Startseite Crystal structure of 4-(((2-(3-(1-(3-(3-cyanophenyl)-6-oxopyridazin-1(6H)-yl)ethyl)phenyl) pyrimidin-5-yl)oxy)methyl)-1-methylpiperidin-1-ium chloride monohydrate, C30H33N6O2Cl
Artikel Open Access

Crystal structure of 4-(((2-(3-(1-(3-(3-cyanophenyl)-6-oxopyridazin-1(6H)-yl)ethyl)phenyl) pyrimidin-5-yl)oxy)methyl)-1-methylpiperidin-1-ium chloride monohydrate, C30H33N6O2Cl

  • Han Yao , Ming Yan ORCID logo EMAIL logo , Xingshu Li und Jinhui Hu ORCID logo
Veröffentlicht/Copyright: 21. Juni 2022

Abstract

C30H33N6O2Cl monoclinic, P21 (no. 4), a = 13.7983(8) Å, b = 7.3771(3) Å, c = 14.3578(7) Å, β = 101.730(5)°, V = 1430.97(12) Å3, Z = 2, R gt (F) = 0.0525, wR ref (F 2) = 0.1285, T = 170 K.

CCDC no.: 2132093

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: Colorless needle
Size: 0.15 × 0.11 × 0.09 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 1.53 mm−1
Diffractometer, scan mode: SuperNova, ω
θ max, completeness: 65.0°, >99%
N(hkl)measured, N(hkl)unique, R int: 4900, 3637, 0.050
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 3225
N(param)refined: 367
Programs: Bruker [1], Olex2 [2], SHELX [3]
Table 2:

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

Atom x y z U iso*/U eq
Cl01 0.91107 (9) −0.02945 (17) 0.10094 (8) 0.0332 (3)
O002 0.7509 (2) 0.5505 (5) 0.3237 (2) 0.0299 (8)
O003 0.5322 (3) 0.5637 (6) 0.9674 (3) 0.0442 (10)
N004 0.6661 (3) 0.6883 (6) 0.5332 (3) 0.0259 (9)
N005 0.4388 (3) 0.7122 (5) 0.7319 (3) 0.0256 (9)
N006 0.8370 (3) 0.6137 (6) 0.5797 (3) 0.0291 (10)
N007 0.8296 (3) 0.3283 (6) 0.0080 (3) 0.0272 (9)
H007 0.860862 0.215316 0.034714 0.033*
N008 0.4900 (3) 0.7014 (5) 0.8226 (3) 0.0240 (9)
C009 0.7486 (4) 0.8309 (7) 0.8836 (3) 0.0277 (11)
H009 0.748720 0.865240 0.945896 0.033*
C00A 0.5637 (3) 0.8460 (7) 0.8516 (3) 0.0257 (10)
H00A 0.578913 0.849418 0.921327 0.031*
C00B 0.6590 (3) 0.8074 (7) 0.8194 (3) 0.0248 (10)
C00C 0.7501 (3) 0.7285 (7) 0.6969 (3) 0.0226 (10)
C00D 0.7521 (4) 0.6720 (7) 0.5983 (3) 0.0264 (10)
C00E 0.6613 (4) 0.7589 (7) 0.7256 (3) 0.0274 (11)
H00E 0.602093 0.746814 0.681648 0.033*
C00F 0.8368 (4) 0.8035 (7) 0.8551 (3) 0.0308 (12)
H00F 0.895897 0.819445 0.898833 0.037*
C00G 0.6694 (4) 0.6435 (7) 0.4444 (3) 0.0280 (11)
H00G 0.611648 0.651261 0.398139 0.034*
C00H 0.8430 (3) 0.5124 (7) 0.2954 (3) 0.0289 (12)
H00B 0.869101 0.396408 0.320795 0.035*
H00C 0.891376 0.605629 0.318926 0.035*
C00I 0.7551 (4) 0.5856 (7) 0.4176 (3) 0.0249 (10)
C00J 0.3689 (4) 0.5913 (7) 0.7021 (4) 0.0279 (11)
C00K 0.8216 (3) 0.5083 (7) 0.1873 (3) 0.0258 (11)
H00K 0.791678 0.624088 0.163453 0.031*
C00L 0.9183 (3) 0.4852 (7) 0.1532 (3) 0.0259 (10)
H00D 0.950111 0.373138 0.178150 0.031*
H00H 0.962575 0.584758 0.176369 0.031*
C00M 0.3174 (4) 0.6102 (7) 0.6014 (4) 0.0332 (12)
C00N 0.8396 (4) 0.5694 (7) 0.4893 (3) 0.0303 (12)
H00N 0.898253 0.527613 0.474484 0.036*
C00O 0.8979 (3) 0.4814 (7) 0.0447 (3) 0.0265 (10)
H00I 0.868233 0.595216 0.019895 0.032*
H00J 0.959692 0.466833 0.023215 0.032*
C00P 0.4783 (4) 0.5657 (7) 0.8874 (3) 0.0328 (12)
C00Q 0.7512 (4) 0.3563 (8) 0.1476 (3) 0.0311 (12)
H00L 0.688455 0.374880 0.166858 0.037*
H00M 0.778335 0.241761 0.174151 0.037*
C00R 0.3692 (4) 0.6787 (7) 0.5348 (4) 0.0336 (12)
H00R 0.435854 0.708270 0.553209 0.040*
C00S 0.8396 (4) 0.7527 (7) 0.7625 (4) 0.0307 (11)
H00S 0.899832 0.734831 0.744324 0.037*
C00T 0.5211 (4) 1.0288 (7) 0.8172 (4) 0.0325 (12)
H00O 0.510106 1.033108 0.748993 0.049*
H00P 0.566696 1.122623 0.843541 0.049*
H00Q 0.459441 1.046593 0.837078 0.049*
O00U 1.0231 (4) 0.4242 (9) 0.6737 (3) 0.086 (2)
H00V 0.961615 0.448626 0.660622 0.129*
H00W 1.047185 0.498214 0.717746 0.129*
C00V 0.3203 (5) 0.7022 (8) 0.4409 (4) 0.0418 (14)
C00W 0.7335 (4) 0.3469 (8) 0.0390 (4) 0.0347 (12)
H00T 0.691427 0.243970 0.016494 0.042*
H00U 0.699960 0.456021 0.011880 0.042*
N00X 0.4191 (6) 0.8427 (8) 0.3222 (4) 0.0723 (19)
C00Y 0.3472 (4) 0.4531 (8) 0.7635 (4) 0.0368 (12)
H00Y 0.296008 0.371762 0.742116 0.044*
C00Z 0.4006 (4) 0.4399 (7) 0.8528 (4) 0.0392 (13)
H00Z 0.386721 0.347873 0.892421 0.047*
C010 0.8139 (4) 0.3160 (8) −0.0990 (3) 0.0403 (14)
H01A 0.777212 0.419771 −0.127039 0.060*
H01B 0.777690 0.207649 −0.120411 0.060*
H01C 0.876946 0.312914 −0.117562 0.060*
C011 0.3745 (5) 0.7802 (9) 0.3738 (4) 0.0511 (17)
C012 0.2180 (4) 0.5650 (8) 0.5724 (4) 0.0423 (14)
H012 0.182465 0.520608 0.615972 0.051*
C013 0.2218 (5) 0.6568 (9) 0.4113 (4) 0.0501 (16)
H013 0.189744 0.673327 0.348364 0.060*
C014 0.1722 (5) 0.5871 (9) 0.4767 (5) 0.0530 (18)
H014 0.106258 0.553391 0.456972 0.064*

Source of material

The compound was synthesized according to the procedure in our previous work [4]. A mixture of 3-(6-oxo-1,6-dihydropyridazin-3-yl)benzonitrile (197.2 mg, 1 mmol), (S)-1-(3-(5-((1-methylpiperidin-4-yl)methoxy)pyrimidin-2-yl)phenyl) ethan-1-ol (327.4 mg, 1 mmol), and PPh3 (393.4 mg, 1.5 mmol) in anhydrous tetrahydrofuran (THF) (8.0 mL) were added diisopropyl azodicarboxylate (DIAD) (303.3 mg, 1.5 mmol) slowly at 0 °C. The reaction mixture was allowed to warm to room temperature. After 1 h, the reaction was quenched with ice water (20.0 mL) and the mixture was extracted with CH2Cl2 (20.0 × 3). The organic layers were separated, dried and concentrated under reduced pressure. The crude products were purified by flash column chromatography using CH2Cl2/CH3OH (20/1, v/v) as eluents to give (R)-3-(1-(1-(3-(5-((1-methylpiperidin-4-yl)methoxy)pyrimidin-2-yl) phenyl)ethyl)-6-oxo-1,6-dihydropyridazin-3-yl)benzonitrile. The hydrochloride salt of the title compound (506.6 mg, 1 mmol) was obtained by adding hydrogen chloride solution in ethyl acetate (1.0 M, 1 mL) to ethanol. After drying at the rotavapor, the solid product was recrystallized from a mixture of CH2Cl2 and ethyl acetate (v/v, 1/3, 20 mL). Pale yellow block crystals were obtained after three days.

Experimental details

Hydrogen atoms were placed in their geometrically idealized positions and constrained to ride on their parent atoms.

Comment

Chirality is the basic feature of nature, and the main substances that makeup life, such as amino acids, carbohydrates, nucleic acids, proteins, enzymes, and receptors are chiral [5]. Enantiomers do not differ in their physical and chemical properties but could differ in their pharmacological activity, metabolic process, metabolic rate, and toxicity [6, 7]. Pyridazine and its derivatives have attracted wide increasing attention due to its biological activities, such as anticancer and antibacterial [8, 9]. As a part of our current research interest in the exploration of the chiral compounds with anticancer activities [10], we herein report the molecular structure of a new chiral pyridazine derivative.

The asymmetric unit of the title compound contains the hydrochloride of (R)-3-(1-(1-(3-(5-((1-methylpiperidin-4-yl)methoxy)pyrimidin-2-yl) phenyl)ethyl)-6-oxo-1,6-dihydropyridazin-3-yl)benzonitrile and an additional water molecule. The single-crystal structure of this salt monhydrate with (R)-configuration is shown in the figure. A classical hydrogen bond of the N–H⃛Cl type is observed in the structure. All bond lengths and angles of this molecule are in the expected ranges.


Corresponding author: Ming Yan, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China, E-mail:

Funding source: Foundation of Guangdong Basic and Applied Basic Research

Award Identifier / Grant number: 2019A1515110266

Funding source: Foundation for Young Talents

Award Identifier / Grant number: 2019KQNCX159

Funding source: Jiangmen Program for Young Talents

Award Identifier / Grant number: 2019td04

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

  2. Research funding: This work was financially supported by the Foundation of Guangdong Basic and Applied Basic Research (2019A1515110266), the Foundation for Young Talents (2019KQNCX159), and Jiangmen Program for Young Talents (2019td04). We also thank Guangzhou Synmepilin Pharmaceuticals Co. Ltd. for the support of the fund.

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

References

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Received: 2022-02-22
Accepted: 2022-05-30
Published Online: 2022-06-21
Published in Print: 2022-10-26

© 2022 Han Yao et al., published by De Gruyter, Berlin/Boston

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

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of 3-(1-(2-((5-methylthiophen-2-yl)methylene)hydrazinyl)ethylidene)chroman-2,4-dione, C17H14N2O3S
  4. Crystal structure of chlorido-(η 6-toluene)(5,5′-dimethyl-2,2′-bipyridine-κ2 N,N′)ruthenium(II) hexafluoridophosphate(V) ─ acetone (1/1) C22H26ClN2ORuPF6
  5. Crystal structure of 4-(((2-(3-(1-(3-(3-cyanophenyl)-6-oxopyridazin-1(6H)-yl)ethyl)phenyl) pyrimidin-5-yl)oxy)methyl)-1-methylpiperidin-1-ium chloride monohydrate, C30H33N6O2Cl
  6. The crystal structure of 2-chloro-N-((2-chlorophenyl)carbamoyl)nicotinamide, C13H9Cl2N3O2
  7. Crystal structure of 9-(t-butyl)-3,11-dihydro-6H-pyrazolo [1,5-a]pyrrolo[3′,2′:5,6]pyrido[4,3-d]pyrimidin-6-one hemihydrate, C30H32N10O3
  8. Crystal structure of di-μ2-hydroxido-tetrakis(6-methylpyridine-2-carboxylato-k2 N,O) diiron(III) trihydrate C28H32Fe2N4O13
  9. Crystal structure of catena-poly[qua-(μ2-2-aminoisophthalat-κ3 O,O′:O′′)(1,10-phenanthroline-κ2 N,N′)manganese(II)] C20H15MnN3O5
  10. Crystal structure of poly[(bis(isothiocyano)-bis(μ 2-(E)-N′-(pyridin-4-ylmethylene)isonicotinohydrazide))iron(II) – methanol – 1,4-dioxane (1/2/2), C36H44FeN10O8S2
  11. Crystal structure of (E)-N′-(1-(5-chloro-2-hydroxyphenyl)propylidene)-4-hydroxybenzohydrazide, C16H15ClN2O3
  12. Crystal structure of bis(μ2-benzoato-k2O:O′)-bis(μ2-benzoato-k3O,O′:O′)dinitrato-k2O,O′-bis(phenanthroline-k2 N,N′)dierbium(III), C52H36Er2N6O14
  13. Crystal structure of 4-ethyl-2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-1,6-dihydropyrimidine-5-carbonitrile, C14H12N4O3S
  14. Synthesis and crystal structure of 1-((3R,10S,13R,17S)-10,13-dimethyl-3- (phenylamino)hexadecahydro-1H-cyclopenta[α] phenanthren-17-yl)ethan-1-one, C27H39NO
  15. Crystal structre of 1,4-bis(bromomethyl)-2,3,5,6-tetramethylbenzene, C12H16Br2
  16. Crystal structure of 2-(adamantan-1-yl)-5-(3,5-dinitrophenyl)-1,3,4-oxadiazole, C18H18N4O5
  17. Crystal structure of (E)-N′-benzylidene-4-nitrobenzohydrazide – methanol (1/1), C15H15N3O4
  18. The crystal structure of 3-(2-bromophenyl)-1,5-di-p-tolylpentane-1,5-dione, C25H23BrO2
  19. Crystal structure of catena-poly[(μ 2-4,4′-bipyridine-κ2 N:N′)-bis(4-bromobenzoato-κ1 O)zinc(II)], C24H16Br2N2O4Zn
  20. Crystal structure of 1,1′-(1,2-ethanediyl)bis(pyridin-1-ium) bis(1,2-dicyanoethene-1,2-dithiolato-κ2 S:S)zinc(II), C20H14N6ZnS4
  21. Crystal structure of pentacarbonyl-(μ2-propane-1,3-dithiolato-κ4 S:S,S′:S′)-(diphenyl(o-tolyl)phosphine-κ1 P)diiron (Fe-Fe), C27H23Fe2O5PS2
  22. The crystal structure of the cocrystal 4-hydroxy-3,5-dimethoxybenzoic acid–pyrazine-2-carboxamide(1/1), C14H15N3O6
  23. The crystal structure of dichlorido-bis((RS)-2-(4-chlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)hexanenitrile-κ1 N)zinc(II), C30H34Cl4N8Zn
  24. Crystal structure of the cocrystal 2,4,6-triamino-1,3,5-triazine – 1H-isoindole-1,3(2H)-dione – methanol (1/1/1), C12H15N7O3
  25. The crystal structure of methyl 4-((3,5-di-tert-butyl-4-oxocyclohexa-2,5-dien-1-ylidene)methyl) benzoate, C23H28O3
  26. Crystal structure of (poly[µ2-(1H-pyrazol-1-yl)methyl]-1H-benzotriazole-κ 2 N:N)-(nitrato-κ 2 O:O′) silver(I), C9H8AgN7O3
  27. Crystal structure of tetraaqua-bis[4-(1H-1,2,4-triazol-1-yl)benzoato-k1 N]cadmium(II), C18H20CdN6O8
  28. The crystal structure of diaqua-bis(pyrazolo[1,5-a]pyrimidine-3-carboxylato-κ2N,O)nickel(II) dihydrate, C14H16N6O8Ni
  29. Crystal structure of poly[μ2-aqua-aqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2 N:N′)-(μ2-4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ2 O:O′)-(μ4-4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ5 O,O′:O″:O′″:O′″)dicobalt(II)] – water – dimethylformamide (1/1/1) C44H43N11O12Co2
  30. Crystal structure of N-((Z)-amino(((E)-amino(phenylamino)methylene) amino)methylene)benzenaminium chloride – benzo[f]isoquinolino[3,4-b][1,8]naphthyridine – tetrahydrofurane (1/2/2), C60H54ClN11O2
  31. The crystal structure of Chrysosplenol D, C18H16O8
  32. Crystal structure of poly[deca aqua-bis(μ 4-2-(triazol-1-yl)-benzene-1,3,5-tricarboxylato)- bis(μ 5-2-(triazol-1-yl)-benzene-1,3-dicarboxylato-5-carboxyl acid) pentamanganese(II)] dihydrate, C44H42Mn5N12O36
  33. Synthesis and crystal structure of (E)-1-(4-(((E)-3-(tert-butyl)-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-methyl oxime, C20H24N2O2
  34. The crystal structure of 4,4′-dichloro-6,6′-dimethoxy-2,2′,3,3′,5,5′- hexanitroazobenzene, C14H6N8O14Cl2
  35. Crystal structure of N 2,N 4-dimesitylpentane-2,4-diamine, C23H34N2
  36. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ 6O6)potassium(2-methylphenylamino)ethyl-2-methylphenylamide ammoniate (1/3.5), [K(18-crown-6)](o-CH3C6H4)NH(CH2)2N(o-CH3C6H4) 3.5 NH3, C28H53.5KN5.5O6
  37. The crystal structure of N′,N″,2-tris((E)-5-chloro-2-hydroxybenzylidene)hydrazine-1-carbohydrazonhydrazide hydrochloride – methanol (1/3), C25H30Cl4N6O6
  38. Crystal structure of (E)-7-bromo-2-(3,5-dimethoxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C19H17BrO3
  39. Crystal structure of (E)-N′-(1-(5-chloro-2-hydroxyphenyl) ethylidene)-4-hydroxybenzohydrazide, C15H13ClN2O3
  40. {2-(((2-aminoethyl)imino)methyl)-6-bromophenolato-κ3 N,N′,O}iron(III) nitrate, C18H20Br2FeN5O5
  41. Crystal structure of 2-(tert-pentyl)anthracene-9,10-dione, C19H18O2
  42. Crystal structure of 5,5′-(1,4-phenylene)bis(1H-imidazol-3-ium) bis(2-(2-(carboxymethyl)phenyl)acetate), C32H30N4O8
  43. Crystal structure of N 2,N 6-bis(2-(((E)-naphthalen-1-ylmethylene)amino)phenyl)pyridine-2,6-dicarboxamide, C41H29N5O2
  44. The crystal structure of 3-amino-1,2,4-triazolium 2,4,5-trinitroimidazolate, C5H5O6N9
  45. Hydrogen bonded dimers in the crystal structure of 2-chloro-N-(phenylcarbamoyl)nicotinamide, C26H20Cl2N6O4
  46. The crystal structure of 4,4′-bipyridine-5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one-water(1/2/2), C40H32N2O12
  47. Crystal structure of N,N'-bis(4-fluoro-salicylaldehyde)-3,6-dioxa-1,8-diaminooctane, C20H22F2N2O4
  48. Crystal structure of 3-(1,3-dinitropropan-2-yl)-4H-chromen-4-one, C12H10N2O6
  49. The crystal structure of (4-(2-bromoethoxy)-phenyl)(phenyl)methanone, C15H13BrO2
  50. Crystal structure of (E)-7-bromo-2-(4-methoxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C18H15BrO2
  51. Crystal structure of dichlorido-tetrakis((E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ 1 N)cadmium(II), C60H68O4N12Cl10Cd
  52. Crystal structure of diaqua-diphenanthroline-κ2 N,N′-bis(μ2-2-carboxy-3,4,5,6-tetrafluorobenzoato-κ2 O:O′)-bis(μ2-tetrafluorophthalato-κ3 O,O′:O′)didysprosium(III) – phenanthroline (1/2), C80H38Dy2F16N8O18
  53. Crystal structure of bis(μ2-2-oxido-2-phenylacetato-κ3 O,O′:O′)-bis(N-oxido-benzamide-κ2 O,O′)-bis(propan-2-olato-κ1 O)dititanium(IV), C36H38N2O12Ti2
  54. Crystal structure of poly[diaqua-(μ2-1H-benzo[d][1,2,3]triazole-5-carboxylato-κ2 O:O′)(μ2-oxalato-κ4O,O:O″,O′″)europium(III)] monohydrate, C9H10N3O9Eu
  55. Crystal structure of bis((N-methyl-2-oxyethyl)amine)-bis(μ 2-N,N,N-tris(2-oxoethyl)amine)-bis(isopropoxy)-bis(μ 3-oxo)tetratitanium(IV)– isopropanol (1/2), C34H76N4O16Ti4
  56. Synthesis and crystal structure of ethyl 4-((4-iodobenzyl)amino)benzoate, C16H16INO2
  57. Crystal structure of (Z)-2-(tert-butyl)-5-((5-(tert- butyl)-2H-pyrrol-2-ylidene)(mesityl)methyl)-1H-pyrrole, C26H34N2
  58. Crystal structure of dimethylammonium poly[μ4-1,1′-(1,4- phenylenebis(methylene))bis(1H-pyrazole-3,5-dicarboxylato-κ6 N,O:O′:N′,O″:O‴) manganese(II)], C22H26MnN6O8
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