Home The crystal structure of 2-(2-((4,6-dimethoxypyrimidin-2-yl)oxy)phenyl)-4-(piperidin-1-yl)-5H-chromeno[2,3-d]pyrimidine, C28H27N5O4
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The crystal structure of 2-(2-((4,6-dimethoxypyrimidin-2-yl)oxy)phenyl)-4-(piperidin-1-yl)-5H-chromeno[2,3-d]pyrimidine, C28H27N5O4

  • Dongtai Xie , Sufang Lei and Yuanxiang Li ORCID logo EMAIL logo
Published/Copyright: January 24, 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

C28H27N5O4, monoclinic, P21/c (no. 14), a = 11.3563(15) Å, b = 17.547(2) Å, c = 12.8390(16) Å, β = 101.385(3)°, V = 2508.1(6) Å3, Z = 4, R gt (F) = 0.0538, wR ref (F2) = 0.1329, T = 292(2) K.

CCDC no.: 2308860

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 block
Size: 0.20 × 0.20 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.09 mm−1
Diffractometer, scan mode: Bruker Apex Duo, φ and ω
θmax, completeness: 27.0°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 14,614, 5449, 0.044
Criterion for Iobs, N(hkl)gt: Iobs  >  2σ(Iobs), 2939
N(param)refined: 336
Programs: Bruker [1], SHELX [2], [3], [4], DIAMOND [5], Olex2 [6]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.17728 (19) 0.27665 (12) 0.56693 (17) 0.0551 (5)
C2 0.0971 (2) 0.24144 (14) 0.48560 (17) 0.0662 (6)
H2 0.022092 0.262790 0.459805 0.079*
C3 0.1304 (2) 0.17439 (15) 0.44365 (18) 0.0742 (7)
H3 0.077794 0.150122 0.388995 0.089*
C4 0.2419 (2) 0.14333 (15) 0.48290 (19) 0.0786 (7)
H4 0.264408 0.097776 0.455353 0.094*
C5 0.3199 (2) 0.18013 (14) 0.56321 (18) 0.0690 (6)
H5 0.394791 0.158615 0.589189 0.083*
C6 0.29017 (18) 0.24792 (12) 0.60616 (16) 0.0532 (5)
C7 0.37539 (18) 0.28781 (12) 0.69300 (17) 0.0628 (6)
H7A 0.452785 0.292979 0.672537 0.075*
H7B 0.386581 0.257134 0.757051 0.075*
C8 0.33056 (17) 0.36523 (11) 0.71590 (15) 0.0494 (5)
C9 0.21584 (18) 0.38842 (13) 0.67250 (16) 0.0527 (5)
C10 0.24280 (17) 0.50487 (12) 0.74479 (14) 0.0489 (5)
C11 0.40089 (17) 0.42197 (12) 0.77654 (15) 0.0499 (5)
C12 0.59641 (18) 0.47693 (13) 0.85035 (19) 0.0707 (7)
H12A 0.583757 0.496962 0.917691 0.085*
H12B 0.574806 0.516186 0.796789 0.085*
C13 0.72641 (19) 0.45537 (15) 0.85922 (18) 0.0724 (7)
H13A 0.739684 0.439142 0.790245 0.087*
H13B 0.776501 0.499599 0.880900 0.087*
C14 0.7620 (2) 0.39222 (16) 0.93841 (19) 0.0827 (8)
H14A 0.761489 0.411086 1.009328 0.099*
H14B 0.843026 0.375657 0.936365 0.099*
C15 0.6773 (2) 0.32542 (16) 0.9148 (2) 0.0868 (8)
H15A 0.688820 0.300724 0.849914 0.104*
H15B 0.695664 0.288639 0.972072 0.104*
C16 0.54952 (19) 0.34998 (13) 0.90246 (16) 0.0658 (6)
H16A 0.497183 0.306465 0.882791 0.079*
H16B 0.535621 0.369446 0.969715 0.079*
C17 0.19220 (18) 0.58015 (13) 0.76475 (14) 0.0536 (5)
C18 0.07511 (19) 0.58296 (15) 0.78227 (16) 0.0675 (7)
H18 0.029905 0.538434 0.776973 0.081*
C19 0.0248 (2) 0.65030 (18) 0.80730 (18) 0.0815 (8)
H19 −0.053328 0.650773 0.819319 0.098*
C20 0.0897 (3) 0.71659 (18) 0.81449 (18) 0.0850 (8)
H20 0.056075 0.762040 0.831802 0.102*
C21 0.2059 (2) 0.71548 (14) 0.79580 (16) 0.0718 (7)
H21 0.250553 0.760237 0.800565 0.086*
C22 0.25494(19) 0.64809 (13) 0.77023 (15) 0.0547 (5)
C23 0.39494 (19) 0.63025 (11) 0.65720 (16) 0.0499 (5)
C24 0.3302 (2) 0.59504 (12) 0.48912 (16) 0.0549 (5)
C25 0.44549 (19) 0.59362 (13) 0.47232 (16) 0.0605 (6)
H25 0.463224 0.581841 0.406489 0.073*
C26 0.53323 (19) 0.61072 (12) 0.55901 (17) 0.0546 (5)
C27 0.1226 (2) 0.57030 (17) 0.4302 (2) 0.0922 (9)
H27A 0.100392 0.617573 0.458638 0.138*
H27B 0.121288 0.530275 0.480891 0.138*
H27C 0.066736 0.558680 0.365704 0.138*
C28 0.74143 (19) 0.62000 (15) 0.63716 (18) 0.0805 (8)
H28A 0.727443 0.589569 0.695662 0.121*
H28B 0.742319 0.672924 0.656249 0.121*
H28C 0.817380 0.606409 0.620274 0.121*
N1 0.16781 (14) 0.45542 (10) 0.68711 (13) 0.0560 (5)
N2 0.35774 (14) 0.49187 (10) 0.78870 (12) 0.0514 (4)
N3 0.30243 (14) 0.61377 (9) 0.58206 (12) 0.0526 (4)
N4 0.51060 (15) 0.63006 (9) 0.65404 (13) 0.0525 (4)
N5 0.52072 (14) 0.40917 (10) 0.82101 (13) 0.0579 (5)
O1 0.13623 (12) 0.34326 (9) 0.60523 (12) 0.0699 (5)
O2 0.37364 (12) 0.65199 (8) 0.75377 (10) 0.0583 (4)
O3 0.24081 (13) 0.57683 (9) 0.40819 (10) 0.0732 (5)
O4 0.64781 (13) 0.60674 (10) 0.54673 (11) 0.0711 (5)

1 Source of materials

To a stirred mixture of 2-((4,6-dimethoxypyrimidin-2-yl)oxy)benzaldehyde (0.519 g, 2 mmol), and malononitrile (0.1455 g, 2.2 mmol), piperidine (0.186 g, 2.2 mmol) in 15 mL EtOH was added. After stirring at room temperature for 30 min, 2-hydroxybenzaldehyde (0.269 g, 2.2 mmol) was added, and the mixture was stirred at room temperature for 10 h. After completion of the reaction, the solvent was evaporated to afford a crude mixture, which was further purified by flash chromatography (petroleum ether/ethyl acetate, V/V = 4:1) to get the title compound as a white solid (0.64 g, yield: 64 %). Crystals of the title compound were grown through slow evaporation of a petroleum ether/dichloromethane (V/V = 8:1) at 25/% for 3 days.

2 Experimental details

All H atoms were treated as riding, with C–H distances of 0.93 Å (aromatic), 0.97 Å (methylene) and 0.96 Å (methyl). The thermal factors of hydrogen atoms were set 1.2 times of their parent atoms (for aromatic and methylene) or 1.5 times of their parent atoms (for methyl).

3 Comment

As a continuation of our work on nitrogen-containing heterocyclic compounds which can be potentially applied in the fields of medical and organic chemistry [7], we have recently extended our synthesis work into deeper areas such as pyrimidine derivatives. The synthesis of pyrimidine-involved complexes are representing a challenge from both academic and industrial perspectives [8], [9], [10]. Especially, 5H-chromeno[2,3-d]pyrimidine derivatives have been emerged as promising and attractive scaffold in the development of potent anti-tumor and antimicrobial agents in recent years. In a classical approach, the skeleton construction of 5H-chromeno[2,3-d]pyrimidine is accessible through three-component one-pot reaction in which ferric or sodium complexes were used as the catalyst. As an improved method with high yields, we have changed the earlier used 2-hydroxybenzaldehyde to 2-((4-hydroxy-6-methoxypyrimidin-2-yl)oxy)benzaldehyde. In this reaction, the catalysts can be avoided aiming to achieve the purpose of green environmental protection and economy. As a representative, the title compound was synthesized in a similar way with a yield up to 94 %. Herein, its crystal structure was reported.

The title molecule is shown in the figure. Relative to the middle benzene ring, the 5H-chromeno[2,3-d]pyrimidine and dimethoxypyrimidin moieties present a curved or highly distorted spatial configuration with the dihedral angle of 51.8(1)° between them. And each of the two parts are twisted away from the central benzen rings by 44.2(1)° and 64.5(1)°, respectively. It should be noted that the whole V-shaped spatial structure of the title compound is mainly determined by the spatial arrangement of each molecular group. For example, the distance between the N2 atom of pyrimidine and the ether O2 atom is only about 2.885(1) Å apart which is smaller than the van der Waals half-valence sum of these two atoms (3.28 Å) [11]. Due to the delocalization effects of the C17–C22 benzene and C23–C26/N3/N4 pyridine rings adjacent to the oxygen O2 atom, it may carry some π electrons which can interact with the pyridine N2 atoms via the π⋯π interaction. This delocalization can also be reflected by the two short C–O bond distances around O2 (1.364(2) and 1.407(2) Å), which is apparently shorter than the normal C–O single bond distance, for instance dc27–03 and dc28–04 is 1.430(2) Å in the title compound.

In the crystal packing, the DPPP molecules are mainly linked together by the intermolecular C–H⋯O, C–H⋯N and C–H⋯π stacking into the final three-dimensional network. Although several aromatic rings exist, no apparent π⋯π stacking interactions are observed by a analysis of PLATON [12].

Corresponding author: Yuanxiang Li, College of Chemistry and Materials Engineering, Huaihua University, Huaihua 418008, P.R. China, E-mail:

Funding source: Huaihua Key Laboratory project

Award Identifier / Grant number: 2023R2206

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

  2. Research funding: Huaihua Key Laboratory project (No. 2023R2206).

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

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Received: 2023-11-21
Accepted: 2023-12-30
Published Online: 2024-01-24
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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https://doi.org/10.1515/ncrs-2023-0511
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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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