Home Physical Sciences Crystal structure of 9-chloro-2,3,4,4a,5,6-hexahydro-1H-pyrido [1′,2′:1,6]pyrazino[2,3-b]quinoxaline, C14H15ClN4
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Crystal structure of 9-chloro-2,3,4,4a,5,6-hexahydro-1H-pyrido [1′,2′:1,6]pyrazino[2,3-b]quinoxaline, C14H15ClN4

  • Qiang Chen ORCID logo , Xian Wu Fu and Yu Yu EMAIL logo
Published/Copyright: January 8, 2025
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 240 Issue 2

Abstract

C14H15ClN4, triclinic, P 1 ‾ (no. 2), a = 7.4938(4) Å, b = 9.1046(5) Å, c = 11.0448(5) Å, α = 113.516(5)°, β = 91.811(4)°, γ = 109.583(5)°, V = 638.98(6) Å3, Z = 2, Rgt(F) = 0.0700, wRref(F2) = 0.1909, T = 100 K.

CCDC no.: 2406336

The crystal structure of title compound 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: Colourless block
Size: 0.16 × 0.11 × 0.09 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 2.57 mm−1
Diffractometer, scan mode: XtaLAB Synergy R, ω
θmax, completeness: 73.0°, 99 %
N(hkl)measured, N(hkl)unique, Rint: 7,238, 2,458, 0.060
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 2,286
N(param)refined: 172
Programs: CrysAlisPRO 1 , Olex2 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
Cl1 −0.04253 (7) 0.12554 (7) 0.88545 (5) 0.0253 (3)
N1 0.3746 (3) 0.1969 (2) 0.45489 (19) 0.0206 (5)
N2 0.0894 (3) 0.3428 (2) 0.5252 (2) 0.0198 (4)
N3 0.1452 (3) 0.4434 (3) 0.3648 (2) 0.0232 (5)
H3 0.050794 0.480993 0.383064 0.028*
N4 0.4363 (3) 0.3142 (2) 0.3003 (2) 0.0210 (5)
C1 0.2728 (3) 0.1793 (3) 0.5537 (2) 0.0201 (5)
C2 0.3114 (3) 0.0878 (3) 0.6215 (2) 0.0225 (5)
H2 0.404596 0.036990 0.597245 0.027*
C3 0.2155 (3) 0.0712 (3) 0.7228 (2) 0.0236 (5)
H3A 0.243060 0.010694 0.769097 0.028*
C4 0.0770 (3) 0.1447 (3) 0.7561 (2) 0.0205 (5)
C5 0.0315 (3) 0.2317 (3) 0.6900 (2) 0.0212 (5)
H5 −0.065792 0.277621 0.712674 0.025*
C6 0.1315 (3) 0.2511 (3) 0.5886 (2) 0.0187 (5)
C7 0.1856 (3) 0.3583 (3) 0.4308 (2) 0.0184 (5)
C8 0.3338 (3) 0.2844 (3) 0.3952 (2) 0.0184 (5)
C9 0.2518 (3) 0.4750 (3) 0.2653 (2) 0.0207 (5)
H9A 0.358919 0.589792 0.308908 0.025*
H9B 0.165650 0.476905 0.196519 0.025*
C10 0.3328 (3) 0.3373 (3) 0.1976 (2) 0.0221 (5)
H10 0.223270 0.225461 0.140989 0.027*
C11 0.4636 (3) 0.3888 (3) 0.1064 (2) 0.0234 (5)
H11A 0.558803 0.508514 0.158341 0.028*
H11B 0.384966 0.386715 0.031580 0.028*
C12 0.5702 (4) 0.2671 (4) 0.0489 (3) 0.0299 (6)
H12A 0.476389 0.147711 −0.006697 0.036*
H12B 0.655359 0.304378 −0.008677 0.036*
C13 0.6885 (3) 0.2718 (3) 0.1645 (2) 0.0264 (5)
H13A 0.785368 0.390640 0.217107 0.032*
H13B 0.758466 0.193407 0.128661 0.032*
C14 0.5629 (3) 0.2174 (3) 0.2563 (2) 0.0219 (5)
H14A 0.482658 0.092197 0.208192 0.026*
H14B 0.646687 0.235919 0.336369 0.026*

1 Source of material

2,3,6-Trichloroquinoxaline (7.08 g, 30.3 mmol), potassium bicarbonate (12.57 g, 91.0 mmol) and 2-(aminomethyl)piperidine (5.21 g, 45.6 mmol) were added successively to the solution of DMF (150 mL) stirring for 3 h at 90 °C. After cooling the reaction mixture to room temperature, water (300 mL) was added under stirring. The precipitate formed was filtered and dried. The filter cake was pulverized with ethyl acetate (5 × 20 mL) at room temperature overnight till the isomer impurity was basically removed. Finally, the crude product (pink solid) was recrystallized from dichloromethane and methanol (3:2, v/v). Colorless crystal, yield 40.8 %.

2 Experimental details

Single-crystal X-ray data of title compound was collected on a SuperNova four-circle diffractometer at 100 K. 1 Using Olex2, the structure was solved with SHELXT program and refined with the SHELXT refinement package. 2 , 3 Finally, the crystal structure of title compound was visualized using Ortep3 software. 4 All of the hydrogen atoms were placed in the calculated positions.

3 Comment

Tetrazanbigen (TNBG) studied by our research group is a aza-sterane compound with quinoxaline as the core structure, which is designed and synthesized by our own innovation. It has good anti-tumor activity in vitro and in vivo. 5 Based on SAR, our research team has reported a series of derivatives with improved physical properties and biological effect comparing to TNBG. 6 , 7 , 8 In this study, in order to diminish molecular weight and structural rigidity, an attempt was carried out to modify the main scaffold of TNBG by deducting a benzene ring. 9 It is a novel tetrazanbigen derivative in which an electron drawing group, chloride, was introduced at position C4 (see the Figure). In conclusion, we report the synthesis and crystal structure of the title compound which is a potential anti-tumor drug and consists of 2-(aminomethyl) piperidine and quinoxaline. Their atoms almost lie on the same plane. The key lengths and angles obtained from the title structure are within the normal range. 10

Corresponding author: Yu Yu, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P.R. China, E-mail:

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

  2. Research funding: National Natural Science Foundation of China (30772595, 30371632, 30171070).

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

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Received: 2024-10-27
Accepted: 2024-11-29
Published Online: 2025-01-08
Published in Print: 2025-04-28

© 2024 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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  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of N-(3-bromo-4-fluorophenyl)-N′-hydroxy-4-{[2-(4-methylphenyl)ethyl]amino}-1,2,5-oxadiazole-3-carboximidamide, C18H17BrFN5O2
  4. Synthesis and crystal structure of ethyl (2S,4aS,6aS,6bR,8aR,12aS,12bR,14bR,E)-10-(((3,4-dichlorobenzyl)oxy)imino)-2,4a,6a,6b,9,9,12a-heptamethyl-13-oxo-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-2-carboxylate
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  7. Crystal structure of catena-poly[μ3-iodido-(4-bromopyridine-κ1N)copper(I)], C5H4BrNCuI
  8. The crystal structure of cyclopentadienyl Co–P–C complexes by benzylideneacetone addition, C38H38CoO2P
  9. Synthesis and crystal structure of-(3S,10S,13S,17S)-N-(2-methoxyphenyl)-10,13-dimethyl-17-((R)-1-(phenylamino)ethyl)hexadecahydro-1H-cyclopenta[α]phenanthren-3-amine, C34H48N2O
  10. The crystal structure of (E)-3-((E)-3-(4-ethoxy-3-methoxyphenyl)-1-hydroxyallylidene) chroman-2,4-dione, C21H18O6
  11. The crystal structure of trans–L/D-[bis-(2-methyl-8-hydroxyquinoline-κ2 N,O) bis-(1,3,5-triaza-7-phosphaadamantane-κ2 P)cobalt(III)] tetrafluoroborate
  12. Crystal structure of 9-chloro-2,3,4,4a,5,6-hexahydro-1H-pyrido [1′,2′:1,6]pyrazino[2,3-b]quinoxaline, C14H15ClN4
  13. Crystal structure of 7-(diethylamino)-3-(benzoyl)-2 H -chromen-2-one, C20H19NO3
  14. The crystal structure of 4–bromo-3,5-dinitropyrazole
  15. Crystal structure of 8-hydroxy-3,5,8a-trimethyl-7,8,8a,9-tetrahydronaphtho[2,3-b]furan-4,6-dione, C15H16O4
  16. Crystal structure of 5-hydroxy-3,5,8a-trimethyl-4a,5,6,7,8a,9-hexahydronaphtho[2,3-b]furan-4,8-dione, C15H18O4
  17. Synthesis and crystal structure of-(3S,10S,13S,17S)-N-(2-methoxyphenyl)-10,13-dimethyl-17-((R)-1-(p-tolylamino)ethyl)hexadecahydro-1H-cyclopenta[α]phenanthren-3-amine, C35H50N2O
  18. The crystal structure of catena-poly((μ2-1,3,5-tri(1H- imidazol-1-yl)benzene κ2N:N′)-bis(4-hydroxbenzoato-κ1O)-zinc(II) monohydrate), C29H24N6O7Zn
  19. Crystal structure of 2-(benzo[d]oxazol-2-yl)acetonitrile, C9H6N2O
  20. Crystal structure of 1,3-dihydroxy-6,8-dimethoxy-2-(6-methyltetrahydro-2Hpyran-2-yl)-4a,9a-dihydroanthracene-9,10-dione, C22H22O7
  21. The crystal structure of the double salt potassium 1-methylpiperazine-1,4-di-ium trinitrate, C5H14KN5O9
  22. Crystal structure of 5′-hydroxy-6′-methoxy-1′-methyl-2′,3′,8′,8a′-tetrahydro-1′H-spiro[cyclohexane-1,7′-cyclopenta[ij]isoquinoline]-2,5-dien-4-one, C18H19NO3
  23. The crystal structure of 1,1′-(2,3,5,6-tetramethylpyrazine-1,4-diyl)bis(ethan-1-one), C12H18N2O2
  24. Crystal structure of [μ2-piperazine-1,4-bis(2-hydroxypropanesulfonato-κ2O:O′)] bis(μ2-4,4′-trimethylenedipyridyl-κ2N:N′)disilver(I), C18H24AgN3O4S
  25. Crystal structure of bis ((1-((E)-((4-methoxyphenyl)imino)methyl)naphthalen-2-yl)oxy) copper(II), C36H28CuN2O4
  26. Synthesis and crystal structure of 6,6′-((1E,11E)-5,8-dioxa-2,11-diazadodeca-1,11-diene-1,12-diyl) bis(2,4-di-tert-butylphenol), C36H56N2O4
  27. The crystal structure of barium hexahydroxidoiridate(IV) dihydroxide, Ba2[Ir(OH)6](OH)2
  28. Crystal structure of cinnamoyl ferrocene, C19H16FeO
  29. Crystal structure of (E)-3-(4-butoxyphenyl)acryloylferrocene, C23H24FeO2
  30. Crystal structure of 7-(dimethylamino)-2-hydroxy-2-(trifluoromethyl)-2H-chromene-3-ethyl carboxylate, C15H16F3NO4
  31. The crystal structure of 1-phenylethan-1-aminium 4-hydroxy-3,5-dimethoxybenzoate C17H21NO5
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  33. The crystal structure of tris(μ2-bromido)-bis(η6-p-cymene)-diosmium(II) tetrafluoroborate, C20H28BBr3F4Os2
  34. Crystal structure of new barium lithium manganese fluorides: Ba14Li1.87Mn14.13F68 with a Jarlite–related structure
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  36. The crystal structure of calcitriol–chloroform (1/1), C27H44O3⋅CHCl3
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  43. Synthesis and crystal structure of 4-(difluoromethyl)-1-methyl-N-(pyridin-3-yl)-1H-pyrazole-3-carboxamide hydrate, C11H12F2N4O2
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https://doi.org/10.1515/ncrs-2024-0422
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of N-(3-bromo-4-fluorophenyl)-N′-hydroxy-4-{[2-(4-methylphenyl)ethyl]amino}-1,2,5-oxadiazole-3-carboximidamide, C18H17BrFN5O2
  4. Synthesis and crystal structure of ethyl (2S,4aS,6aS,6bR,8aR,12aS,12bR,14bR,E)-10-(((3,4-dichlorobenzyl)oxy)imino)-2,4a,6a,6b,9,9,12a-heptamethyl-13-oxo-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-2-carboxylate
  5. The crystal structure of pyrazole nitrate
  6. Crystal structure of tetramethyl-bis(μ2-2-(2-hydroxy-3-methoxybenzylidene)-1-(6-(2-(2-hydroxy-3-methoxybenzylidene)hydrazine-1-carbonyl)picolinoyl)hydrazin-1-ido-κ4O,N,O′:O′)ditin(II) ─ ethanol (1/2), C54H62N10O14Sn2
  7. Crystal structure of catena-poly[μ3-iodido-(4-bromopyridine-κ1N)copper(I)], C5H4BrNCuI
  8. The crystal structure of cyclopentadienyl Co–P–C complexes by benzylideneacetone addition, C38H38CoO2P
  9. Synthesis and crystal structure of-(3S,10S,13S,17S)-N-(2-methoxyphenyl)-10,13-dimethyl-17-((R)-1-(phenylamino)ethyl)hexadecahydro-1H-cyclopenta[α]phenanthren-3-amine, C34H48N2O
  10. The crystal structure of (E)-3-((E)-3-(4-ethoxy-3-methoxyphenyl)-1-hydroxyallylidene) chroman-2,4-dione, C21H18O6
  11. The crystal structure of trans–L/D-[bis-(2-methyl-8-hydroxyquinoline-κ2 N,O) bis-(1,3,5-triaza-7-phosphaadamantane-κ2 P)cobalt(III)] tetrafluoroborate
  12. Crystal structure of 9-chloro-2,3,4,4a,5,6-hexahydro-1H-pyrido [1′,2′:1,6]pyrazino[2,3-b]quinoxaline, C14H15ClN4
  13. Crystal structure of 7-(diethylamino)-3-(benzoyl)-2 H -chromen-2-one, C20H19NO3
  14. The crystal structure of 4–bromo-3,5-dinitropyrazole
  15. Crystal structure of 8-hydroxy-3,5,8a-trimethyl-7,8,8a,9-tetrahydronaphtho[2,3-b]furan-4,6-dione, C15H16O4
  16. Crystal structure of 5-hydroxy-3,5,8a-trimethyl-4a,5,6,7,8a,9-hexahydronaphtho[2,3-b]furan-4,8-dione, C15H18O4
  17. Synthesis and crystal structure of-(3S,10S,13S,17S)-N-(2-methoxyphenyl)-10,13-dimethyl-17-((R)-1-(p-tolylamino)ethyl)hexadecahydro-1H-cyclopenta[α]phenanthren-3-amine, C35H50N2O
  18. The crystal structure of catena-poly((μ2-1,3,5-tri(1H- imidazol-1-yl)benzene κ2N:N′)-bis(4-hydroxbenzoato-κ1O)-zinc(II) monohydrate), C29H24N6O7Zn
  19. Crystal structure of 2-(benzo[d]oxazol-2-yl)acetonitrile, C9H6N2O
  20. Crystal structure of 1,3-dihydroxy-6,8-dimethoxy-2-(6-methyltetrahydro-2Hpyran-2-yl)-4a,9a-dihydroanthracene-9,10-dione, C22H22O7
  21. The crystal structure of the double salt potassium 1-methylpiperazine-1,4-di-ium trinitrate, C5H14KN5O9
  22. Crystal structure of 5′-hydroxy-6′-methoxy-1′-methyl-2′,3′,8′,8a′-tetrahydro-1′H-spiro[cyclohexane-1,7′-cyclopenta[ij]isoquinoline]-2,5-dien-4-one, C18H19NO3
  23. The crystal structure of 1,1′-(2,3,5,6-tetramethylpyrazine-1,4-diyl)bis(ethan-1-one), C12H18N2O2
  24. Crystal structure of [μ2-piperazine-1,4-bis(2-hydroxypropanesulfonato-κ2O:O′)] bis(μ2-4,4′-trimethylenedipyridyl-κ2N:N′)disilver(I), C18H24AgN3O4S
  25. Crystal structure of bis ((1-((E)-((4-methoxyphenyl)imino)methyl)naphthalen-2-yl)oxy) copper(II), C36H28CuN2O4
  26. Synthesis and crystal structure of 6,6′-((1E,11E)-5,8-dioxa-2,11-diazadodeca-1,11-diene-1,12-diyl) bis(2,4-di-tert-butylphenol), C36H56N2O4
  27. The crystal structure of barium hexahydroxidoiridate(IV) dihydroxide, Ba2[Ir(OH)6](OH)2
  28. Crystal structure of cinnamoyl ferrocene, C19H16FeO
  29. Crystal structure of (E)-3-(4-butoxyphenyl)acryloylferrocene, C23H24FeO2
  30. Crystal structure of 7-(dimethylamino)-2-hydroxy-2-(trifluoromethyl)-2H-chromene-3-ethyl carboxylate, C15H16F3NO4
  31. The crystal structure of 1-phenylethan-1-aminium 4-hydroxy-3,5-dimethoxybenzoate C17H21NO5
  32. The crystal structure of 1,3,5-trichloro-2-nitrobenzene
  33. The crystal structure of tris(μ2-bromido)-bis(η6-p-cymene)-diosmium(II) tetrafluoroborate, C20H28BBr3F4Os2
  34. Crystal structure of new barium lithium manganese fluorides: Ba14Li1.87Mn14.13F68 with a Jarlite–related structure
  35. Crystal structure of (4-fluorobenzyl)triphenylphosphonium chloride, C25H21ClFP
  36. The crystal structure of calcitriol–chloroform (1/1), C27H44O3⋅CHCl3
  37. The crystal structure of (E)-1-((3)-nitrophenyl)pyren-3-(pyren-1-yl)prop-2-en-1-one, C25H15NO3
  38. Crystal structure of (E)-2-hydroxy-N′-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H16N2O3
  39. Crystal structure of (E)-(3-(thiophen-2-yl)acryloyl)ferrocene, C17H14FeOS
  40. Crystal structure of (E)-(3-(furan-2-yl)acryloyl)ferrocene, C17H14FeO2
  41. Synthesis and crystal structure poly[diaqua(μ3-3-(((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl) methyl)ammonio)propanoate-κ3 O:O′:O″) sodium(I)] monohydrate, C20H24NNaO12S
  42. Crystal structure of 9-methoxy-4-(2-methoxypyridin-3-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine C19H18N4O2
  43. Synthesis and crystal structure of 4-(difluoromethyl)-1-methyl-N-(pyridin-3-yl)-1H-pyrazole-3-carboxamide hydrate, C11H12F2N4O2
  44. The crystal structure of caesalfurfuric acid B, C22H32O4
  45. The crystal structure of 2-bromo-2-(5-bromo-2-methyl-4-nitro-1H-imidazol-1-yl)-1-phenylethanone, C12H9Br2N3O3
  46. The crystal structure of bis{chlorido-[μ2-(1-oxidopyridin-2-yl)(pyridin-2-yl)amido-κ3 O,N, N′]copper(II)}, C20H16Cl2Cu2N6O2
  47. The crystal structure of 3-amino-2-formyl-1-phenyl-9,10-dihydrophenanthrene-4-carbonitrile, C22H16N2O
  48. The crystal structure of 1,1′-(2,5-dimethylpyrazine-1,4-diyl)bis(ethan-1-one), C10H14N2O2
  49. Crystal structure of 5′-(9-phenyl-9H-carbazol-3-yl)-[2,2′-bithiophene]-5-carbaldehyde, C27H17NOS2
  50. The crystal structure of the double salt dipyridin-1-ium bromide tribromide
  51. Crystal structure of (E)-(3-(3-methylthiophen-2-yl)acryloyl)ferrocene, C18H16FeOS
  52. Crystal structure of (E)-(3-(4-phenoxyphenyl)acryloyl)ferrocene, C25H20FeO2
  53. Crystal structure of (E)-(3-(3,4-dimethylphenyl)acryloyl)ferrocene, C21H20FeO
  54. Crystal structure of [(1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N‴)tetracyanidodiplatinum(II)] dimethyl sulfoxide solvate, C18H36N8O2Pt2S2
  55. Crystal structure of (4-ethoxybenzyl)triphenylphosphonium bromide ethanol solvate, C29H32BrO2P
  56. Crystal structure of (1-naphthalen-1-yl-methyl)triphenylphosphonium chloride ethanol solvate, C31H30ClOP
  57. Crystal structure of (1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N″,N‴)platinum(II) bis[tribromido(dimethyl sulfoxide-κS)platinate(II)], C14H36Br6N4O2Pt3S2
  58. Crystal structure of (2-methylbenzyl)triphenylphosphonium chloride ethanol solvate, C28H30ClOP
  59. Crystal structure of bis(η2, σ1-8-methoxycyclooct-4-enyl)(μ2-1,4,8,11-tetraazacyclotetradecane-κ4 N, N′, N″, N‴)diplatinum(II) dibromide, C28H54Br2N4O2Pt2
  60. Crystal structure of (1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N″,N‴)palladium(II) tetrabromidopalladate(II), C10H24Br4N4Pd2
  61. Crystal structure of (1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N″,N‴)palladium(II) bis[trichlorido(dimethyl sulfoxide-κS)platinate(II)], C14H36Cl6N4O2PdPt2S2
  62. Crystal structure of (1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N″,N‴)palladium(II) tetraiodidopalladate(II), C10H24I4N4Pd2
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