Home Physical Sciences 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
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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

  • Hai-Lin Chen ORCID logo , Yan-Ping Wang EMAIL logo , Qing-Yan Sun and Ze-Ping Luo
Published/Copyright: February 12, 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

C20H24NNaO12S, monoclinic, P21/c (no. 14), a = 16.3424(5) Å, b = 9.2619(2) Å, c = 16.1782(5) Å, β = 115.163(4)°, V = 2216.38(13) Å3, Z = 4, Rgt (F) = 0.0368, wRref (F2) = 0.1024, T = 100 K.

CCDC no.: 2419847

The title crystal 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: Clear light colourless block
Size: 0.13 × 0.12 × 0.10 mm
Wavelength:

μ:		 Mo Kα radiation (0.71073 Å)

0.24 mm−1
Diffractometer, scan mode:

θmax, completeness:		 ROD, Synergy Custom DW system, HyPix, φ and ω 29.4°, 100 %
N(hkl)measured, N(hkl)unique, Rint: 28159, 5258, 0.039
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 4288
N(param)refined: 335
Programs: Rigaku, 1 Diamond, 2 SHELX 3 , 4
Table 2:

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

x y z Uiso*/Ueq
S1 0.20410 (2) 0.82080 (4) 0.62971 (2) 0.01432 (10)
Na1 1.03550 (5) 0.16850 (7) 0.96725 (4) 0.02143 (16)
O1 0.76978 (8) 0.62158 (12) 0.44136 (8) 0.0198 (2)
H1 0.7619 (16) 0.677 (3) 0.3968 (16) 0.042 (7)*
O2 0.46047 (7) 0.83155 (11) 0.55342 (8) 0.0185 (2)
O3 0.62083 (7) 0.47185 (11) 0.61946 (7) 0.0159 (2)
O4 0.24901 (7) 0.62582 (12) 0.79070 (7) 0.0190 (2)
O5 0.21054 (8) 0.88837 (12) 0.55172 (7) 0.0227 (3)
O6 0.21169 (8) 0.92782 (11) 0.69963 (7) 0.0190 (2)
O7 0.12420 (8) 0.73075 (12) 0.60457 (8) 0.0245 (3)
O8 1.08306 (8) 0.18983 (13) 0.85518 (8) 0.0243 (3)
O9 1.10195 (9) 0.26213 (16) 0.73379 (9) 0.0358 (3)
O10 1.0692 (2) 0.4067 (4) 0.9980 (7) 0.0314 (15)
H10A 1.118657 0.451834 1.005910 0.047*
H10B 1.030966 0.475160 0.993266 0.047*
O11 1.06123 (8) 0.04275 (12) 1.10017 (7) 0.0193 (2)
H11A 1.077562 0.103736 1.147720 0.029*
H11B 1.101432 −0.032784 1.116100 0.029*
N1 0.83388 (9) 0.44336 (15) 0.65434 (8) 0.0179 (3)
H1A 0.857426 0.532132 0.653617 0.021*
H1B 0.812541 0.444375 0.697932 0.021*
C1 0.70598 (10) 0.64710 (17) 0.47177 (10) 0.0160 (3)
C2 0.65035 (11) 0.77022 (16) 0.44455 (11) 0.0192 (3)
H2 0.656656 0.836790 0.402956 0.023*
C3 0.58690 (11) 0.79470 (16) 0.47784 (10) 0.0168 (3)
H3 0.550421 0.879006 0.459683 0.020*
C4 0.57524 (10) 0.69664 (16) 0.53839 (10) 0.0135 (3)
C5 0.63020 (10) 0.57482 (16) 0.56294 (10) 0.0136 (3)
C6 0.69690 (10) 0.54743 (16) 0.53233 (10) 0.0142 (3)
C7 0.50832 (10) 0.72228 (15) 0.57451 (10) 0.0140 (3)
C8 0.50387 (10) 0.61012 (15) 0.63737 (10) 0.0139 (3)
C9 0.55828 (10) 0.49344 (16) 0.65269 (10) 0.0153 (3)
H9 0.552071 0.419529 0.690335 0.018*
C10 0.44014 (10) 0.61904 (15) 0.68071 (10) 0.0143 (3)
C11 0.36217 (10) 0.70485 (15) 0.64395 (10) 0.0137 (3)
H11 0.351774 0.763358 0.592205 0.016*
C12 0.29966 (10) 0.70657 (15) 0.68124 (10) 0.0140 (3)
C13 0.31347 (10) 0.62179 (16) 0.75816 (10) 0.0151 (3)
C14 0.39218 (11) 0.53989 (17) 0.79676 (10) 0.0178 (3)
H14 0.403635 0.483692 0.849670 0.021*
C15 0.45395 (10) 0.53921 (16) 0.75910 (10) 0.0172 (3)
H15 0.507338 0.482928 0.787239 0.021*
C16 0.26449 (11) 0.53417 (17) 0.86828 (11) 0.0204 (3)
H16A 0.270074 0.433625 0.852518 0.031*
H16B 0.213556 0.542894 0.884826 0.031*
H16C 0.320322 0.563867 0.920087 0.031*
C17 0.75639 (10) 0.41608 (16) 0.56301 (10) 0.0159 (3)
H17A 0.720587 0.332722 0.567517 0.019*
H17B 0.780027 0.392385 0.517539 0.019*
C18 0.90741 (11) 0.33369 (18) 0.67971 (11) 0.0216 (3)
H18A 0.925156 0.321406 0.628747 0.026*
H18B 0.885318 0.239550 0.691008 0.026*
C19 0.98924 (11) 0.3817 (2) 0.76541 (11) 0.0244 (4)
H19A 0.972485 0.389850 0.817278 0.029*
H19B 1.010245 0.477433 0.755153 0.029*
C20 1.06458 (11) 0.27036 (19) 0.78733 (11) 0.0233 (4)
O12 0.74451 (8) 0.77857 (12) 0.29391 (8) 0.0247 (3)
H12A 0.786555 0.759813 0.275924 0.037*
H12B 0.749545 0.871553 0.300574 0.037 (6)*
O10A 1.0737 (2) 0.3869 (4) 1.0423 (6) 0.0217 (10)
H10C 1.078393 0.390036 1.097874 0.033*
H10D 1.121582 0.431646 1.044984 0.033*

  1. aOccupancy: 0.522 (14).

1 Source of materials

The title compound was synthesized via a Mannich reaction. A formaldehyde solution (5 mL, 37 %), water (5 mL), 3-aminopropionic acid (0.668 g, 0.075 mol) and sodium 5-(7-hydroxy-4-oxo-4H-chromen-3-yl)-2-methoxybenzenesulfonate (1.85 g, 0.005 mol) were added to ethanol (50 mL, 99.5 %) and stirred for 10 min at 328 K. Then, hot water was added until a clear solution was immediately obtained. After 12 h reaction time, the mixture was filtered. The residue was washed with ethanol and collected. The residue was dried at 373 K. Sodium 5-(8-(((2-carboxyethyl)amino)methyl)-7-hydroxy-4-oxo-4H-chromen-3-yl)-2-methoxybenzenesulfonate (2.076 g) was obtained. The sodium salt described before (0.0229 g) and water (1.5 mL) were mixed and stirred for 10 min. After filtration, a transparent solution was obtained. Colorless block crystals of the title compound were obtained by vapor diffusion of ethanol into a water solution of the title product for 2 days. NMR spectra were recorded on a Bruker AV400 instrument. 1H NMR (400 MHz, D2O) δ: 8.47 (s, 1H, H9), 8.28 (d, J = 8.8 Hz, 1H, H15), 8.28 (d, J = 2.3 Hz, 1H, H11), 7.77 (d, J = 8.6 Hz, 1H, H3), 7.40 (d, J = 8.8 Hz, 1H, H14), 7.39 (d, J = 8.6 Hz, 1H, H2), 4.79 (s, 2H, H17A, H17B), 4.28 (s, 3H, H16A, H16B, H16C), 3.74 (t, J = 6.4 Hz, 2H, H18A, H18B), 3.11 (t, J = 6.4 Hz, 2H, H19A, H19B); 13C NMR (100 MHz, D2O) δ: 178.16 (C20), 176.85 (C7), 161.77 (C1), 155.94 (C5), 155.57 (C13), 154.13 (C9), 133.04 (C15), 129.67 (C12), 128.24 (C3, C11), 122.38 (C10), 122.17 (C8), 116.01 (C4), 114.79 (C14), 112.37 (C2), 104.78 (C6), 55.65 (C16), 44.28 (C18), 39.12 (C17), 31.85 (C19). IR spectra (potassium bromide pellet) were recorded on a Nicolet 6700. IR (v/cm−1): 3506, 3045, 2835, 1632, 1606, 1560, 1495, 1452, 1413, 1373, 1360, 1327, 1286, 1265, 1219, 1184, 1103, 1094, 1031, 1004, 981, 944, 897,823, 7 775, 722, 668, 636, 622, 584, 546.

2 Experimental details

Carbon-bound H atoms were placed in calculated positions and were included in the refinement in the riding model approximation, with Uiso(H) set to 1.2 Ueq(C). The oxygen-bound and nitrogen-bond H atoms were located on a difference Fourier map and refined freely.

3 Comment

Recently, we have improved the water solubility of formononetin by introducing a sulfo-group at the C-3′ position and synthesized a series of new C-8 formononetin derivatives through the Mannich reaction. 5 , 6 , 7 Some derivatives of formononetin derivatives possess antitumor acitivity. When the sulfo-group and carboxyl group are introduced to formononetin, they can coordinate with some metal ions directly. To extend this research, we used sodium 5-(7-hydroxy-4-oxo-4H-chromen-3-yl)-2-methoxybenzenesulfonate to react with a 3-aminopropanoic acid by Mannich reaction and got the title compound.

The asymmetric unit of the title structure contains one sodium ion, one ligand, two coordinated water molecules and one uncoordinated water molecule (cf.the figure). The dihedral angle between planar rings B (C10–C15) and C (C7–C9/O3/C5/C4) is 21.39°. The sodium ion is six-coordination and resides in a distorted octahedral environment defined by three oxygen atoms from three ligands and the three oxygen atoms from three coordinated water molecules. Two coordinated water molecules were shared with another sodium ion. The sodium ions are linked with the neighboring sodium ions through the bridging of oxygen atoms and forming four-member rings. The Na–O bond lengths are Na1–O1A = 2.9155(13) Å, Na1–O7A = 2.4321(13) Å, Na1–O8 = 2.2647(13) Å, Na1–O10 = 2.277(3) Å, Na1–O11 = 2.32141(2) Å, Na1–O11A = 2.4598(13) Å, respectively. The bond distances and bond angles are in normal ranges. 7 , 8 , 9 There exist various O–H⋯O and N–H⋯O hydrogen bonds. The nitrogen atom N1 is protonated. The sodium coordination polymer is extended to a three-dimensional framework structure. It is obvious that the hydrogen bonds play important roles in the self-assembly and enhance stability of the resultant title structure.

Corresponding author: Yan-Ping Wang, Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China, E-mail:

Acknowledgments

This work was financially supported by Guangxi Collaborative Innovation Center of Modern Sericulture and Silk (2022GXCSSC17) and the Foundation of Hechi University (2020XJYB004).

References

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Supplementary Material

This article contains supplementary material (https://doi.org/10.1515/ncrs-2024-0483).

Received: 2024-12-19
Accepted: 2025-01-27
Published Online: 2025-02-12
Published in Print: 2025-04-28

© 2025 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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  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
https://doi.org/10.1515/ncrs-2024-0483
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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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