrazoles can be synthesized depending on the experimental conditions: 3,5-Diisopropylpyrazole 3a. Clean sodium (3.9 g, 169 mmol) is powdered under nitrogen ¯ow by

0022-2860/01/$ - see front matter q 2001 Elsevier Science B.V. All rights reserved. PII: S 0022-286 0(00)00766-3

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L.E. Ochando, et al. / Journal of Molecular Structure 562 (2001) 11±17

Scheme 1.

melting and agitating it during cooling. To the gray powder is added 200 ml of dry diethylether. Then, under re¯ux, 10 ml (1 eq.) of ethanol (dried over Ê molecular sieves) is added dropwise. The solution 4A is left under re¯ux for 4 h. The reaction mixture being then a suspension of a white solid. The diethylether is distilled off. To the dry sodium ethoxide, heated to 808C, is added 45 ml (approximately 2 eq.) of ethyl 2-methyl propionate in one portion. Immediately, a dropwise addition of 18.8 ml (1 eq.) of 3-methyl-2butanone is started. At that stage, the reaction should be protected from moisture with a silica gel drying tube. After the completion of the addition the solution is heated for 1 h and left for cooling. Upon cooling the reaction mixture becomes a solid. Water is added and the organic layer is separated and dissolved in diethylether. The organic layer is extracted several times with water. Combined aqueous layers are acidi®ed with 10% sulfuric acid. The diketone is extracted with diethylether. Special care must be taken when

concentrating the ethereal solution due to volatility of the product. 17.2 g of the yellow oil containing 2,5-dimethyl-hepta-3,5-dione are obtained. The oil is dissolved in 200 ml of ethanol. 9.5 ml (more than 1.5 eq.) hydrazine hydrate and 1 ml concentrated hydrochloric acid are added. The reaction mixture is heated under re¯ux overnight and then concentrated to dryness. The oily residue, dissolved in dichloromethane, is washed with a saturated solution of sodium bicarbonate. The aqueous layer is extracted with dichloromethane. Combined organic layers are washed with water and brine. After drying over sodium sulfate and evaporation of the solvent, 1.8 g (6%) of an oil that solidi®es slowly is obtained, m.p. 788C. Attempts to crystallize it reverts it to its syrupy appearance. 1 H NMR (d ppm, CDCl3): 8.10 (br, 1H), 5.88 (s, 1H), 2.96 (h, 2H), 1.26 (s, 12H). 13C NMR (d ppm, CDCl3): 98.3 (C4), 26.8, 22.6 (3,5-iPr groups). 3,5-Diisopropyl-4-bromopyrazole 3b. To a solution

Scheme 2.

L.E. Ochando, et al. / Journal of Molecular Structure 562 (2001) 11±17 Table 1 X-ray powder diffraction data of 3,5-di-isopropyl-4-nitropyrazole hkl

2u obs (8)

2u calc (8)

Ê) dobs (A

Iobs

200 002 22 0 2 110 011 202 21 1 2 211 112 400 310 004 22 0 4 23 1 2 22 1 3 402 213 204 411 24 1 3 510 26 0 2 22 1 5 413 22 0 6 512 26 1 1 23 2 1 25 1 4 222 26 0 4 123 206 024 116 22 2 4 613 24 2 4 23 2 5

10.681 11.640 14.324 16.746 16.896 17.193 19.881 20.595 20.989 21.448 22.641 23.386 23.941 24.144 24.702 26.294 27.344 27.512 28.282 29.921 31.397 32.459 33.576 34.294 35.087 35.339 35.807 36.056 36.358 36.546 36.642 37.616 38.965 40.036 40.311 40.369 43.175 43.695 45.107

10.685 11.637 14.333 16.741 16.900 17.187 19.873 20.594 20.984 21.463 22.640 23.395 23.939 24.142 24.699 26.290 27.349 27.511 28.274 29.929 31.396 32.468 33.585 34.304 35.117 35.301 35.815 36.028 36.371 36.568 36.647 37.613 38.977 40.040 40.315 40.378 43.178 43.673 45.114

9.6101 8.8206 7.1745 6.1426 6.0884 5.9840 5.1815 5.0038 4.9108 4.8068 4.5567 4.4135 4.3125 4.2769 4.1817 3.9326 3.7842 3.7616 3.6612 3.4649 3.3058 3.2004 3.0968 3.0339 2.9674 2.9469 2.9096 2.8902 2.8670 2.8527 2.8455 2.7744 2.6819 2.6130 2.5959 2.5923 2.4311 2.4036 2.3321

100 19 6 10 4 3 56 2 22 ,1 4 10 5 4 81 8 7 4 6 14 3 2 5 2 2 4 1 ,1 4 2 2 1 1 3 1 1 2 2 3

of 0.56 g (3.7 mmol) 3,5-diisopropylpyrazole 3a in 5 ml glacial acetic acid is added 0.2 ml (1 eq.) bromine via a syringe. The solution is re¯uxed for 3 h and becomes brown. After cooling, the reaction mixture is concentrated, dissolved in dichloromethane and washed with a saturated solution of sodium bicarbonate, with water and ®nally with brine. After drying over sodium sulfate and evaporation under reduced pressure a brown oil is obtained. Discoloration by activated

13

carbon in ethanol affords 0.52 g (52%) of a slightly yellow oil. 1 H NMR (d ppm, CDCl3): 10.65 (br, 1H), 3.07 (h, 2H), 1.30 (d, 12H). 13C NMR (d ppm, CDCl3): 90.6 (C-4), 26.1, 21.2 (3,5-iPr groups). 3,5-Diisopropyl-4-nitropyrazole 3c. To 0.5 g (3.3 mmol) of 3,5-diisopropylpyrazole 3a in a 25 ml round-bottom ¯ask cooled to 08C is added slowly 1.4 ml of 96% sulfuric acid. Once the entire product dissolved, 0.7 ml of 90% nitric acid is added. The reaction mixture is left at 08C for 30 min and then heated to 1008C for 2 h. Thin Layer Chromatography (TLC) analysis shows the completion of the reaction. The reaction mixture once cold is neutralized with a saturated solution of sodium bicarbonate. The resulting suspension is extracted with dichloromethane. The organic layer is dried over sodium sulfate and yields after evaporation 0.54 g (83%) of a white powdered solid, m.p. 1128C. 1 H NMR (d ppm, CDCl3): 3.72 (h, 2H), 1.36 (d, 12H). 13C NMR (d ppm, CDCl3): 153.4 (C-3 and C5), 128.9 (C-4), 26.4, 21.0 (3,5-iPr groups). Of these three compounds, only 3c yields a microcrystalline powder by slow evaporation of a saturated solution in ethanol. Two powder diffraction data sets were used for the study. For indexing purposes and, also, to have a reference material for the calibration of the second instrument, data set (I) was collected with a high-resolution powder diffractometer (Siemens D500) using the parafocusing Bragg±Brentano Geometry. Pure  radiation was produced CuKa1 …l ˆ 1:5405981 A† with an incident-beam curved-crystal Ge monochromator and asymmetric focusing (short focal distance, 124 mm; long focal distance, 216 mm). The instrument resolution function has been described elsewhere [7] and the alignment of the diffractometer was checked with standard reference materials [8]. To reduce peak displacements due to the effect of specimen transparency in re¯ection geometry, a thin layer of the powder was deposited on a silicon plate. The powder diffraction pattern was scanned in steps of 0.028 (2u ) with a ®xed counting time 27 s per step. Peak positions were obtained with the pro®le ®tting program pro®le from Socabim. The second data set (II) was collected with a highresolution powder diffractometer using the Debye±  Scherrer Geometry. Pure CoKa1 …l ˆ 1:78892 A†

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L.E. Ochando, et al. / Journal of Molecular Structure 562 (2001) 11±17

Table 2 Details of the rigid-body least-squares re®nement from X-ray powder data of 3,5-di-isopropyl-4-nitropyrazole. s…f†; s…c†; s…w† are the estimated standard deviations of the Euler angles describing the molecular rotation Range of 2u (8) Space group Z Ê) Unit cell dimensions (A

Ê 3) Volume (A Number of re¯ections Scale factor FWHM (8) Ê 2) Overall B (A s (f ) (8) s (c ) (8) s (w ) (8) Residuals Rp a Rwp b RB c x 2d

8±59 I2/a 8 a ˆ 19.530(5) b ˆ 6.485(1) c ˆ 17.937(3) b ˆ 100.32(1) 2234.6(4) 91 (unambig.) 0.8579 0.089 6.33 0.253 0.204 0.235 0.144 0.197 0.306 4.619

a

R-pattern: X uyo …i† 2 yc …i†u Rp ˆ i X : yo …i† i

b

R-weighted pattern: 0X 11=2 w…i†…yo …i† 2 yc …i††2 B i C C X Rwp ˆ B @ A w…i†yo …i†2 i

with w…i† ˆ 1=yo …i†: c R-Bragg factor: nref X

RB ˆ

j

uIo …j† 2 Ic …j†u nref X j

d

is

: Io …j†

Chi-squared factor: x2 ˆ Rwp =Rexp ; where the R-expected factor

Rexp

0

11=2

B …N 2 P† C C : ˆB @X A w…i†yo …i†2 i

radiation was produced with an incident-beam curved-crystal quartz monochromator and asymmetric focusing (short focal distance, 180 mm; long focal distance, 560 mm) with a capillary sample. The powder diffraction pattern was scanned in steps of 0.0258 (2u ) with a ®xed counting time of 200 s per step in the range from 8 to 308 and 400 s per step in the range from 30.025 to 598 (2u ). Then, the full pattern was scaled to the lower counting times. Such a procedure improves signi®cantly the counting statistics at high angles. After data collection the stability of the X-ray source was checked by recording the ®rst lines of the pattern. Peak positions were obtained with the pro®le ®tting program pro®le from Socabim. 3. Structure solution The powder diffraction data (data set I) were indexed with the two programs dicvol91 [9] and treor90 [10]. The same monoclinic unit cell, with high ®gures of merit M20 ˆ 29 and F20 ˆ 64…0:004; 78† for dicvol91 and M18 ˆ 27 and F18 ˆ 56…0:0042; 77† for treor90, was obtained from both programs. After a least-squares reviewing of the data available of the pattern, the re®ned unit cell para b ˆ 6:485…1† A  and meters were: a ˆ 19:530…5† A;  3:  b ˆ 100:32…1†8; V ˆ 2234:6…4† A c ˆ 17:937…3† A; The ®nal ®gures of merit are M20 ˆ 20:3 and F30 ˆ 35:1…0:0067; 127†; the list of observed and calculated peak positions is given in Table 1. The most probable space group is I2/a (C2/c). Ninety-one unambiguously indexed and 106 systematically overlapped integrated intensities were extracted from data set II by means of the whole pattern ®tting program ajust [11] in the range of 8± 598 (2u ). Patterson search methods have been widely used for solving crystal structures from powder data when, as in the present case, only low-resolution diffraction data are available [12]. The molecular fragment used for the Patterson search was taken from the compound 3,5-di-tert-buthyl-4-nitropirazole (C11H19N3O2) [6], which crystallizes in a monoclinic  b ˆ 9:6180…4† A;  cˆ structure [a ˆ 10:6407…4† A;  3 ],  12:6649…5† A; b ˆ 107:962…3†8; V ˆ 1233:0…1† A space group P21/c, with four molecules in the asymmetric unit …Z ˆ 4†:

L.E. Ochando, et al. / Journal of Molecular Structure 562 (2001) 11±17 Table 3 Fractional coordinates of non-methyl-hydrogen atoms for 3,5-diisopropyl-4-nitropyrazole with e.s.d.'s in parentheses Atom

x/a

y/b

z/c

N1 H1 N2 C3 C4 C5 C6 C7 H8 C9 N10 O11 O12 C13 H14 C15 C16

0.4349 (4) 0.4204 0.5023 (4) 0.5067 (4) 0.4397 (4) 0.3943 (4) 0.3168 (4) 0.2770 (4) 0.3012 0.3022 (4) 0.4223 (4) 0.3622 (4) 0.4687 (4) 0.5745 (4) 0.5987 0.6211 (4) 0.5612 (4)

0.4644 (4) 0.5652 0.4003 (4) 0.2493 (4) 0.2211 (4) 0.3593 (4) 0.4021 (4) 0.2739 (4) 0.3691 0.6304 (4) 0.0826 (4) 0.0732 (4) 20.0195 (4) 0.1326 (4) 0.1872 0.1599 (4) 20.0979 (4)

0.4268 (4) 0.4509 0.4402 (4) 0.3910 (4) 0.3469 (4) 0.3718 (4) 0.3491 (4) 0.3989 (4) 0.2954 0.3609 (4) 0.2838 (4) 0.2508 (4) 0.2651 (4) 0.3926 (4) 0.3534 0.4697 (4) 0.3795 (4)

15

The search model was oriented and placed in the monoclinic unit cell by the program rots96 [13]. The subsequent rigid-body Rietveld re®nement was performed with the program ribols [14] using a Pearson-VII pro®le function with the shape parameter m ˆ 1:6; which dropped to a pro®le factor Rwp ˆ 19:7%: As shown in Table 2, the parameters re®ned are the angles describing the molecular orientations. To complete the structure, the hydrogen atoms of the central atom of the isopropyl groups and of the nitrogen atom were generated geometrically by the shelxl-93 program [15]. The details of the ®nal re®nement are given in Table 2. The ®nal coordinates including three hydrogen atoms are listed in Table 3. The observed X-ray diffraction pattern and the difference pro®le between observed and calculated patterns are shown in Fig. 1. The molecular conformation with atom labeling and the unit

Fig. 1. Observed diffraction pattern and difference pro®le between observed and calculated patterns for 3,5-di-isopropyl-4-nitropyrazole.

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L.E. Ochando, et al. / Journal of Molecular Structure 562 (2001) 11±17

Fig. 2. Molecular conformation of the title compound, with atom labeling.

cell packing of the ®nal crystal structure of the title compound are represented in Figs. 2 and 3, respectively. 4. Discussion One of the most fascinating properties of N-unsubstituted pyrazole crystals is the possibility that they present dynamic disorder involving the NH proton of the N±H´ ´´N hydrogen bond. This only happens in cyclic structures (dimers, trimers and tetramers) and never in catemers. Moreover, in most cases, the substituents at positions 3 and 5 should be identical [1,2,16]. Therefore, the dimer formed by 3,5-diisopropyl-4-nitropyrazole was a good candidate for

Fig. 3. Unit cell view of the title compound, along the b-axis.

SSPT (solid state proton transfer) considering that 3,5-di-tert-butyl-4-nitropyrazole, a dimer [6], shows proton disorder [17]. Unfortunately, compound 3c does not present SSPT and the N±H proton is clearly localized, may be due to the fact that the two isopropyl groups have different orientations. Even in the case where only one position for the proton is found, the possibility exists to study the disorder by looking at the internal angles of the pyrazole pentagon, especially those at N1 and N2 [18]. In compound 3c these angles amount to 113.69(^0.65)8 and 106.45(^0.36)8, respectively. The difference is 7.28, instead of 98 for a pyrazole in the gas phase (ED, MW or high level ab initio calculations) [18]. Therefore, a small amount of disorder cannot be ruled out. Acknowledgements The authors acknowledge the EU for the network Location and Transfer of Hydrogen (No. CHRX CT 940582). LEO, JMA, JR and DL are also indebted to the D.G.E.S. for economic support (AccioÂn Integrada Hispano-Francesa number HF1997-0226/Action InteÂgreÂe PICASSO No. 98149). References [1] V. Bertolasi, P. Gilli, V. Ferretti, G. Gilli, C. FernaÂndezCastanÄo, Acta Crystallogr. B 55 (1999) 985. [2] C. Foces-Foces, I. Alkorta, J. Elguero, submitted for publication. [3] J.A.S. Smith, B. Wehrle, F. Aguilar-Parrilla, H.H. Limbach, C. Foces-Foces, F.H. Cano, J. Elguero, A. Baldy, M. Pierrot, M.M.T. Khurshid, J.B. Larcombe, J. Am. Chem. Soc. 111 (1989) 7304. [4] I. Hargittai, J. Brunvoll, C. Foces-Foces, A.L. Llamas-Saiz, J. Elguero, J. Mol. Struct. 291 (1993) 211. [5] F. Aguilar-Parrilla, O. Klein, J. Elguero, H.H. Limbach, Ber. Bunsenges. Phys. Chem. 101 (1997) 889. [6] A.L. Llamas-Saiz, C. Foces-Foces, F.H. Cano, P. JimeÂnez, J. Laynez, W. Meutermans, J. Elguero, H.H. Limbach, F. Aguilar-Parrilla, Acta Crystallogr. B 50 (1994) 746. [7] D. LoueÈr, J.I. Langford, J. Appl. Crystallogr. 21 (1988) 430. [8] D. LoueÈr, Mater. Sci. Forum 79±82 (1986) 17. [9] A. Boultif, D. LoueÈr, J. Appl. Crystallogr. 24 (1991) 987. [10] P.-E. Werner, L. Erikson, M. Westdahl, J. Appl. Crystallogr. 18 (1985) 367. [11] J. Rius, J. SanÄeÂ, C. Miravitlles, J.M. AmigoÂ, M.M. ReventoÂs, D. LoueÈr, An. Quim. Int. Ed. 92 (1996) 223.

L.E. Ochando, et al. / Journal of Molecular Structure 562 (2001) 11±17 [12] J. Rius, C. Miravitlles, J. Appl. Crystallogr. 20 (1987) 261. [13] J. Rius, L.E. Ochando, ROTS96, Program System for Solving Molecular Structures by Patterson Search Methods, ICMABCSIC, Catalunya, Spain, 1996. [14] J. Rius, RIBOLS: Rigid-Body Least-Squares Program for Powder Data, ICMAB-CSIC, Catalunya, Spain, 1989. [15] G.M. Sheldrick. SHELXL93: Program for the Re®nement of Crystal Structures, University of GoÈttingen, Germany, 1993.

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[16] F. Aguilar-Parrilla,, G. Scherer, H.H. Limbach, C. FocesFoces, F.H. Cano, J. Elguero, J. Am. Chem. Soc. 114 (1992) 9657. [17] O. Klein, M. Minguet-BonvehõÂ, F. Aguilar-Parrilla, N. Jagerovic, J. Elguero, H.H. Limbach, Israel J. Chem. 39 (1999) 291. [18] I. Alkorta, J. Elguero, B. Donnadieu, M. Etienne, J. Jaffart, D. Schagen, H.H. Limbach, New J. Chem. 23 (1999) 1231.