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The crystal structure of zwitterionic 3-aminoisonicotinic acid, C6H6N2O2

  • Xinsheng Wang EMAIL logo and Xiuge Wang
Published/Copyright: March 27, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 3

Abstract

C6H6N2O2, monoclinic P21/c (no. 14), a = 6.7909(2) Å, b = 23.9261(7) Å, c = 7.5103(2) Å, β = 95.265(2)°, V = 1215.12(6) Å3, Z = 8, R gt(F) = 0.0574, wR ref(F 2) = 0.1439, T = 293.

CCDC no.: 2326984

The 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: Yellow plate
Size: 0.15 × 0.13 × 0.09 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 0.99 mm−1
Diffractometer, scan mode: SuperNova, ω-scans
θ max, completeness: 71,5°, >99 %
N(hkl)measured, N(hkl)unique, R int: 5419, 2278, 0.033
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 1330
N(param)refined: 181
Programs: CrysAlisPRO [1], OLEX2 [2], SHELX [3, 4]
Table 2:

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

x y z U iso*/U eq
O1 0.7517 (3) 0.78844 (11) 1.1216 (3) 0.0529 (6)
O2 0.7655 (3) 0.69649 (11) 1.1192 (3) 0.0599 (7)
N1 0.4589 (5) 0.63808 (13) 0.9789 (4) 0.0659 (9)
H1A 0.393541 0.608200 0.949171 0.079*
H1B 0.575262 0.635733 1.034047 0.079*
N2 0.1042 (3) 0.73829 (14) 0.8086 (3) 0.0583 (8)
H2 −0.012341 0.737810 0.753127 0.070*
C1 0.6792 (4) 0.74113 (14) 1.0819 (4) 0.0386 (7)
C2 0.4735 (3) 0.73988 (13) 0.9852 (3) 0.0329 (6)
C3 0.3766 (4) 0.78897 (14) 0.9390 (4) 0.0432 (7)
H3 0.436982 0.823053 0.968251 0.052*
C4 0.1877 (4) 0.78778 (19) 0.8483 (4) 0.0601 (9)
H4 0.121445 0.820798 0.816118 0.072*
C5 0.1904 (4) 0.69034 (18) 0.8498 (4) 0.0560 (10)
H5 0.124523 0.657174 0.818855 0.067*
C6 0.3790 (4) 0.68844 (14) 0.9391 (4) 0.0398 (7)
O3 0.2262 (3) 0.54899 (10) 0.8283 (3) 0.0542 (6)
O4 0.2557 (4) 0.45760 (10) 0.8737 (3) 0.0542 (6)
N3 0.2149 (4) 0.38967 (11) 0.5879 (3) 0.0510 (7)
H3A 0.206906 0.358277 0.531879 0.061*
H3B 0.210339 0.390469 0.701898 0.061*
N4 0.2533 (3) 0.48043 (12) 0.2136 (3) 0.0430 (6)
H4A 0.257206 0.476959 0.099979 0.052*
C7 0.2422 (4) 0.50017 (12) 0.7751 (3) 0.0348 (6)
C8 0.2440 (3) 0.49113 (12) 0.5756 (3) 0.0298 (6)
C9 0.2558 (4) 0.53756 (14) 0.4669 (4) 0.0381 (6)
H9 0.261222 0.573126 0.517130 0.046*
C10 0.2597 (4) 0.53129 (15) 0.2837 (4) 0.0458 (7)
H10 0.266691 0.562496 0.210724 0.055*
C11 0.2413 (4) 0.43485 (14) 0.3112 (4) 0.0395 (7)
H11 0.237271 0.400159 0.255112 0.047*
C12 0.2343 (4) 0.43735 (13) 0.4974 (3) 0.0335 (6)

1 Source of materials

Method-1: A mixture of FeSO4·7H2O (0.1190 g) and 3-aminoisonicotinic acid (0.0690 g) was stirred in 15 mL aqueous solution for 6 h at 60 °C. Then the resulting mixture slowly cooled to room temperature was filtrated and volatilized in the air. The yellow stick crystals of the titled compound were isolated directly.

Method-2: Cadmium acetate dihydrate (0.0533 g) and 3-aminoisonicotinic acid (0.0552 g) in a mixture of H2O (6 mL) and ethanol (3 mL) were sonicated for 1 h, then two drops of 1 mol/L HNO3 were added into the mixture. The homogeneous mixture was sealed in a 20 mL solvothermal vial, and heated at 120 °C for 48 h, then cooled to room temperature at 5 °C/h. The powder XRD of obtained yellow stick crystals is identical to that prepared in the method-1.

2 Experimental details

Crystal data, data collection and structure refinement details are provided in Table 1. All hydrogen atoms were placed in calculated positions and refined using a riding-model approximation with C–H = 0.93 Å and Uiso(H) = 1.2Ueq(C), N–H = 0.86 Å and Uiso(H) = 1.2Ueq(N).

3 Comment

Amino-functionalized isonicotinic acids are important medical intermediates and isoniazid derivatives in the synthesis and pharmacology [5]. In addition, as the one-center-acceptor–donor ligand they can react with the metal ion to construct a series of unique diamondoid network metal-organic frameworks (MOFs). For example, the acentric framework reported by Zhou et al. [6] exhibits potential 2nd-harmonic-generation response, ferroelectric behaviors and photoluminescence. Although the crystal structures of nicotinic acid and isonicotinic acid as pure organic room-temperature phosphorescences have been reported in the neutral form and zwitterion [7, 8], however, the crystal structure of amino-functionalized isonicotinic acid is not available. In our attempt to synthesize the MOFs containing the 3-aminoisonicotinic acid, we unexpectedly obtained the single-crystal of 3-aminoisonicotinic acid.

The determined results indicated that 3-aminoisonicotinic acid crystallizes as a zwitterion in the space group P21/c without any other solvent molecules, which often were directly involved in the formation of hydrogen bonds or as the filler of void space. Its asymmetric unit includes two independent 3-aminoisonicotinic acids. The pyridine ring, the carboxylate group, and the –NH2 group are in the same plane, similar to bis(4-aminopyridin-1-ium) iodide triiodide [9]. The existence of the zwitterionic form of 3-aminoisonicotinic acid is confirmed by the presence of an H atom bonded to the N1 or N4 atom in the difference Fourier map. All of the C–O band distances, less than 1.27 Å, also agree with this result. Specifically, the C1–O1, C1–O2, C7–O4, and C7–O3 bond distances are 1.259(4), 1.238(4), 1.258(3), and 1.242(3) Å, respectively. In the crystal of 3-aminoisonicotinic acid, all nitrogen and oxygen atoms are involved in N⋯O hydrogen bonds with distances in the range between 2.612(3) Å and 3.317(3) Å. The head-to-tail N2–H2⋯O2 and N2–H2⋯O1 interactions form one chain running parallel to the a axis, and the N⋯O distances are 3.025(4) Å and 2.738(4) Å, respectively. Another chain formed by very strong head-to-tail N4–H4A⋯O4 interactions with a N⋯O distance of 2.612(3) Å extends along the c axis. These two kinds of chains are mutually perpendicular and further interact by the N–H⋯O hydrogen bonds between carboxyl groups and neighboring amino groups. In addition, the weak C–H⋯O hydrogen bonds are also found in the crystal packing. The combination of these interactions builds an intricate three-dimensional assembly of a hydrogen bond network. Theoretical calculations at the ωB97XD/6–311++G** level have shown that in the gas phase the energy of the neutral form of 3-aminonicotinic acid is lower by about 92 kJ/mol than that of inner salt. However, in water the zwitterion becomes the favorable form with a difference in energy of 14 kJ/mol. From a structural point of view, zwitterion is stabilized by the strong head-to-tail N–H⋯O hydrogen bonds between the –NH2 and carboxyl group. This is in agreement with the calculated changes in bond distance and other reported spectrophoto-chemical results in the case of 2-aminonicotinic acid with a similar structure [10].

Corresponding author: Xinsheng Wang, School of Biological Engineering, Xinxiang Institute of Engineering, Xinxiang 453700, P.R. China, E-mail:

Funding source: The School-level Innovation Fund project of Xinxiang Institute of Engineering

Award Identifier / Grant number: (2023ZK-1)

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

  2. Research funding: The School-level Innovation Fund project of Xinxiang Institute of Engineering (2023ZK-1) is gratefully acknowledged.

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

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Received: 2024-01-24
Accepted: 2024-03-01
Published Online: 2024-03-27
Published in Print: 2024-06-25

© 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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https://doi.org/10.1515/ncrs-2024-0040
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of tris((Z)-2-hydroxy-N-((E)-pyridin-2-ylmethylene)benzohydrazonato-k2O,N)europium(III), C39H30N9O6Eu
  4. Crystal structure of (E)-3-(benzylideneamino)-2-phenylthiazolidin-4-one, C16H14N2OS
  5. The crystal structure of (E)-4-fluoro-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H15FN2O
  6. Crystal structure of (6-chloropyridin-3-yl)methyl 2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  7. Crystal structure of methyl 3-methoxy-4-(2-methoxy-2-oxoethoxy)benzoate, C12H14O6
  8. The crystal structure of bis[(4-methoxyphenyl)(picolinoyl)amido-κ2 N:N′]copper(II), C26H22CuN4O4
  9. The crystal structure of poly[di(μ2-aqua)-diaqua-bis(3-aminopyridine-4-carboxylate-κ2 O: O′)-tetra(μ2-3-aminopyridine-4-carboxylate-κ2 O: O′)-dineodymium(III), [Nd2(C6H5N2O2)6(H2O)4] n
  10. The crystal structure of t-butyl 7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoate, C28H34FNO4
  11. Crystal structure of catena-poly[(benzylamine-κ1 N)-(sorbato-κ1 O)-(μ2-sorbato-κ2 O,O′)-copper(II), C19H23CuNO4
  12. Crystal structure of (4-(2-chlorophenyl)-1H-pyrrol-3-yl)(ferrocenyl) methanone, C21H16ClFeNO
  13. The crystal structure of N-[4-(4-bromophenyl)-1,3-thiazol-2-yl]-3-(2-methylphenyl)-2-sulfanylprop-2-enamide hydrate, C19H17BrN2O2S2
  14. The crystal structure of 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 hydrate
  15. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C26H24O3
  16. Crystal structure of naphthalen-1-ylmethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C25H22O3
  17. Crystal structure of poly[diaqua- (μ4-5-(1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ5N:O,O’:O’’:O’’’)calcium(II), C10H9CaN3O6
  18. Crystal structure of (E)-N′-(4-((E)-3-(dimethylamino)acryloyl)-3-hydroxyphenyl)-N, N-dimethylformimidamide, C14H19N3O2
  19. Crystal structure of (E)-3-(dimethylamino)-1-(2-hydroxy-4,6-dimethoxyphenyl)prop-2-en-1-one, C13H17NO4
  20. Crystal structure of (2-chloropyridin-3-yl)methyl-2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  21. The crystal structure of diethyl 4-(3,4-dimethylphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, C21H27NO4
  22. Crystal structure of (8R,9S,10R,13S,14S,17S)-17-hydroxy-10,13-dimethyl-17-((4-(2-phenylpropyl)phenyl)ethynyl)-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H42O2
  23. Synthesis and crystal structure of 4-(4-cyclopropylnaphthalen-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C15H13N3S
  24. Crystal structure of catena-poly[aqua-(2,6-di-(2-pyridyl)-pyridine-κ3 N,N′, N″)(μ2-1,4-naphthalene dicarboxylato-κ2 O,O′)nickel(II)], C27H19NiN3O5
  25. Crystal structure of 3-(diphenylphosphoryl)-3-hydroxy-1-phenylpropan-1-one, C21H19O3P
  26. The crystal structure of R,S-{N-[(2-oxidonaphthalen-1-yl)methylidene]phenylglycinato}divinylsilicon, C23H19NO3Si
  27. The crystal structure of 1,2,4-tris(bromomethyl)benzene, C9H9Br3
  28. Crystal structure of chlorido-[4-(pyridin-2-yl)benzaldehyde-κ2 N,C]-(diethylamine-κ1 N)platinum(II), C16H18ClN2OPt
  29. Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9
  30. The crystal structure of 1-(2-chlorobenzyl)-3-(3-chlorophenyl)urea, C14H12Cl2N2O
  31. Hydrothermal synthesis and crystal structure of aqua-tris(4-acetamidobenzoato-κ2 O,O′)-(1,10-phenanthroline-κ2 N,N′)terbium(III) hydrate C39H36N5O11Tb
  32. The crystal structure of zwitterionic 3-aminoisonicotinic acid, C6H6N2O2
  33. The crystal structure of bis{[monoaqua-μ2-4-[(pyridine-4-carbonyl)-amino]-phthalato-κ3 N:O,O′-(2,2′-bipyridine κ2 N,N′)copper(II)]}decahydrate, C48H56N8O22Cu2
  34. Crystal structure of poly[μ10-4,4′-methylene-bis(oxy)benzoatodipotassium], C15H10K2O6
  35. The crystal structure of catena-poly[[tetraaqua[(μ2-1,4-di(4-methyl-1-imidazolyl)benzene] cobalt(II)]bis(formate)], C16H24CoN4O8
  36. The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2
  37. The crystal structure of (E)-1-(((2-amino-4,5-dimethylphenyl)iminio)methyl)naphthalen-2-olate, C19H18N2O
  38. Crystal structure of N-(acridin-9-yl)-2-(4-methylpiperidin-1-yl) acetamide monohydrate, C21H25N3O2
  39. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2 O,O′)-zinc(II), C14H20Cl2N4O4Zn
  40. The crystal structure of 2,8-diethyl-1,3,7,9-tetramethyl-4λ4,5λ4-spiro[dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinine-5,2′-naphtho[1,8-de][1,3,2]dioxaborinine], C25H29BN2O2
  41. The crystal structure of 5-tert-butyl-2-(5-tert-butyl-3-iodo-benzofuran-2-yl)-3-iodobenzofuran, C24H24I2O2
  42. Synthesis and crystal structure of methyl 2-{[4-(4-cyclopropyl-1-naphthyl)-4H-1,2,4-triazole-3-yl]thio} acetate, C18H17N3O2S
  43. The crystal structure of n-propylammonium bis(2,3-dimethylbutane-2,3-diolato)borate-boric acid (1/1), [C3H10N][C12H24BO4]·B(OH)3
  44. Crystal structure of methyl 1-(2-bromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C19H17BrN2O2
  45. Crystal structure of (4-bromobenzyl)triphenylphosphonium bromide ethanol solvate, C52H48Br4OP2
  46. The crystal structure of unsymmetrical BOPHY C26H27BN4
  47. The crystal structure of Tb3B5O11(OH)2
  48. The crystal structure of (Z)-4-ethyl-2-((4-ethyl-3,5-dimethyl-1H-pyrrol-2-yl)methylene)-3,5-dimethyl-2H-pyrrol-1-ium 2,2'-spirobi[naphtho[1,8-de][1,3,2]dioxaborinin]-2-uide, C37H37BN2O4
  49. Crystal structure of bis(methylammonium) hexadecaselenidopalladate(II), (CH3NH3)2PdSe16
  50. The crystal structure of (2-diphenylphosphanylphenyl) 2-[7-(dimethylamino)-2-oxochromen-4-yl]acetate, C31H26NO4P
  51. Crystal structure of (E)-6-(4-ethylpiperazin-1-yl)-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C23H25FN2O
  52. The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers
  53. Crystal structure of 4-amino-3,5-dibromobenzonitrile, C7H4Br2N2
  54. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-acetoxybenzoate, C21H18O4
  55. Single-crystal structure determination of Tm3B12O19(OH)7
  56. Crystal structure determination of NdB3.6O7
  57. The crystal structure of NdB6O8(OH)5·H3BO3
  58. Crystal structure of 2-(5-ethylpyridin-2-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C23H25NO3
  59. Crystal structure of N-(1-(3,4-dimethoxyphenyl)-2-methylpropyl)aniline, C18H23NO2
  60. Crystal structure of Ba6Cd12Mn4SiF48
  61. Synthesis and crystal structure of 5-fluoro-1-methyl-2-oxo-3-(2-oxochroman-4-yl)indolin-3-yl acetate, C20H16FNO5
  62. The crystal structure of 6-methacryloylbenzo[d][1,3]dioxol-5-yl 4-nitrobenzenesulfonate, C17H13NO8S
  63. Crystal structure of ethyl 2-(3-benzyl-4-oxo-3,4-dihydrophthalazin-1-yl)- 2,2-difluoroacetate, C19H16F2N2O3
  64. The crystal structure of tetrakis(μ 2-(1H-benzimidazole-2-methoxo-κ2 N,O:O:O)-(n-butanol-κO)-chlorido)-tetranickel(II), C48H68Cl4N8O8Ni4
  65. Synthesis and crystal structure of trans-tetraaqua-bis((1-((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carbonyl)oxy-κO)zinc(II)hexahydrate, C46H64N2O28S2Zn
  66. The crystal structure of 1-(4-carboxybutyl)-3-methyl-1H-imidazol-3-ium hexafluoridophosphate, C9H15F6N2O2P
  67. Crystal structure of 1-(4-chlorophenyl)-4-(2-furoyl)-3-phenyl-1H-pyrazol-5-ol, C20H13ClN2O3
  68. Crystal structure of dimethyl (R)-2-(3-(1-phenylethyl)thioureido)-[1,1′-biphenyl]-4,4′-dicarboxylate, C25H24N2O4S
  69. The crystal structure of 1-(3-carboxypropyl)-1H-imidazole-3-oxide, C7H10N2O3
  70. Synthesis and crystal structure of dimethyl 4,4′-(propane-1,3-diylbis(oxy))dibenzoate, C19H20O6
  71. Crystal structure of methyl-1-(p-tolyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C20H20N2O2
  72. The crystal structure of 1-(1-adamantan-1-yl)ethyl-3-(3-methoxyphenyl)thiourea, C20H28N2OS
  73. The crystal structure of N,N′-carbonylbis(2,6-difluorobenzamide), C15H8F4N2O3
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