Startseite Crystal structure of 6,9-diamino-2-ethoxyacridinium 3,5-dinitrobenozate — dimethylsulfoxide — water (1/1/1), C24H27N5O9S
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Crystal structure of 6,9-diamino-2-ethoxyacridinium 3,5-dinitrobenozate — dimethylsulfoxide — water (1/1/1), C24H27N5O9S

  • Artur Mirocki ORCID logo EMAIL logo
Veröffentlicht/Copyright: 17. Mai 2022

Abstract

C24H27N5O9S, triclinic, P 1 (no. 2), a = 7.5749(4) Å, b = 10.0368(5) Å, c = 17.9111(10) Å, α = 87.224(4)°, β = 83.678(4)°, γ = 85.414(4)°, V = 1348.04(12) Å3, Z = 2, R gt (F) = 0.0562, wR ref (F2) = 0.1477, T = 295(2) K.

CCDC no.: 2169898

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: Yellow needle
Size: 0.42 × 0.25 × 0.09 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.18 mm−1
Diffractometer, scan mode: Oxford diffraction ruby, ω
θmax, completeness: 25.0°, >99%
N(hkl)measured, N(hkl)unique, Rint: 18,840, 4726, 0.037
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 3319
N(param)refined: 386
Programs: CrysAlis [1], SHELX [2, 3], ORTEP-II [4]
Table 2:

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

Atom x y z Uiso*/Ueq
O1W 0.7318 (4) 0.1341 (2) 0.38546 (13) 0.0731 (6)
H1W 0.793 (4) 0.071 (4) 0.3891 (18) 0.080 (12)*
H2W 0.687 (5) 0.135 (4) 0.343 (2) 0.105 (13)*
C1 0.8596 (3) 0.6705 (2) 0.44288 (12) 0.0406 (5)
H1A 0.899496 0.631291 0.397487 0.049*
C2 0.8831 (3) 0.8019 (2) 0.45149 (13) 0.0423 (5)
C3 0.8260 (3) 0.8619 (2) 0.52019 (14) 0.0488 (6)
H3A 0.843426 0.951428 0.525687 0.059*
C4 0.7454 (3) 0.7899 (2) 0.57858 (14) 0.0471 (6)
H4A 0.707587 0.830287 0.623806 0.056*
C5 0.5242 (3) 0.3870 (2) 0.68933 (13) 0.0450 (6)
H5A 0.492404 0.432940 0.733239 0.054*
C6 0.4900 (3) 0.2546 (2) 0.68768 (14) 0.0460 (6)
C7 0.5369 (3) 0.1868 (2) 0.61980 (14) 0.0479 (6)
H7A 0.512541 0.097744 0.617645 0.057*
C8 0.6165 (3) 0.2498 (2) 0.55824 (13) 0.0435 (6)
H8A 0.645714 0.202972 0.514493 0.052*
C9 0.7419 (3) 0.4554 (2) 0.49519 (12) 0.0369 (5)
N10 0.6365 (2) 0.5839 (2) 0.62940 (12) 0.0427 (5)
H10A 0.600 (3) 0.621 (3) 0.6684 (15) 0.046 (7)*
C11 0.7753 (3) 0.5937 (2) 0.50233 (12) 0.0368 (5)
C12 0.7191 (3) 0.6539 (2) 0.57073 (12) 0.0384 (5)
C13 0.6568 (3) 0.3857 (2) 0.55845 (12) 0.0376 (5)
C14 0.6055 (3) 0.4530 (2) 0.62626 (12) 0.0390 (5)
N15 0.7899 (3) 0.3967 (2) 0.43089 (12) 0.0461 (5)
H15A 0.765 (3) 0.314 (3) 0.4262 (15) 0.065 (9)*
H15B 0.840 (3) 0.441 (3) 0.3920 (16) 0.051 (8)*
N16 0.4102 (3) 0.1874 (3) 0.74878 (15) 0.0650 (7)
H16A 0.390 (4) 0.228 (3) 0.7893 (18) 0.078*
H16B 0.402 (4) 0.102 (3) 0.7495 (17) 0.078*
O17 0.9597 (2) 0.88627 (16) 0.39651 (9) 0.0519 (4)
C18 1.0196 (3) 0.8305 (3) 0.32493 (14) 0.0523 (6)
H18A 0.921682 0.792703 0.304783 0.063*
H18B 1.111008 0.759103 0.332091 0.063*
C19 1.0909 (4) 0.9401 (3) 0.27360 (17) 0.0769 (9)
H19A 1.135541 0.904707 0.225752 0.115*
H19B 1.185597 0.977456 0.295143 0.115*
H19C 0.997388 1.008646 0.266940 0.115*
C20 0.4250 (3) 0.8183 (2) 0.87314 (13) 0.0489 (6)
C21 0.3201 (3) 0.9241 (3) 0.90505 (15) 0.0550 (7)
H21A 0.264189 0.988947 0.875000 0.066*
C22 0.2998 (3) 0.9320 (3) 0.98266 (16) 0.0617 (8)
C23 0.3796 (4) 0.8388 (3) 1.02930 (16) 0.0678 (8)
H23A 0.363562 0.845236 1.081267 0.081*
C24 0.4833 (4) 0.7364 (3) 0.99612 (15) 0.0630 (7)
C25 0.5067 (4) 0.7241 (3) 0.91954 (14) 0.0567 (7)
H25A 0.577624 0.652328 0.898883 0.068*
C26 0.4524 (4) 0.8048 (3) 0.78883 (14) 0.0559 (7)
O27 0.3892 (3) 0.8980 (2) 0.74987 (11) 0.0800 (6)
O28 0.5351 (3) 0.7005 (2) 0.76663 (10) 0.0846 (7)
N29 0.1918 (4) 1.0471 (3) 1.0164 (2) 0.0857 (9)
O30 0.1335 (4) 1.1341 (3) 0.97468 (18) 0.1085 (9)
O31 0.1675 (4) 1.0493 (3) 1.08421 (16) 0.1292 (11)
N32 0.5765 (5) 0.6351 (3) 1.04375 (16) 0.0856 (8)
O33 0.6839 (4) 0.5532 (3) 1.01343 (16) 0.1097 (9)
O34 0.5397 (5) 0.6401 (3) 1.11118 (15) 0.1347 (11)
S35a 0.91775 (19) 0.48519 (17) 0.21541 (8) 0.0899 (7)
S35Ab 1.0676 (3) 0.4653 (2) 0.21896 (14) 0.0777 (10)*
O36 0.9633 (4) 0.5044 (3) 0.29074 (13) 0.1162 (9)
C37 1.0633 (11) 0.5732 (7) 0.1553 (3) 0.215 (4)
H37A 1.038831 0.667222 0.162712 0.323*
H37B 1.049005 0.554808 0.104265 0.323*
H37C 1.183293 0.546662 0.165257 0.323*
C38 0.9980 (8) 0.3198 (5) 0.1953 (4) 0.182 (3)
H38A 1.006934 0.308948 0.142027 0.274*
H38B 0.917494 0.258810 0.220362 0.274*
H38C 1.113454 0.301585 0.212543 0.274*
  1. aOccupancy: 0.635 (3).bOccupancy: 0.365 (3).

Source of material

All compounds were purchased from Sigma-Aldrich and used without purification. 6,9-Diamino-2-ethoxyacridine-dl-lactate monohydrate (0.03 g, 0.083 mmol) and 3,5-dinitrobenzoic acid (0.035 g, 0.165 mmol) were dissolved in 12 mL of an ethanol/water mixture (5:1 v/v) and heated in order to dissolve the sample. The solution was allowed to evaporate for a few days. Next recrystallization was performed. The sample was dissolved in 10 mL of methanol and added a few drops of CH2Cl2 and 3 mL dimethylsulfoxide (DMSO). The solution was allowed to evaporate for a few days to give yellow crystals (m.p. = 260.2 °C).

Experimental details

The solvent molecule is disordered. The site-occupancy factors are 0.635(3) and 0.365(3). All H atoms bound to N/O-atoms were located on a difference Fourier map and refined freely. All H atoms bound to aromatic C atoms were placed geometrically (C–H = 0.93 Å) and refined using a riding model with Uiso(H) = 1.2Ueq(C). All H atoms from the methyl group were positioned geometrically (C–H = 0.98 Å) and refined using a riding model, with Uiso(H) = 1.5Ueq(C).

Comment

An acridine derivative – 6,9-diamino-2-ethoxyacridine – has antiviral and antibacterial properties, and it is also helpful in curing various infections [5], [6], [7]. As a continuation of my recent study on the acridine derivatives [8], [9], [10], in this paper, the crystal structure of 6,9-diamino-2-ethoxyacridinium 3,5-dinitrobenozate dimethylsulfoxide monosolvate monohydrate is described.

The title compound crystallizes in the triclinic P 1 space group with one 6,9-diamino-2-ethoxyacridinium cation, one 3,5-dinitrobenzoate anion, a dimethylsulfoxide (DMSO) molecule and water molecule in the asymmetric unit (Figure). The C–O bond lengths in the carboxylic group (1.236–1.237 Å) indicating a proton transfer occurring between the carboxylic group of 3,5-dinitrobenzoic acid and the endocyclic N-atom of 6,9-diamino-2-ethoxyacridine. The 6,9-diamino-2-ethoxyacridinium cation interacts with the 3,5-dinitrobenzoate anion through the N(acridine)–H⃛O(carboxylate) hydrogen bond between the endocyclic N-atom and the carboxylate group [d(H10A⃛O28) = 1.96(3) Å, and angle (N10–H10A⃛O28) = 174(3)°] to form a heterodimer. The adjacent heterodimers are linked via the O(water)–H⃛O(carboxylate) hydrogen bond between water molecule and carboxylate group [d(H2W⃛O27) = 1.87(4) Å, and angle (O1W–H2W⃛O27) = 169(4)°] and the N(amino)–H⃛O(water) hydrogen bond between C9-amino group and water molecule [d(H15A⃛O1W) = 2.02(3) Å, and angle (N15–H15A⃛O1W) = 164(2)°] to form a heterohexamer. The same or similar heterohexamers have appeared in earlier works about on acridines [8], [9], [10], [11]. The adjacent 6,9-diamino-2-ethoxyacridinium cations involved in hetetrohexameric synthon interact with each other via ππ interactions (with the distance between centroids (Cg⃛Cg) ranging from 3.915(1) Å to 3.979(1) Å and separation 3.450 Å between the mean planes of the 6,9-diamino-2-ethoxyacridine skeleton) to form π-stacked columns. The neighbouring columns are lined via the O(water)–H⃛O(ethoxy) hydrogen bond [d(H1W⃛O17) = 2.17(4) Å, and angle (O1W–H1W⃛O17) = 177(4)°] between the water molecule and the ethoxy group from the acridinium cation, the N(amino)–H⃛O(carboxylate) hydrogen bond between the C6-amino group and the carboxylate group [d(H16B⃛O27) = 2.06(3) Å, and angle (N16–H16B⃛O27) = 179(4)°], and the N(amino)–H⃛O(nitro) hydrogen bond between the C6-amino group and the O-atom of one of the nitro groups [d(H16A⃛O34) = 2.40(3) Å, and angle (N16–H16A⃛O34) = 156(3)°] to form blocks. Moreover, the neighbouring anions are linked via N(nitro)–O⃛N(nitro) interactions [d(O30⃛N29) = 3.163(4) Å, and angle (N29–O30⃛N29) = 83(1)°], [d(O33⃛N32) = 3.121(5) Å, and angle (N32–O33⃛N32) = 99(6)°], which have appeared in earlier works about intermolecular interactions involving nitroarene fragments in the crystal structures of molecular complexes of acridines with dinitrobenzoic acids [12, 13]. Furthermore, the dimethylsulfoxide (DMSO) molecule interacts only with the 6,9-diamino-2-ethoxyacridinium cation via the N(amino)–H⃛O(DMSO) hydrogen bond [d(H15B⃛O36) = 2.04(3) Å, and angle (N15–H15B⃛O36) = 167(3)°] between the C9-amino group and the O-atom of DMSO to form a 3D framework structure (Figure).


Corresponding author: Artur Mirocki, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland, E-mail:

Funding source: University of Gdańsk

Award Identifier / Grant number: 539-T080-B027-22

Award Identifier / Grant number: DS 531-T080-D738-22

Acknowledgements

I am grateful to Professor Artur Sikorski for critically reading and feedback on an early version of the manuscript.

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

  2. Research funding: Research of Young Scientists grant (BMN) no. 539-T080-B027-22 (University of Gdańsk) and DS 531-T080-D738-22 (University of Gdańsk).

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

References

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Received: 2022-04-05
Accepted: 2022-05-02
Published Online: 2022-05-17
Published in Print: 2022-08-26

© 2022 Artur Mirocki, published by De Gruyter, Berlin/Boston

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

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  54. The crystal structure of diaqua-bis(6-phenylpyridine-2-carboxylato-κ2N,O) manganese(II) — water — dimethylformamide (1/2/1), C27H31N3O9Mn
  55. The crystal structure of bis(pyrazolo[1,5-a]pyrimidine-3-carboxylato-κ2N,O)-copper(ii), C14H8N6O4Cu
  56. Crystal structure of poly[(μ2-1-(1-imidazolyl)-4-(imidazol-1-ylmethyl)benzene-κ2N:N′)-(μ3-pyridazine-4,5-dicarboxylate-κ3O:O′:N)]copper(II) hydrate, C19H16CuN6O5
  57. Crystal structure of acrinidinium tetrafluorohydrogenphthalate, C21H11F4NO4
  58. Crystal structure of 2-(1H-pyrazol-3-yl-κN)pyridine-κN-bis(2-(2,4-difluorophenyl)pyridinato-κ2C,N)iridium(III) sesquihydrate, C30H18F4IrN5·1.5[H2O]
  59. Crystal structure of 2-(2-hydroxy-5-nitrophenyl)-5-methyl-1,3-dioxane-5-carboxylic acid, C12H13N1O7
  60. The crystal structure of 1,2-bis(pyridinium-4-yl)ethane diperchlorate, C12H14N2·2ClO4 – a second polymorph
  61. The crystal structure of [(1,10-phenantroline-κ2N,N′)-bis(6-phenylpyridine-2-carboxylato-κ2N,O)manganese(II)] monohydrate, C36H26N4O5Mn
  62. Crystal structure of 1,2-bis(2,2,3,3,5,5,5-heptamethyl-1,1,4,4- tetrakis(trimethylsilyl)pentasilan-1-yl)ditellane, C38H114Si18Te2
  63. Crystal structure of 1,2-bis(2,4-dinitro-1H-imidazol-1-yl)ethane – dimethylformamide (1/1), C11H13N9O9
  64. Crystal structure of (Z)-3-((tert-butylamino) methylene)-2-(2-hydroxynaphthalen-1-yl) chroman-4-one, C24H23NO3
  65. Synthesis and crystal structure of (E)-1-(4-(((E)-3-(tert-butyl)-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-ethyl oxime, C21H26N2O2
  66. Crystal structure of the double salt bis(5-amino-1,2,4-triazol-4-ium-3-yl)methane hydrogen oxalate hemioxalate, C8H11N8O6
  67. Hydrothermal synthesis and crystal structure of catena-poly[diaqua-bis(μ2-4-[(4-pyridinylmethyl)amino]benzoato-κ2N:O)cobalt(II)]–1,2bi(4-pyridyl)ethene–water (1/1/1), C50H50N8O8Co
  68. Crystal structure of 3-(3-bromophenyl)-1′,3′-dimethyl-2′H,3H,4H-spiro[furo[3, 2-c]chromene-2,5′-pyrimidine]-2′,4,4′,6′(1′H,3′H) tetraone, C22H15BrN2O6
  69. The crystal structure of poly[aqua-(μ2-4,4′- bis(imidazolyl)biphenyl-κ2N:N′)-(μ2-3-nitrobenzene-1,2-dicarboxylato-κ2O:O′)]copper (II) hydrate, C26H21N5O8Cu
  70. The crystal structure of bis(4-(6-carboxy-8-ethyl-3-fluoro-5-oxo-5,8-dihydro-1,8-naphthyridin-2- yl)piperazin-1-ium) adipate tetrahydrate, C36H52F2N8O14
  71. Synthesis and crystal structure of poly[aqua(μ4-(1R,2S,4R)-4-hydroxy-1-((7-hydroxy-3-(4-hydroxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)pyrrolidin-1-ium-2-carboxylate-κ4O:O′:O″:O‴)sodium(I)] monohydrate, C21H22NNaO12S
  72. Crystal structure of chlorido-(η6-toluene)(2,2′-bipyridine-κ2N,N′)ruthenium(II) hexafluorophosphate, C17H16ClN2RuPF6
  73. The crystal structure of (R)-6-hydroxy-8-methoxy-3-methylisochroman-1-one, C11H12O4
  74. Crystal structure of catena-poly[(5,5,7,12,12,14-hexamethyl -1,4,8,11-tetraazacyclotetradecane- κ4N,N′,Nʺ,N‴)nickel(II)-(μ2-perchlorato-κ2O:O′)] 3,5-dicarboxybenzoate – methanol (1/2), C27H49ClN4NiO12
  75. The crystal structure of 4-(chloromethyl)benzonitrile, C8H6ClN
  76. The crystal structure of dimethylammonium 8-[(7,9-dioxo-6,10-dioxaspiro[4.5]decan-8-ylidene)methyl]-9-oxo-6,10-dioxaspiro[4.5]dec-7-en-7-olate, C19H25NO8
  77. Crystal structure of (2R,3S,4S,5R,6S)-2-(acetoxymethyl)-6-((1-acetyl-5-bromo-4-chloro-1H-indol-3-yl)oxy)tetrahydro-2H-pyran-3,4,5-triyl triacetate hemihydrate C24H25BrClNO11
  78. The crystal structure of the co-crystal tetrakis[2-(tris(4-methoxyphenyl)stannyl)ethyl]silane – tetrahydrofuran – toluene – tetrahydrofurane (1/1/1), C103H116O13SiSn4
  79. Crystal structure of methyl 3-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)propanoate, C16H13NO4
  80. Crystal structure of ethyl (Z)-3-amino-2-cyano-3-(2-oxo-2H-chromen-3-yl)acrylate, C15H12N2O4
  81. Crystal structure of methyl 2-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)acetate, C15H11NO4
  82. Crystal structure of catena-poly[diaqua-bis(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2N:N′)cobalt(II)] tetrafluoroterephthalate, C26H28N8O6F4Co
Heruntergeladen am 6.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2022-0174/html
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