Home Crystal structure of 2-((2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)amino)-N-(2-(4-methylpiperazin-1-yl)ethyl)benzamide hydrate, C25H37Cl2N5O6
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Crystal structure of 2-((2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)amino)-N-(2-(4-methylpiperazin-1-yl)ethyl)benzamide hydrate, C25H37Cl2N5O6

  • Xiaona Xu , Wenqiang Tang ORCID logo , Zhoujing Zhu and Bin Liu ORCID logo EMAIL logo
Published/Copyright: February 6, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 2

Abstract

C25H37Cl2N5O6, triclinic, P 1 ‾ (no. 2), a = 8.115(4) Å, b = 8.656(4) Å, c = 22.641(9) Å, α = 81.344(9)°, β = 80.173(9)°, γ = 65.833(8)°, V = 1423.9(10) Å3, Z = 2, R gt (F) = 0.0652, wR ref (F 2) = 0.2010, T = 173 K.

CCDC no.: 2294528

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 needle
Size: 0.18 × 0.12 × 0.05 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.28 mm−1
Diffractometer, scan mode: Bruker APEX-II, φ and ω
θ max, completeness: 27.5°, 99 %
N(hkl)measured, N(hkl)unique, R int: 12,547, 6361, 0.067
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 3543
N(param)refined: 358
Programs: Bruker [1], SHELX [2], [3], Olex2 [4]
Table 2:

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

Atom x y z U iso*/U eq
C1 0.2267 (5) 0.1911 (4) 0.68834 (19) 0.0335 (9)
C2 0.2241 (5) 0.0190 (4) 0.69663 (17) 0.0277 (8)
C3 0.2422 (5) −0.0965 (4) 0.65821 (16) 0.0255 (8)
C4 0.2218 (6) −0.3958 (5) 0.6819 (2) 0.0423 (11)
C5 0.2246 (5) −0.2340 (4) 0.69660 (17) 0.0314 (9)
C6 0.2714 (5) −0.0807 (4) 0.59140 (16) 0.0236 (8)
C7 0.4049 (5) −0.2104 (4) 0.56055 (16) 0.0252 (8)
C8 0.4295 (5) −0.1983 (4) 0.49845 (16) 0.0240 (8)
C9 0.3158 (5) −0.0610 (4) 0.46343 (15) 0.0233 (8)
C10 0.1884 (5) 0.0723 (4) 0.49577 (16) 0.0226 (8)
C11 0.1651 (5) 0.0664 (4) 0.55827 (16) 0.0248 (8)
C12 0.3072 (4) −0.1664 (4) 0.36895 (16) 0.0233 (8)
C13 0.2783 (5) −0.3089 (4) 0.39809 (17) 0.0271 (8)
C14 0.2629 (5) −0.4253 (5) 0.36652 (19) 0.0327 (9)
C15 0.2782 (6) −0.4041 (5) 0.3045 (2) 0.0392 (10)
C16 0.3011 (6) −0.2609 (5) 0.27477 (18) 0.0334 (9)
C17 0.3131 (5) −0.1394 (4) 0.30578 (16) 0.0257 (8)
C18 0.3189 (5) 0.0237 (4) 0.27291 (16) 0.0292 (9)
C19 0.3863 (5) 0.1719 (5) 0.17742 (18) 0.0350 (10)
C20 0.2186 (6) 0.2555 (5) 0.14340 (18) 0.0357 (10)
C21 0.1123 (7) 0.5418 (5) 0.16926 (18) 0.0454 (11)
C22 0.0787 (6) 0.7234 (5) 0.1473 (2) 0.0430 (11)
C23 0.0328 (6) 0.6803 (5) 0.05183 (18) 0.0387 (10)
C24 0.0688 (6) 0.4953 (4) 0.07252 (18) 0.0373 (10)
C25 −0.0860 (6) 0.9651 (5) 0.0821 (2) 0.0463 (11)
Cl1 0.05030 (13) 0.25476 (10) 0.45630 (4) 0.0340 (3)
Cl2 0.61309 (12) −0.36043 (10) 0.46347 (4) 0.0298 (2)
H 0.618570 0.658869 0.143450 0.055*
HA 0.715241 0.766987 0.129489 0.055*
HB 0.348281 0.034573 0.379750 0.034*
HC 0.431636 −0.078185 0.198393 0.039*
HD 0.078225 0.161089 0.578234 0.030*
HE 0.481066 −0.309303 0.582355 0.030*
HF 0.308793 −0.245095 0.232101 0.040*
HG 0.269124 −0.325938 0.440770 0.032*
HH 0.656574 0.385797 0.111920 0.102*
HI 0.715134 0.353972 0.169830 0.102*
HJ 0.241591 −0.520320 0.387457 0.039*
HK 0.497752 0.142093 0.148136 0.042*
HL 0.387910 0.253884 0.203240 0.042*
HM 0.234313 0.188489 0.109556 0.043*
HN 0.109640 0.255475 0.170805 0.043*
HO 0.148443 0.690318 0.033794 0.046*
HP −0.050975 0.721082 0.020568 0.046*
HQ 0.102562 0.276792 0.686468 0.050*
HR 0.302944 0.202749 0.650809 0.050*
HS 0.276510 0.207710 0.722278 0.050*
HT −0.047950 0.484368 0.088116 0.045*
HU 0.124875 0.425970 0.037827 0.045*
HV 0.273191 −0.486829 0.282394 0.047*
HW 0.196223 0.502625 0.200430 0.054*
HX −0.004020 0.534232 0.187957 0.054*
H0AA −0.162658 1.001257 0.049409 0.069*
HY 0.028535 0.978792 0.067579 0.069*
HZ −0.149651 1.034933 0.115720 0.069*
H1AA 0.028113 0.794505 0.181654 0.052*
H2AA 0.195335 0.731931 0.129594 0.052*
H3AA 0.339564 −0.462592 0.660192 0.063*
H4AA 0.125317 −0.369220 0.656554 0.063*
H5AA 0.198854 −0.461564 0.719156 0.063*
N1 0.2009 (5) −0.2055 (4) 0.75334 (14) 0.0369 (8)
N2 0.3271 (4) −0.0511 (3) 0.40063 (13) 0.0283 (7)
N3 0.3863 (4) 0.0193 (4) 0.21460 (14) 0.0327 (8)
N4 0.1909 (4) 0.4304 (4) 0.12006 (13) 0.0298 (7)
N5 −0.0475 (4) 0.7861 (4) 0.10239 (14) 0.0329 (8)
O1 0.2023 (4) −0.0436 (3) 0.75422 (12) 0.0416 (7)
O2 0.2588 (4) 0.1560 (3) 0.29803 (12) 0.0409 (7)
O3 0.6078 (4) 0.7639 (3) 0.13587 (15) 0.0461 (8)
O4 0.6582 (7) 0.4326 (4) 0.1431 (2) 0.0850 (14)
O5 0.5212 (4) 0.3765 (4) 0.04784 (13) 0.0429 (7)
H5A 0.532098 0.320348 0.017641 0.052*
H5B 0.414799 0.397558 0.068571 0.052*
O6 0.5522 (6) 0.1276 (5) −0.02736 (19) 0.0807 (12)
H6A 0.437943 0.149220 −0.006993 0.097*
H6B 0.543859 0.168144 −0.062273 0.097*

1 Source of materials

A mixture of 2-((2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)-phenyl)amino) benzoic acid (3.76 g, 10 mmol), pyrrolidine (1.57 g, 11 mmol), 2-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetra-methyluronium hexafluorophosphate (HATU) (4.18 g, 11 mmol) and N,N-diisopropylethylamine (2.58 g, 20 mmol) was dissolved in N,N-dimethylformamide (25 mL). The mixture was stirred for 3 h at room temperature, until the TLC indicated the reaction was completed. The mixture was diluted with brine, and then extracted with ethyl acetate (3 × 30 mL). The organic phase was washed with brine (30 mL), dried with anhydrous sodium sulfate, and then concentrated under pressure. The title compound was separated by silica-gel column chromatography with ethyl dichloromethane-methanol (10 %) gradient solvent system. The target product was obtained as a white solid. Yield: 89.7 %.

2 Experimental details

The SHELXT [2] program was employed for the initial structure solution, followed by refinement using full-matrix least-squares procedures in Shelxl [3], within the OLEX2 program [4].

3 Comment

Benzamide is a type of aromatic amide containing a carboxylic acid group, commonly used for synthesizing a variety of compounds. Halogen-substituted derivatives of benzamide exhibit notable properties such as antipsychotic, anticancer, and antiemetic effects, and show potential for treating human tumors [5]. There are numerous similar structures reported in literature [6], [7], [8], [9]. This article reports the comprehensive single crystal structure of a newly identified benzamide compound.

In the molecular structure of the titled organic compound, the piperazine hexagonal ring adopts a chair conformation, while the five-membered ring of isoxazolidine exhibits almost planar characteristics with the atoms lying in the same plane. The dihedral angle of C2–C3–C5–O1 is only 1.0(3)°, indicating minimal torsion. The two benzene rings in the molecule are non-coplanar and display evident torsion. All bond lengths, bond angles, and dihedral angles in the molecule fall within reasonable ranges, resembling similar structures reported in the literature [10], [11], [12], [13], [14], [15].

Within the molecule, a hydrogen bond (N2–HB⋯O2) is formed, with a bond angle of 127.3(3)° and a bond length of 2.075(3) Å, which also contributes to the relatively small dihedral angle (27.3(4)°) of N2–C12–C18–O2. Water molecules in the crystal structure are stabilized by hydrogen bonding interactions with hydrogen atoms in the organic compound, as well as with other water molecules.

Corresponding author: Bin Liu, Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang, Shaanxi, China, E-mail:

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

  2. Research funding: Natural Science Foundation of Shannxi Province (2021JM-561), Doctoral research fund project of Xianyang Vocational and Technical College (2021BK01) and the Key Laboratory of Molecular Imaging and Drug Synthesis of Xianyang City (2021QXNL–PT-0008).

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

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Received: 2023-11-29
Accepted: 2024-01-17
Published Online: 2024-02-06
Published in Print: 2024-04-25

© 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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  52. The crystal structure of [hexaaquamagnesium(II)] 4-[(pyridine-4-carbonyl)-amino]-phthalate trihydrate, C14H26N2O14Mg
  53. Crystal structure of 1-(p-tolylphenyl)-4-(2-furoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O3
  54. The crystal structure of bis(1,4,7,10,13-pentaoxacyclopentadecane)-potassium(I) dichloridocopper(I), C20H40Cl2CuKO10
  55. The crystal structure of tris(tetra-n-butylammonium) hexanitrato-κ2O,O′-lanthanium(III) C48H108N9O18La
https://doi.org/10.1515/ncrs-2023-0525
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Solvothermal synthesis and crystal structure of aqua-tris(p-acetamidobenzoate-κ2O,O′)-(2,2′-bipyridine-κ2N,N′)terbium(III) - water - methanol (1/1/1)
  4. Crystal structure of hexaaquazinc(II) catena-poly[bis(1-(3-carboxyphenyl)-5-methyl-4-oxo-1,4-dihydropyridazine-3-carboxylato-κ2O,O′)-bis(μ2-1-(3-carboxyphenyl)-5-methyl-4-oxo-1,4-dihydropyridazine-3-carboxylato-κ2O:O′)trizinc(II)] hexahydrate C26H36N4O20Zn2
  5. The crystal structure of valinyl-N-ium-4-(5-(thiophen-2-yl)isoxazol-3-yl)phenyl trifluoroacetate
  6. Crystal structure of bis(3,5-diisopropyl-1H-pyrazol-4-ammonium) tetrafluoroterephthalate, 2[C9H18N3][C8F4O4]
  7. Crystal structure of aqua-octakis(μ3-salicylato)-(1,10-phenanthroline)-(acetonitrile)-dicobalt(II)-trititanium(IV), C70H45N3O25Co2Ti3
  8. Crystal structure of catena-poly[aqua-(μ2-4,4′-diimidazole diphenyl ether-κ2N:N′)-(sulfato-κ1O)-cobalt(II)] – dimethylformamide (2/1), C39H37CoN9O8S
  9. Crystal structure of (5R,8R,9R,10R,12R, 13R,14R,17S)-2-(E-3-fluorobenzylidene)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl) hexadecahydro-3H-cyclopenta[a]phenanthren-3-one, C37H53FO3
  10. Crystal structure of (Z)-4-((4,5,6-trimethoxy-3-oxobenzofuran-2(3H)-ylidene)methyl)phenyl diphenylphosphinate, C30H25O7P
  11. Crystal structure of 3-((5-methylpyridin-2-yl)amino)-1-phenylpropan-1-one, C15H16N2O
  12. The crystal structure of (R)-9-(5-methoxy-2-methyl-2,3-dihydro-1H-cyclopenta[a]naphthalen-1-ylidene)-9H-thioxanthene, C28H22OS
  13. Crystal structure of diaqua-bis[1-(1-(hydroxymethyl)-1H-pyrazol-3-yl)-5-methyl-1H-1,2,3-triazole-4-carboxylato-κ2N,O)] manganese(II), C16H20MnN10O8
  14. The crystal structure of t-butyl 7-[4-(4-fluorophenyl)-2-[(methanesulfonyl)(methyl)amino]-6-(propan-2-yl)pyrimidin-5-yl]-3,5-dihydroxyhept-6-enoate, C26H36FN3O6S
  15. The crystal structure of samarium sulfate pentahydrate, Sm2(SO4)3(H2O)5
  16. The crystal structure of [triaqua-(8-carboxymethoxy-quinoline-2-carboxylate-κ 4 N,O,O,O)-zinc(II)] monohydrate, C12H15NO9Zn
  17. The crystal structure of 2,3-difluoro-11H-benzo-[4,5]imidazo[2,1-a]isoindol-11-one, C14H6F2N2O
  18. The crystal structure of 2,3-di(9H-carbazol-9-yl)-9H-fluoren-9-one, C37H22N2O
  19. The crystal structure of 5-(2-chloro-3-(3,6-di-tert-butyl-9H-carbazol-9-yl)phenyl)-10,11-dihydro-5H-dibenzo[b,f]azepine, C40H39ClN2
  20. Crystal structure of 2-bromo-1-hydroxy-3-(3-methylbut-2-enyloxy)-9H-xanthen-9-one, C18H15BrO4
  21. Crystal structure of bis(μ2-benzenesulfonato-κ2O:O′)-bis(μ2-6,6′-((ethane-1,2-diylbis(azaneylylidene))bis(methaneylylidene))-bis(2-methoxyphenolato-κ6O,O′:O′,N,N′,O′′:O′′,O′′′))disodium(I)dicopper(II)
  22. The crystal structure of (E)-1,2-bis(benzo[e][1,2]azaborinin-2(1H)-yl)ethene, C18H16B2N2
  23. Crystal structure of 3-oxo-urs-12-en-28-benzyl ester, C37H52O3
  24. The crystal structure of ethyl (E)-1-chloro-3-(4-chloro-1-methyl-1H-indole-2-carbonyl)-4-oxo-2-phenylcyclooct-2-ene-1-carboxylate, C27H25Cl2NO4
  25. The crystal structure of 4,4′-((5-bromo-2-iodo-1,3-phenylene)bis(oxy))bis(tert-butylbenzene) ─ ethanol (2/1), C26H28BrIO2
  26. Crystal structure of (E)-1-(4-(benzyloxy)-2-hydroxyphenyl)-3-(dimethylamino)prop-2-en-1-one, C18H19NO3
  27. The crystal structure of N1,N3-bis(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)\ propanediamide hydrate, C25H26N6O4, 2(H2O)
  28. The crystal structure of 2,5-bis[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)amino]cyclohexa-2,5-diene-1,4-dione, C28H26N6O4
  29. Crystal structure of 3,4-bis[2-(hydroxymethyl)-pyrrolidin-1-yl] cyclobut-3-ene-1,2-dione hydrate, C14H22N2O5
  30. The crystal structure of 2-(3,4–dichlorobenzyl)-1H-benzimidazole, C14H10Cl2N2
  31. The crystal structure of 2-(2-((4,6-dimethoxypyrimidin-2-yl)oxy)phenyl)-4-(piperidin-1-yl)-5H-chromeno[2,3-d]pyrimidine, C28H27N5O4
  32. The crystal structure of 6-(benzofuran-2-yl)-2-oxo-4,5-diphenyl-3,4-dihydro-2H-pyran-3-carbonitrile, C26H17NO3
  33. Crystal structure of N-(4-bromobenzyl)-3-(difluoromethyl)-1-methyl-N-(pyridin-2-yl)-1H-pyrazole-4-carboxamide, C18H15BrF2N4O
  34. The crystal structure of the host-guest complex: N′-{5-[2-(2,6-dimethylphenoxy)acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide-diethyl ether (2/1)
  35. The crystal structure of (Z)-4-amino-N′-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H17N3O2
  36. The crystal structure of diethyl 1,4-dihydro-2,6-dimethyl-4-(3-cyanophenyl)-3,5-pyridinedicarboxylate, C20H22N2O4
  37. Crystal structure of 3-(5-((4-(difluoromethoxy)phenyl) sulfonyl)-3,4,5,6-tetrahydropyrrolo[3,4-c]pyrrol-2(1H)-yl) oxetane-3-carboxamide, C17H19F2N3O5S
  38. Crystal structure of 2-((2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)amino)-N-(2-(4-methylpiperazin-1-yl)ethyl)benzamide hydrate, C25H37Cl2N5O6
  39. Crystal structure of 3-(benzo[d]thiazol-2-yl)-5-bromo-2-hydroxybenzaldehyde, C14H8BrNO2S
  40. Crystal structure of 3-(difluoromethyl)-1-methyl-N-(pyridin-2-yl)-1H-pyrazole-4-carboxamide, C11H10F2N4O
  41. Crystal structure of 3-(2-ethoxy-2-oxoethyl)-1-isopropyl-1H-imidazol-3-ium hexafluoridophosphate(V), C20H34F12N4P2
  42. Crystal structure of ethyl 5,6-dichloro-2-methyl-2,3-dihydro-1 H-benzo[d]imidazole-2-carboxylate, C11H12Cl2N2O2
  43. The crystal of structure of (OC-6-22)-pentakis(acetonitrile)bromidoruthenium(II)bromide monohydrate, C10H15Br2N5Ru
  44. Crystal structure of (2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(((4aS,5R,6S)-1-oxo-5-vinyl-4,4a,5,6-tetrahydro-1H,3H-pyrano[3,4-c]pyran-6-yl)oxy)tetrahydro-2H-pyran-3-yl 2,3-dihydroxybenzoate hydrate, C23H26O12·H2O
  45. The crystal structure of (E)-4-amino-N′-(1-(4-fluorophenyl)propylidene)benzohydrazide, C16H16FN3O
  46. The crystal structure of 2′-(9H-carbazol-9-yl)-[1,1′-binaphthalen]-2-amine, C32H22N2
  47. Crystal structure of poly[μ3-diiodido-[μ2-di(1H-pyrazol-1-yl)methane-κ2N,N′)]dicopper(I)], C7H8Cu2I2N4
  48. Crystal structure of 3-amino-N′-hydroxy-1H-pyrazole-4-carboximidamide, C4H7N5O
  49. The crystal structure of 1,3-diacetyltetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione, C8H10O4N4
  50. Crystal structure of catena-poly[aqua-(μ2-1,4-diazabicyclo[2.2.2]octane-k2N: N′)-bis(sorbato-κ1O)-copper(II), C18H28CuN2O5
  51. Crystal structure of catena-poly[triaqua-(μ2 -1-(4-carboxylatophenyl)-4-oxo-1,4-dihydropyridazine-3-carboxylato-κ3O,O′:O′′)manganese(II)], C12H12N2O8Mn
  52. The crystal structure of [hexaaquamagnesium(II)] 4-[(pyridine-4-carbonyl)-amino]-phthalate trihydrate, C14H26N2O14Mg
  53. Crystal structure of 1-(p-tolylphenyl)-4-(2-furoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O3
  54. The crystal structure of bis(1,4,7,10,13-pentaoxacyclopentadecane)-potassium(I) dichloridocopper(I), C20H40Cl2CuKO10
  55. The crystal structure of tris(tetra-n-butylammonium) hexanitrato-κ2O,O′-lanthanium(III) C48H108N9O18La
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