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Crystal structure of 4-methyl-4-nitropentanoic acid, C6H11NO4

  • Hongjuan Tong ORCID logo EMAIL logo and Wenqiang Tang ORCID logo
Published/Copyright: March 7, 2022
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 237 Issue 3

Abstract

C6H11NO4, monoclinic, P21/c (no. 14), a = 19.1903(7) Å, b = 18.4525(6) Å, c = 9.2197(3) Å, β = 95.879(1)°, V = 3247.61(19) Å3, Z = 16, Rgt(F) = 0.0495, wRref (F2) = 0.1194, T = 173 K.

CCDC no.: 1974921

The asymmetric unit (four molecules) of 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: Colourless block
Size: 0.19 × 0.12 × 0.08 mm
Wavelength: MoKα radiation (0.71073 Å)
μ: 0.11 mm−1
Diffractometer, scan mode: D8 VENTURE, φ and ω
θmax, completeness: 25.7°, >99%
N(hkl)measured, N(hkl)unique, Rint: 34982, 6176, 0.065
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ (Iobs), 4192
N(param)refined: 409
Programs: Bruker [1], Olex2 [2], SHELX [3, 4]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.75608 (11) 0.64871 (12) −0.0723 (2) 0.0367 (5)
C2 0.73326 (14) 0.72754 (13) −0.0825 (3) 0.0585 (7)
H2A 0.706299 0.739142 −0.000821 0.088*
H2B 0.704067 0.735546 −0.174664 0.088*
H2C 0.774710 0.758787 −0.078538 0.088*
C3 0.80611 (13) 0.63013 (15) −0.1853 (3) 0.0565 (7)
H3A 0.847565 0.661336 −0.170800 0.085*
H3B 0.782473 0.637847 −0.283447 0.085*
H3C 0.820428 0.579287 −0.174277 0.085*
C4 0.69429 (11) 0.59658 (12) −0.0813 (2) 0.0359 (5)
H4A 0.665347 0.604531 −0.175119 0.043*
H4B 0.712503 0.546397 −0.081792 0.043*
C5 0.64757 (11) 0.60351 (11) 0.0415 (2) 0.0350 (5)
H5A 0.675130 0.590960 0.134848 0.042*
H5B 0.632397 0.654583 0.047987 0.042*
C6 0.58415 (11) 0.55602 (11) 0.0218 (2) 0.0337 (5)
C7 0.92257 (10) 0.44876 (11) 0.0671 (2) 0.0296 (5)
C8 0.86350 (10) 0.40871 (11) 0.1245 (2) 0.0293 (5)
H8A 0.846285 0.437086 0.204732 0.035*
H8B 0.881073 0.361752 0.165345 0.035*
C9 0.80290 (10) 0.39479 (11) 0.0083 (2) 0.0306 (5)
H9A 0.821137 0.368898 −0.073968 0.037*
H9B 0.784470 0.442072 −0.029089 0.037*
C10 0.74218 (10) 0.35086 (11) 0.0585 (2) 0.0293 (5)
C11 0.67860 (11) 0.35406 (13) −0.0543 (3) 0.0433 (6)
H11A 0.638989 0.329650 −0.015980 0.065*
H11B 0.689465 0.329817 −0.143807 0.065*
H11C 0.666394 0.404785 −0.075686 0.065*
C12 0.76261 (12) 0.27347 (11) 0.0974 (3) 0.0439 (6)
H12A 0.802466 0.273427 0.172937 0.066*
H12B 0.775717 0.248413 0.010533 0.066*
H12C 0.722874 0.248497 0.134020 0.066*
C13 0.56382 (12) 0.35839 (13) 0.3456 (3) 0.0472 (6)
H13A 0.600837 0.321590 0.353621 0.071*
H13B 0.584818 0.406546 0.361079 0.071*
H13C 0.538046 0.356125 0.248310 0.071*
C14 0.55212 (12) 0.34131 (13) 0.6122 (3) 0.0478 (6)
H14A 0.519089 0.328427 0.682318 0.072*
H14B 0.572771 0.388805 0.637438 0.072*
H14C 0.589296 0.304768 0.615088 0.072*
C15 0.51379 (10) 0.34429 (11) 0.4602 (2) 0.0329 (5)
C16 0.45390 (10) 0.39909 (11) 0.4473 (2) 0.0325 (5)
H16A 0.473254 0.447322 0.476092 0.039*
H16B 0.434680 0.402127 0.343691 0.039*
C17 0.39417 (11) 0.38264 (11) 0.5381 (2) 0.0354 (5)
H17A 0.375231 0.333948 0.511865 0.043*
H17B 0.412538 0.381622 0.642437 0.043*
C18 0.33636 (11) 0.43665 (11) 0.5171 (2) 0.0323 (5)
C19 0.82245 (11) 0.43839 (11) 0.5703 (2) 0.0315 (5)
C20 0.88257 (10) 0.38917 (11) 0.6127 (2) 0.0331 (5)
H20A 0.866486 0.338432 0.598889 0.040*
H20B 0.897645 0.396017 0.717734 0.040*
C21 0.94537 (10) 0.40079 (11) 0.5274 (2) 0.0333 (5)
H21A 0.966544 0.448418 0.554780 0.040*
H21B 0.928839 0.402546 0.422200 0.040*
C22 1.00167 (11) 0.34277 (11) 0.5520 (2) 0.0331 (5)
C23 1.05905 (12) 0.35373 (13) 0.4508 (3) 0.0503 (6)
H23A 1.092088 0.313142 0.461992 0.075*
H23B 1.083956 0.399105 0.475913 0.075*
H23C 1.037897 0.355992 0.349520 0.075*
C24 1.03104 (13) 0.33656 (13) 0.7097 (3) 0.0503 (6)
H24A 0.993059 0.325579 0.769665 0.075*
H24B 1.053214 0.382466 0.741832 0.075*
H24C 1.065913 0.297617 0.720061 0.075*
N1 0.79737 (9) 0.63679 (11) 0.0767 (2) 0.0426 (5)
N2 0.72169 (9) 0.38875 (10) 0.1960 (2) 0.0354 (4)
N3 0.96799 (10) 0.26962 (10) 0.5037 (2) 0.0436 (5)
N4 0.48169 (10) 0.26949 (10) 0.4223 (2) 0.0402 (5)
O1 0.80612 (10) 0.68733 (11) 0.1613 (2) 0.0805 (7)
O2 0.81854 (9) 0.57622 (10) 0.1064 (2) 0.0614 (5)
O3 0.55162 (8) 0.54987 (9) 0.13922 (16) 0.0439 (4)
H3 0.515449 0.524521 0.120596 0.066*
O4 0.56416 (8) 0.52655 (9) −0.09352 (16) 0.0455 (4)
O5 0.97344 (7) 0.46448 (9) 0.16907 (15) 0.0397 (4)
H5 1.005219 0.486990 0.131798 0.059*
O6 0.92375 (7) 0.46551 (8) −0.06038 (15) 0.0372 (4)
O7 0.69537 (9) 0.44870 (9) 0.18189 (19) 0.0539 (5)
O8 0.73406 (9) 0.35905 (9) 0.31411 (17) 0.0511 (4)
O9 0.50447 (10) 0.21668 (9) 0.4906 (2) 0.0674 (5)
O10 0.43602 (9) 0.26558 (9) 0.3203 (2) 0.0580 (5)
O11 0.34033 (8) 0.49239 (8) 0.44751 (17) 0.0440 (4)
O12 0.28062 (8) 0.41778 (8) 0.57958 (17) 0.0411 (4)
H12 0.249494 0.449598 0.563435 0.062*
O13 0.76674 (7) 0.42231 (8) 0.63628 (16) 0.0407 (4)
H13 0.733639 0.450048 0.606388 0.061*
O14 0.82438 (7) 0.48858 (8) 0.48409 (17) 0.0411 (4)
O15 0.99058 (12) 0.21474 (9) 0.5639 (2) 0.0753 (6)
O16 0.92169 (9) 0.26922 (10) 0.4027 (2) 0.0699 (6)

Source of material

A mixture of methyl 4-methyl-4-nitropentanoate (13.6 g, 77.7 mmol), H2O (20 mL), and sodium hydroxide (6.2 g, 155.0 mmol) was stirred in methanol (200 mL) at 25 °C for 4 h. The reaction was monitored by thin-layer chromatography. The solution was concentrated and diluted with water, and the pH was adjusted to two by adding hydrochloric acid solution (4 mol/L). Then the mixture was extracted with ethyl acetate and washed with brine. The organic layer was concentrated under reduced pressure, and the residue was purified by column chromatography using petroleum ether and ethyl acetate (5:1, v/v) as eluent. Crystals were obtained by slow evaporation of the aforementioned mixed solution at room temperature after a week.

Experimental details

All hydrogen atoms were placed in theoretical positions and refined in riding models with the U iso values set to 1.2 or 1.5 times of those of the attached atoms. The distances of C–H bonds were constrained from 0.98 to 0.99 Å. Oxygen-bound H atoms were also included in the refinement in the riding model with O–H = 0.84 Å and their U iso  = 1.5 U eq (O).

Comment

The γ-aminobutyric acid (GABA) is a kind of non-protein amino acid widely distributed in nature, such as in plants, animals, and microorganisms. It can be produced by plant extraction, isolation, microbial fermentation, and chemical synthesis [5, 6]. Some γ-aminobutyric acids are the primary inhibitory transmitters of the mammalian central nervous system. They have significant physiological functions such as lowering blood pressure, sedation, anti-anxiety, anti-epilepsy, enhancing memory, preventing diabetes, and regulating insomnia [7], [8], [9], [10], [11]. Therefore, γ-aminobutyric acid and its derivatives have broad application prospects in pharmaceutical research [12, 13]. The 4-methyl-4-nitro-pentanoic acid is an essential intermediate for the synthesis of γ- aminobutyric acid derivatives. In addition, it has been widely used in the preparation of lactam, nitro acid, and nitro amide. As a precursor of γ-amino acid, the crystal structure of the title compound would provide a crucial pharmacodynamic fragment for drug molecular design and synthesis.

The asymmetric unit contains four crystallographically independent molecules, as shown in the figure. The bond lengths of C6–O4, C7–O6, C18–O11, and C19–O14 in the title molecule are 1.221(3), 1.218(3), 1.219(3), and 1.223(3) Å, respectively. It illustrated characteristic C=O double bonds. In addition, the bond length of N1–O1, N1–O2, N2–O7, N2–O8, N3–O15, N3–O16, N4–O9, N4–O10 in the title molecule are in the range of 1.211(3)–1.220(3) Å. The bond lengths of C–C, C–N are in the range of 1.489–1.529 Å and 1.531–1.542 Å, respectively. These bond distances are all in their normal ranges. The molecules are connected to each other through hydrogen bonds between carboxyl groups and carboxyl groups, including O3…H3…O4, O13…H13…O11, O12…H12…O14, and O5…H5…O6. The lengths of hydrogen bonds are 1.7906 (16), 1.8015 (15), 1.8374 (14), and 1.8010 (15) Å. It can be seen that the hydrogen bonds are stable and strong.

Corresponding author: Hongjuan Tong, Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi’an, China, E-mail:

Funding source: Natural Science Foundation of Shannxi Province http://dx.doi.org/10.13039/501100007128

Award Identifier / Grant number: 2019JQ-924, 2021JQ-883

Funding source: Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province http://dx.doi.org/10.13039/501100009103

Award Identifier / Grant number: 2019XT-1–03

Funding source: Shaanxi University Association for Science and Technology Young Talent Support Program Project http://dx.doi.org/10.13039/501100017550

Award Identifier / Grant number: 20210313

Funding source: Key Laboratory of Molecular Imaging and Drug Synthesis of Xianyang City http://dx.doi.org/10.13039/501100011710

Award Identifier / Grant number: 2021QXNL–PT-0008

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

  2. Research funding: This work was financially supported by the projects of Natural Science Foundation of Shannxi Province (2019JQ-924, 2021JQ-883), Key breeding program by Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province (2019XT-1–03), Shaanxi University Association for Science and Technology Young Talent Support Program Project (20210313) and 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: 2022-01-14
Accepted: 2022-02-21
Published Online: 2022-03-07
Published in Print: 2022-06-27

© 2022 Hongjuan Tong and Wenqiang Tang, published by De Gruyter, Berlin/Boston

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

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  46. Crystal structure of 3,6-di-tert-butyl-1-iodo-9-methyl-8-(pyren-1-ylethynyl)-9H-carbazole, C39H34IN
  47. The cocrystal 2-(dimethylammonio)-5-nitrobenzoate – 2-(dimethylamino)-5-nitrobenzoic acid, C9H10N2O4
  48. Crystal structure of 5-nitroquinazolin-4(3H)-one, C8H5N3O3
https://doi.org/10.1515/ncrs-2022-0015
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of (E)-(4-imidazol-1-yl-phenyl)-(2-methoxy-benzylidene)-amine monohydrate, C17H17N3O2
  4. Crystal structure of 6-methyl-3-(pyrrolidine-1-carbonyl)-2H-chromen-2-one, C15H15N1O3
  5. Crystal structure of 4-methyl-4-nitropentanoic acid, C6H11NO4
  6. The crystal structure of (E)-3-(furan-2-yl)acrylonitrile, C7H5NO
  7. Crystal structure of 3-(difluoromethyl)-1-methyl-N-(4,11,11-trimethyl-1,2,3,4-tetrahydro-1,4-methanoacridin-9-yl)-1H-pyrazole-4-carboxamide monohydrate, C23H26F2N4O3
  8. Crystal structure of 2-(4-bromobenzyloxy)-6-chloropyridine, C12H9BrClNO
  9. Crystal structure of N-(4-bromo-2,6-dichloro-phenyl)pyrazin-2-amine, C10H6BrCl2N3
  10. Crystal structure of (E)-1-(2–nitrophenyl)-3-phenylprop-2-en-1-one, C15H11NO3
  11. The crystal structure of (E)-3-chloro-2-(2-(4-fluorobenzylidene)hydrazinyl)pyridine, C12H9ClFN3
  12. Crystal structure of (E)-amino(2-(thiazol-2-ylmethylene)hydrazineyl)methaniminium nitrate, C10H16N12O6S2
  13. Crystal structure of 9-methoxy-2,3,4,4a,5,6-hexahydro-1H-pyrido [1′,2′:1,6]pyrazino[2,3-b]quinoxaline, C15H18N4O
  14. The crystal structure bis(dimethylsulfoxide-κ1O)-dipyridine-κ1 N-bis(m2-(Z)-3-methyl-2-oxido-N-((Z)-oxido(phenyl)methylene)benzohydrazonato-κ5)trinickel(II) - dimethylsulfoxide (1/2), C48H56N6Ni3O10S4
  15. Crystal structure of bis(bis(triphenylphosphine)iminium) tetradecacarbonyltetratelluridopentaferrate(2-), (PPN)2[Fe5Te4(CO)14]
  16. Crystal structure of 4-Hydroxy-3-(naphthalen-2-ylthio)pent-3-en-2-one, C15H14O2S
  17. The crystal structure of [(1,10-phenanthroline-κ2 N,N)-bis(6-phenylpyridine-2-carboxylate-κ2 N,O)nickel(II)] monohydrate, C36H26N4O5Ni
  18. Crystal structure of 3,3′-(pyridine-2,6-diylbis(methylene))bis(1-propyl-1H-imidazol-3-ium) ditetrafluoroborate, C19H27B2F8N5
  19. The crystal structure of (E)-1-(4-aminophenyl)-3-(p-tolyl)prop-2-en-1-one, C16H15NO
  20. The crystal structure of poly[(μ2-terephthalato-κ4O,O′: O″,O‴)-(μ4-terephthalato-κ4O:O′:O″:O‴)-{μ4-(1,2,4,5-tetrakis(1,2,4-triazol-1-ylmethyl)-benzene-κ4O:O′:O″,O‴)}dicadmium(II)] – water – acetronitrile (1/2/2), C38H36N14O10Cd2
  21. The crystal structure of diaqua-bis(6-phenylpyridine-2-carboxylato-κ2 N,O)cobalt(II)–water–N,N-dimethylformamide(1/2/1), C27H31N3O9Co
  22. The co-crystal structure of 4-hydroxy-3-methoxybenzoic acid – 4,4′-bipyridine, C8H8O4·C10H8N2
  23. Crystal structure of catena-poly[(μ2-1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol)-κ2N:N′)-bis(4-bromobenzoate-κ1O)cobalt(II)], C32H22Br2CoN4O4
  24. Crystal structure of (E)-5-propyl-4-((pyridin-2-ylmethylene)amino)-2,4-dihydro-3H-1,2,4-triazole-3-thione – methanol (1/1), C11H13N5S
  25. The crystal structure of (Z)-4-bromo-6-(((1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl)amino)methylene)cyclohexa-2,4-dien-1-one monohydrate, C11H16BrNO5
  26. Crystal structure of bis(tetrapropylammonium) nonaselenidotetrastannate(IV), (Pr4N)2[Sn4Se9]
  27. Crystal structure of 2,6-di-tert-butyl-4-(4-chlorobenzylidene)cyclohexa-2,5-dien-1-one, C21H25ClO
  28. Crystal structure of (2,2′-((naphthalen-1-ylmethyl)azanediyl)diacetato-κ3 N,O,O′)-(1,10-phenanthroline-κ2 N,N′)-copper(II) trihydrate, CuC27H27N3O7
  29. The crystal structure of tetrakis(6-phenylpyridine-2-carboxylato-κ2N,O)-bis(1H-pyrazol-3-ylamine-κ2 N:N)dicobalt(II) dihydrate, C27H23N5O5Co
  30. The crystal structure of bis((E)-2-((tert-butylimino)methyl)-4-chlorophenolato-κ2N,O)zinc(II), C22H26Cl2N2O2Zn
  31. The crystal structure of poly[diaqua-(μ3-5-nitrobenzene-1,2,3-tricarboxylato-κ3O:O′:O′)-(μ2-4,4′-dipyridylamine-κ2N:N′)copper(II)], C38H30Cu3N8O20
  32. The crystal structure of (E)-1-ferrocenyl-3-(naphthalen-1-yl)prop-2-en-1-one, C23H18FeO
  33. The crystal structure of (E)-1-ferrocenyl-3-(4-isopropylphenyl)prop-2-en-1-one, C22H22FeO
  34. Crystal structure of 6-hydroxy-2,2-dimethyl-4Hbenzo[d][1,3]dioxin-4-one, C10H10O4
  35. The crystal structure of (2E,4E)-1-ferrocenyl-5-phenylpenta-2,4-dien-1-one, C21H18FeO
  36. Crystal structure of alaninato-κ2N,O-bis(hydroxylamido-κ2N,O)-oxido-vanadium(V), C3H10N3O5V
  37. Crystal structure of catena-poly[aqua-bis[μ2-6-(1H-imidazol-1-yl)nicotinato-κ2 N,O]copper(II)], C18H14N6O5Cu
  38. Crystal structure of diethyl 4,6-diphenyl-1,9-di-p-tolylhexahydro-3H-2,7,3,5-(epimethanetriyliminomethanetriyl)cyclopenta[b]pyridine-3,5(2H)-dicarboxylate, C42H42N2O4
  39. The crystal structure of cobalt cadmium bis(hydrogenphosphate) bis(phosphate(V)) tetrahydrate, H10O20P4Co3.14Cd1.86
  40. Crystal structure of dimethyl 1,4,6,9-tetraphenylhexahydro-3H-2,7,3,5-(epimethanetriyliminomethanetriyl)cyclopenta[b]pyridine-3,7(2H)-dicarboxylate, C38H34N2O4
  41. Crystal structure of (Z)-4-(furan-2-yl((4-iodophenyl)amino)methylene)-5-methyl-2(p-tolyl)-2,4-dihydro-3H-pyrazol-3-one, C21H16I N3O2
  42. Crystal structure of (E)-1-(4-(3,5-dimethoxystyryl)phenyl)-7-ethylheptanedioate, C25H30O6
  43. Crystal structure of 6-bromo-2-(4-chlorophenyl)chroman-4-one (6-bromo-4′-chloroflavanone), C15H10BrClO2
  44. The crystal structure of 2-(benzhydryloxy)-3-nitropyridine, C18H14N2O3
  45. The crystal structure of 1,3(4,1)-dipyridin-1-iuma-2(1,8)-diethynylanthracena-5(1,3)-benzenacyclohexaphane-11,31-diium bis(hexafluoridophosphate), C36H24F12N2P2
  46. Crystal structure of 3,6-di-tert-butyl-1-iodo-9-methyl-8-(pyren-1-ylethynyl)-9H-carbazole, C39H34IN
  47. The cocrystal 2-(dimethylammonio)-5-nitrobenzoate – 2-(dimethylamino)-5-nitrobenzoic acid, C9H10N2O4
  48. Crystal structure of 5-nitroquinazolin-4(3H)-one, C8H5N3O3
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