Crystal structure of N-(4-methoxybenzyl)pyridazin-3-amine- a rare Z′ = 4 structure, C12H13N3O

Xin-Hua Lou; Qing-Li Zhou; Wen-Yuan Liu; Xue-Qing Hu

doi:10.1515/ncrs-2018-0212

Open Access Published by De Gruyter (O) October 11, 2018

Crystal structure of N-(4-methoxybenzyl)pyridazin-3-amine- a rare Z′ = 4 structure, C₁₂H₁₃N₃O

Xin-Hua Lou , Qing-Li Zhou , Wen-Yuan Liu and Xue-Qing Hu

From the journal Zeitschrift für Kristallographie - New Crystal Structures

https://doi.org/10.1515/ncrs-2018-0212

Abstract

C₁₂H₁₃N₃O, triclinic, P1̄ (no. 2), a = 10.2233(9) Å, b = 10.2902(9) Å, c = 24.2253(19) Å, α = 86.607(7)°, β = 88.529(7)°, γ = 62.515(9)°, V = 2256.9(4) Å³, Z = 8, R_gt(F) = 0.0425, wR_ref(F²) = 0.1239, T = 291(2) K.

CCDC no.: 1848646

One of four crystallographically independent molecules of the title crystal structure is shown in the figure. Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:	Yellow
Size:	0.22 × 0.20 × 0.08 mm
Wavelength:	Cu Kα radiation (1.54184 Å)
μ:	0.68 mm⁻¹
Diffractometer, scan mode:	Xcalibur, ω
θ_max, completeness:	67.1°, >99%
N(hkl)_measured, N(hkl)_unique, R_int:	16086, 8063, 0.022
Criterion for I_obs, N(hkl)_gt:	I_obs > 2 σ(I_obs), 6060
N(param)_refined:	582
Programs:	SHELX [3], CrysAlis^PRO [2]

Table 2:

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

Atom	x	y	z	U_iso*/U_eq
C1	0.7370(2)	0.7842(2)	0.15269(8)	0.0728(5)
H1	0.7456	0.7306	0.1220	0.087*
C2	0.6059(2)	0.9111(2)	0.16011(8)	0.0686(5)
H2	0.5282	0.9417	0.1352	0.082*
C3	0.59494(19)	0.98814(19)	0.20446(7)	0.0597(4)
H3	0.5090	1.0729	0.2116	0.072*
C4	0.71843(17)	0.93578(17)	0.23967(6)	0.0504(4)
C5	0.8386(2)	0.9739(2)	0.32022(7)	0.0619(4)
H5A	0.8428	1.0628	0.3287	0.074*
H5B	0.9288	0.9128	0.3009	0.074*
C6	0.83347(18)	0.89358(17)	0.37390(7)	0.0529(4)
C7	0.7051(2)	0.9008(2)	0.39523(7)	0.0650(5)
H7	0.6176	0.9566	0.3759	0.078*
C8	0.7010(2)	0.8276(2)	0.44467(8)	0.0732(5)
H8	0.6122	0.8342	0.4580	0.088*
C9	0.8294(2)	0.7454(2)	0.47374(8)	0.0688(5)
C10	0.9590(2)	0.7380(2)	0.45353(8)	0.0763(6)
H10	1.0461	0.6832	0.4732	0.092*
C11	0.9608(2)	0.8113(2)	0.40423(8)	0.0684(5)
H11	1.0496	0.8052	0.3911	0.082*
C12	0.7093(4)	0.6651(4)	0.54332(11)	0.1409(13)
H12A	0.6735	0.6252	0.5161	0.211*
H12B	0.6351	0.7624	0.5506	0.211*
H12C	0.7319	0.6041	0.5768	0.211*
N1	0.84907(17)	0.73637(16)	0.18670(7)	0.0698(4)
N2	0.84124(15)	0.81329(15)	0.23115(6)	0.0577(3)
N3	0.71485(16)	1.01291(15)	0.28347(6)	0.0634(4)
H3A	0.6340	1.0900	0.2899	0.076*
O1	0.8376(2)	0.67036(19)	0.52346(6)	0.0985(5)
C1B	0.4090(2)	0.4192(2)	0.32310(8)	0.0712(5)
H1B	0.4765	0.4134	0.3494	0.085*
C2B	0.2806(2)	0.5509(2)	0.31505(8)	0.0691(5)
H2B	0.2620	0.6310	0.3357	0.083*
C3B	0.18461(19)	0.55917(19)	0.27681(8)	0.0621(4)
H3B	0.0968	0.6445	0.2703	0.074*
C4B	0.22180(18)	0.43325(18)	0.24663(7)	0.0538(4)
C5B	0.1490(2)	0.3073(2)	0.17973(8)	0.0647(5)
H5BA	0.0519	0.3168	0.1727	0.078*
H5BB	0.1991	0.2228	0.2052	0.078*
C6B	0.23327(18)	0.27770(18)	0.12613(7)	0.0565(4)
C7B	0.3470(2)	0.3127(2)	0.11518(7)	0.0634(5)
H7B	0.3738	0.3567	0.1421	0.076*
C8B	0.4224(2)	0.2845(2)	0.06546(8)	0.0686(5)
H8B	0.4988	0.3089	0.0594	0.082*
C9B	0.3835(2)	0.2203(2)	0.02514(8)	0.0708(5)
C10B	0.2727(3)	0.1818(3)	0.03546(9)	0.0871(7)
H10B	0.2467	0.1370	0.0086	0.105*
C11B	0.2001(2)	0.2095(2)	0.08547(9)	0.0766(6)
H11B	0.1266	0.1812	0.0920	0.092*
C12B	0.5645(3)	0.2222(4)	−0.03825(11)	0.1223(11)
H12D	0.5989	0.1954	−0.0751	0.183*
H12E	0.6430	0.1666	−0.0124	0.183*
H12F	0.5332	0.3250	−0.0352	0.183*
N1B	0.43940(16)	0.30293(17)	0.29549(6)	0.0675(4)
N2B	0.34526(15)	0.30897(15)	0.25608(6)	0.0605(4)
N3B	0.13124(16)	0.43638(16)	0.20645(6)	0.0658(4)
H3BA	0.0591	0.5196	0.1962	0.079*
O1B	0.44547(19)	0.1924(2)	−0.02649(6)	0.1002(5)
C1A	0.9692(2)	0.3947(2)	0.33888(9)	0.0766(5)
H1A	1.0373	0.3831	0.3659	0.092*
C2A	0.8502(3)	0.5327(2)	0.32878(9)	0.0778(6)
H2A	0.8388	0.6121	0.3485	0.093*
C3A	0.7531(2)	0.54814(19)	0.29005(8)	0.0674(5)
H3AA	0.6725	0.6387	0.2817	0.081*
C4A	0.77627(18)	0.42281(18)	0.26213(7)	0.0551(4)
C5A	0.6891(2)	0.3079(2)	0.19491(8)	0.0720(5)
H5AA	0.5910	0.3162	0.1926	0.086*
H5AB	0.7490	0.2190	0.2170	0.086*
C6A	0.75293(18)	0.29266(19)	0.13758(7)	0.0574(4)
C7A	0.7489(2)	0.4101(2)	0.10585(8)	0.0729(5)
H7A	0.7084	0.5018	0.1208	0.087*
C8A	0.8031(2)	0.3958(2)	0.05241(8)	0.0764(6)
H8A	0.7982	0.4771	0.0318	0.092*
C9A	0.8640(2)	0.2609(2)	0.02995(8)	0.0633(4)
C10A	0.8686(2)	0.1416(2)	0.06093(8)	0.0669(5)
H10A	0.9092	0.0499	0.0460	0.080*
C11A	0.81341(19)	0.15856(19)	0.11366(8)	0.0647(5)
H11A	0.8167	0.0775	0.1339	0.078*
C12A	0.9327(3)	0.3494(3)	−0.05330(10)	0.1070(8)
H12G	0.9791	0.3152	−0.0881	0.161*
H12H	0.9896	0.3837	−0.0334	0.161*
H12I	0.8352	0.4283	−0.0596	0.161*
N1A	0.98913(17)	0.28034(17)	0.31190(7)	0.0712(4)
N2A	0.89252(15)	0.29289(15)	0.27255(6)	0.0603(4)
N3A	0.67961(17)	0.43192(18)	0.22318(7)	0.0720(4)
H3AB	0.6079	0.5169	0.2147	0.086*
O1A	0.92396(17)	0.23344(16)	−0.02212(6)	0.0847(4)
C1C	0.7108(2)	0.2755(2)	0.83158(9)	0.0769(6)
H1C	0.6964	0.3409	0.8588	0.092*
C2C	0.8462(2)	0.1502(2)	0.82919(9)	0.0763(5)
H2C	0.9211	0.1317	0.8542	0.092*
C3C	0.86532(19)	0.0564(2)	0.78953(8)	0.0639(5)
H3C	0.9533	−0.0294	0.7866	0.077*
C4C	0.74780(17)	0.09255(17)	0.75271(7)	0.0531(4)
C5C	0.6475(2)	0.0264(2)	0.67326(7)	0.0655(5)
H5CA	0.5522	0.0846	0.6899	0.079*
H5CB	0.6534	−0.0676	0.6655	0.079*
C6C	0.65765(18)	0.10285(18)	0.61971(7)	0.0541(4)
C7C	0.57760(19)	0.25285(19)	0.61066(7)	0.0612(4)
H7C	0.5147	0.3079	0.6382	0.073*
C8C	0.5884(2)	0.32292(18)	0.56203(7)	0.0624(4)
H8C	0.5332	0.4242	0.5570	0.075*
C9C	0.68056(19)	0.24388(18)	0.52064(7)	0.0573(4)
C10C	0.7607(2)	0.0945(2)	0.52809(8)	0.0714(5)
H10C	0.8225	0.0398	0.5003	0.086*
C11C	0.7486(2)	0.0261(2)	0.57739(8)	0.0697(5)
H11C	0.8037	−0.0752	0.5823	0.084*
C12C	0.7717(3)	0.2490(3)	0.42918(9)	0.0993(8)
H12J	0.8730	0.1972	0.4407	0.149*
H12K	0.7616	0.3184	0.3992	0.149*
H12L	0.7404	0.1804	0.4172	0.149*
N1C	0.60280(18)	0.30503(17)	0.79705(7)	0.0723(4)
N2C	0.61978(15)	0.21435(16)	0.75654(6)	0.0621(4)
N3C	0.76221(16)	0.00257(16)	0.71247(6)	0.0656(4)
H3CA	0.8454	−0.0747	0.7098	0.079*
O1C	0.68404(16)	0.32350(14)	0.47373(5)	0.0784(4)

Source of material

The title compound was obtained from the ruthenium-catalyzed N-alkylation of pyridazin-3-amine and (4-methoxyphenyl)methanol as described in literature [3] and recrystallized from dichloromethane/petroleum ether solution at room temperature to give the desired crystals suitable for single-crystal X-ray diffraction.

Experimental details

Hydrogen atoms were added using the riding models implemented in the SHELX system.

Comment

The C—N bond forming reaction has become widely used in organic synthesis as well as in materials and pharmaceuticals [4], [5]. Among of these routes, the metal-catalyzed hydrogen autotransfer process is highly desirable [6], [7], [8], [9], because the use of alcohols as electrophiles in the C—N bond forming reaction improves the atom efficiency of the process, producing only water as by product. However, the N-alkylation of heteroaryl amines have been relatively less reported [3]. Considering that the pyridazine derivatives are an important class of heterocyclic molecules [10], [11], [12], we prepared the N-alkylation product of pyridazin-3-amine and (4-methoxyphenyl)methanol.

The molecular structure of one of the four crystallographically independent molecules forming the asymmetric unit of the title crystal structure of the title compound is shown in the figure. The pyridazine ring and aryl moiety are not coplanar and their best planes enclose an angle of 72°, which is similar to that of related derivatives [13]. In the crystal there exist intermolecular NH⋯N hydrogen bonds (N⋯H = 2.277 and 2.185 Å) and some weak non classical CH⋯N hydrogen bonds (N⋯H = 2.516 or 2.547 Å), which are attributed to construct the one-dimensional structure. Owing to the CH/π hydrogen bonds (the distance is 3.374 Å) [14], the crystal structure of the title compound is extended into a 2D architecture. This network is very complex as each of the four crystallographically independent molecules shows an at least slightly different surrounding [15].

Acknowledgements

This work was supported by the tackle key problem of science and technology Project of Henan Province (172102210411).

References

1. Sheldrick, G. M.: A short history of SHELX. Acta Crystallogr. A64 (2008) 112–122.10.1107/S0108767307043930Search in Google Scholar PubMed

2. Agilent Technologies: CrysAlis^PRO software system, version 1.171.38.41r, Agilent Technologies UK Ltd, Oxford, UK (2011).Search in Google Scholar

3. Li, H. M.; Xu, C.; Wang, Z. Q.; Fu, W. J.: A half sandwich ruthenium(II) complex with N-4,6-dimethyl-2-pyrimidinylimidazole: synthesis, crystal structure and application in N-alkylation of amines with alcohols. Bull. Korean Chem. Soc. 36 (2015) 2557–2560.10.1002/bkcs.10484Search in Google Scholar

4. Maiti, D.; Fors, B. P.; Henderson, J. L.; Nakamura, Y.; Buchwald, S. L.: Palladium-catalyzed coupling of functionlized primary and secondary amines with aryl and heteroaryl halides: two ligands suffice in most cases. Chem. Sci. 2 (2011) 57–68.10.1039/C0SC00330ASearch in Google Scholar PubMed PubMed Central

5. Ricci, A.: Modern amination reaction. Wiley-VCH, Weinheim (2000).10.1002/9783527613182Search in Google Scholar

6. Guillena, G.; Ramon, D. J.; Yus, M.: Hydrogen autotransfer in the N-alkylation of amines and related compounds using alcohols and amines as electrophiles. Chem. Rev. 110 (2010) 1611–1641.10.1021/cr9002159Search in Google Scholar PubMed

7. Xu, C.; Hao, X. Q.; Xiao, Z. Q.; Wang, Z. Q.; Yuan, X. E.; Fu, W. J.; Ji, B. M.; Song, M. P.: One-pot synthesis of ferrocenyl ketones containing biaryls and 6-aryl-2-ferrocenylquinolines via Ir/Pd-cocatalyzed A-alkylation/Suzuki reaction. J. Org. Chem. 78 (2013) 8730–8738.10.1021/jo401421bSearch in Google Scholar PubMed

8. Cano, R.; Ramon, D. J.; Yus, M.: Impregnated ruthenium on magnetite as a recyclable catalyst for the N-alkylation of amines, sulfonamides, sulfinamides, and nitroarenes using alcohols as electrophiles by a hydrogen autotransfer process. J. Org. Chem. 76 (2011) 5547–5557.10.1021/jo200559hSearch in Google Scholar PubMed

9. Xu, C.; Xiao, Z. Q.; Li, H. M.; Han, X.; Wang, Z. Q.; Fu, W. J.; Ji, B. M.; Hao, X. Q.; Song, M. P.: Ligand-free Pd/C-catalyzed one-pot, three-component synthesis of arylsubstituted benzimidazoles by hydrogen-transfer reaction and Suzuki reaction in water. Eur. J. Org. Chem. 2015 (2015) 7427–7432.10.1002/ejoc.201501169Search in Google Scholar

10. Chelini, A.; Brogi, S.; Paolino, M.; Capua, A. D.; Cappelli, A.; Giorgi, G.; Farzad, M.; Mannelli, L. D. C.; Micheli, L.; Ghelardini, C.; Anzini, M.: Synthesis and biological evaluation of novel neuroprotective pyridazine derivatives as excitatory amino acid transporter 2 (EAAT2) activators. J. Med. Chem. 60 (2017) 5216–5221.10.1021/acs.jmedchem.7b00383Search in Google Scholar PubMed

11. Xu, C.; Li, H. M.; Wang, Z. Q.; Fu, W. J.; Zhang, Y. Q.; Ji, B. M.: N-Heterocyclic carbene adducts of cyclopalladated ferrocenylpyridazine: synthesis, structural characterization and application in A-arylation of ketones with aryl chlorides. Aust. J. Chem. 65 (2012) 366–370.10.1071/CH12035Search in Google Scholar

12. Abed, H. B.; Mammoliti, O.; Bande, O.; Lommmen, G. V.; Herdewijn. P.: Strategy for the synthesis of pyridazine heterocycles and their derivatives. J. Org. Chem. 78 (2013) 7845–7858.10.1021/jo400989qSearch in Google Scholar PubMed

13. Li, H. M.; Zu, E. P.; Xu, C.: Crystal structure of 2-(4-methoxyphenyl)-2,3-dihydro-1H-perimidine, C₁₈H₁₆N₂O. Z. Kristallogr. NCS 231 (2016) 133–134.10.1515/ncrs-2015-0059Search in Google Scholar

14. Nishio, M.: CH/π hydrogen bonds in crystals. CrystEngComm 6 (2004) 130–158.10.1039/b313104aSearch in Google Scholar

15. Steed, K. M.; Steed, J. W.: Packing Problems: high Z′ crystal structures and their relationship to cocrystals, inclusion compounds, and polymorphism. Chem. Rev. 115 (2015) 2895–2933.10.1021/cr500564zSearch in Google Scholar PubMed

Received: 2018-06-17

Accepted: 2018-09-05

Published Online: 2018-10-11

Published in Print: 2018-12-19

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