Crystal structure of dimethyl (3aS,6R,6aS,7S)-2-pivaloyl-2,3-dihydro-1H,6H,7H-3a,6:7,9a-diepoxybenzo[de]isoquinoline-3a1,6a-dicarboxylate, C21H25NO8

Pavel V. Dorovatovskii 1 , Nurlana D. Sadigova 2 , Alakbar E. Huseynzada 2 , Sarvinaz F. Hajiyeva 2 , Alejandro Cárdenas 3 , Jonathan Cisterna 4 , and Iván Brito 4
  • 1 National Research Center Kurchatov Institute, Moscow, Russia
  • 2 Organic Chemistry Department, Baku State University, Z. Xalilov Str. 23, Az, 1148 Baku, Azerbaijan
  • 3 Departamento de Física, Facultad de Ciencias Básicas, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
  • 4 Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
Pavel V. Dorovatovskii, Nurlana D. Sadigova
  • Organic Chemistry Department, Baku State University, Z. Xalilov Str. 23, Az, 1148 Baku, Azerbaijan
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, Alakbar E. Huseynzada
  • Organic Chemistry Department, Baku State University, Z. Xalilov Str. 23, Az, 1148 Baku, Azerbaijan
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, Sarvinaz F. Hajiyeva
  • Organic Chemistry Department, Baku State University, Z. Xalilov Str. 23, Az, 1148 Baku, Azerbaijan
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, Alejandro Cárdenas
  • Departamento de Física, Facultad de Ciencias Básicas, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
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, Jonathan Cisterna
  • Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
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and Iván Brito
  • Corresponding author
  • Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
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Abstract

C21H25NO8 , P21/n, (no. 14), a = 12.905(3) Å, b = 13.370(3) Å, c = 13.090(3) Å, β = 118.19(3)°, V = 1990.5(8) Å3, Z = 4, Rgt(F) = 0.0629, wRref(F2) = 0.1966, T = 100(2) K.

article image

Table 1:

Data collection and handling.

Crystal:Parallelpiped
Size:0.20 × 0.20 × 0.10 mm
Wavelength:Synchrotron radiation (0.9699 Å)
μ:0.25 mm−1
Diffractometer, scan mode:Synchrotron Radiation, ϕ-scan
θmax, completeness:38.5°, 97%
N(hkl)measured, N(hkl)unique, Rint:21424, 4031, 0.074
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2857
N(param)refined:277
Programs:Olex2 [14]

The asymmetric unit of the title crystal structure is shown in the figure. Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 2:

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

AtomxyzUiso*/Ueq
O10.53895(17)0.50371(13)0.14659(14)0.0272(5)
O20.66863(17)0.39465(12)0.32594(14)0.0272(5)
O30.41410(18)0.34009(12)0.36896(15)0.0320(5)
O40.30855(18)0.42559(13)0.19913(15)0.0327(5)
O50.92773(19)0.51245(14)0.25445(17)0.0359(5)
O60.86050(18)0.66528(13)0.26739(17)0.0347(5)
O70.84057(18)0.66491(13)0.47755(16)0.0360(6)
O80.65940(17)0.73253(12)0.38401(14)0.0288(5)
C10.5929(3)0.48200(19)0.4394(2)0.0269(7)
H1A0.5951300.4207580.4829000.032*
H1B0.6070450.5401900.4911180.032*
N20.4770(2)0.49140(15)0.33724(18)0.0258(6)
C30.4601(3)0.57971(18)0.2638(2)0.0276(7)
H3A0.4639680.6409200.3080170.033*
H3B0.3811420.5767360.1953660.033*
C3A0.5521(3)0.58553(18)0.2237(2)0.0248(6)
C40.5559(3)0.67432(19)0.1512(2)0.0289(7)
H40.5262040.7398480.1483930.035*
C50.6094(3)0.6401(2)0.0933(2)0.0306(7)
H50.6272730.6765620.0413090.037*
C60.6365(3)0.5299(2)0.1269(2)0.0283(7)
H60.6450040.4874440.0684820.034*
C6A0.7430(3)0.52286(18)0.2548(2)0.0249(6)
C70.7680(3)0.41286(18)0.3066(2)0.0277(7)
H70.7804700.3617090.2577090.033*
C80.8675(3)0.42068(17)0.4315(2)0.0262(6)
H80.9472770.4012130.4602990.031*
C90.8177(3)0.46082(17)0.4912(2)0.0249(6)
H90.8548800.4762160.5715440.030*
C9A0.6887(3)0.47681(17)0.4033(2)0.0235(6)
C9B0.6833(2)0.56946(17)0.3239(2)0.0234(6)
C100.4013(3)0.41226(18)0.3062(2)0.0253(6)
C110.2027(3)0.3614(2)0.1565(2)0.0298(7)
C120.2313(3)0.2527(2)0.1461(3)0.0422(8)
H12A0.2729110.2488180.0999880.063*
H12B0.1582810.2140610.1079690.063*
H12C0.2812570.2253100.2235320.063*
C130.1456(3)0.3743(2)0.2347(3)0.0371(8)
H13A0.1992810.3498410.3126160.056*
H13B0.0721500.3361680.2029100.056*
H13C0.1289050.4453170.2386350.056*
C140.1251(3)0.4053(3)0.0365(3)0.0463(9)
H14A0.1080580.4754820.0441120.069*
H14B0.0513300.367574−0.0015340.069*
H14C0.1661190.400875−0.0100540.069*
C150.8531(3)0.56548(19)0.2600(2)0.0280(7)
C160.9690(3)0.7089(2)0.2794(3)0.0386(8)
H16A0.9698860.7050790.2050330.058*
H16B1.0363850.6720110.3383150.058*
H16C0.9739210.7790880.3029330.058*
C170.7392(3)0.65990(17)0.4019(2)0.0247(6)
C180.7011(3)0.81678(19)0.4637(2)0.0343(7)
H18A0.6546940.8763430.4254670.051*
H18B0.7840860.8293290.4866580.051*
H18C0.6927290.8014150.5326100.051*

Source of material

Synthesis and characterization by 1H/13C NMR, IR and HRMS methods was reported in [10], [11].

Experimental details

H atoms were located in the difference Fourier map, but refined with fixed individual displacement parameters, using a riding model with C—H distances of 0.95–1.0 Å (for aromatic rings), and C—H distances 0.99, 0.98 Å for methylene nd methyl groups, with U(H) values of 1.2Ueq(CAr and CH2) and 1.5Ueq(C) (for CH3).

Comment

Weak interactions, such as hydrogen, halogen, chalcogen, pnicogen, tetrel and icosagen bonds were extensively used in the synthesis, catalysis, crystal engineering, drug delivery, etc. [1], [2], [3], [4], [5]. Among those, hydrogen bonding has turned out to be particularly suitable for design of organic and coordination compounds [6], [7], [8], [9]. There is one title molecule in the asymmetric unit.

The molecule comprises a fused hexacyclic system containing four five-membered rings in the usual envelope conformations with Cremer and Pople parameters [12] ranging from (Q(2) = 0.517(3)–0.583(3) Å; φ2 = 175.2(3)–181.4(4)°) and one six-membered rings adopting a chair conformation with Cremer and Pople parameters Q = 0.523(3) Å, θ = 6.8(3)°, φ = 52(3)° respectively. In the crystal structure the molecules are linked at least by C—O⋯H intermolecular hydrogen bond which link molecules into centrosymmetric dimers with R22(10) graph-set notation [13]. Other weak intermolecular interactions will contibute to the stability of the packing. The carboxylate groups are α-oriented, meanwhile, the tert-butyl carboxylate group is β-oriented. All distances and angles are normal.

Acknowledgements

X-ray crystallographic studies using synchrotron radiation were performed at the unique scientific facility Kurchatov Synchrotron Radiation Source supported by the Ministry of Education and Science of the Russian Federation (project code RFMEFI61917X0007). This work has also been partially supported by Universidad de Antofagasta, and Baku State University.

References

  • 1.

    Kvyatkovskaya, E. A.; Zaytsev,V.; Zubkov, F. I.; Dorovatovskii, P. V.; Zubavichus, Y. V.; Khrustalev, V. N.: Interaction between maleic acid andN-R-furfurylamines: crystal structure of 2-methyl-N-[(5-phenylfuran-2-yl)methyl]propan-2-aminium (2Z)-3-carboxyacrylate andN-[(5-iodofuran-2-yl)methyl]-2-methylpropan-2-aminium (2Z)-3-carboxyprop-2-enoate. Acta Crystallogr. E73 (2017) 515–519.

  • 2.

    Shixaliyev, N. Q.; Ahmadova, N. E.; Gurbanov, A. V.; Maharramov, A. M.; Mammadova, G. Z.; Nenajdenko, V. G.; Zubkov, F. I.; Mahmudov, K. T.; Pombeiro, A. J. L.: Tetrel, halogen and hydrogen bonds in bis(4-((E)-(2,2-dichloro-1-(4-substitutedphenyl)vinyl)diazenyl)phenyl)methane dyes. Dyes Pigments 150 (2018) 377–381.

    • Crossref
    • Export Citation
  • 3.

    Nasirova, D. K.; Malkova, A. V.; Polyanskii, K. B.; Yankina, K. Y.; Amoyaw, P. N.-A.; Kolesnik, I. A.; Kletskov, A. V.; Godovikov, I. A.; Nikitina, E. V.; Zubkov, F. I.: Rearrangement of 2-azanorbornenes to tetrahydrocyclopenta [c]pyridines under the action of activated alkynes – a short pathway for construction of the altemicidin core. Tetrahedron Lett. 58 (2017) 4384–4387.

    • Crossref
    • Export Citation
  • 4.

    Vandyshev, D. Y.; Shikhaliev, K. S.; Potapov, A. Y.; Krysin, M. Y.; Zubkov, F. I.; Sapronova, L. V.: A novel synthetic approach to hydroimidazo[1,5-b]pyridazines by the recyclization of itaconimides and HPLC–HRMS monitoring of the reaction pathway. Beilstein J. Org. Chem. 13 (2017) 2561–2568.

    • Crossref
    • PubMed
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  • 5.

    Shetne, V. A. A.; Zubkov, F. I.: The latest advances in chemistry of 1,2,4-oxadiazines. Chem. Heterocyclic Compd. 53 (2017) 495–497.

    • Crossref
    • Export Citation
  • 6.

    Desiraju, G. R.: Supramolecular synthons in crystal engineering—a new organic synthesis. Angew. Chem. Int. Ed. 34 (1995) 2311–2327.

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    • Export Citation
  • 7.

    Mahmudov, K. T.; Pombeiro, A. J. L.: Resonance–assisted hydrogen bonding as a driving force in synthesis and a synthon in the design of materials. Chem. Eur. J. 22 (2016) 16356–16398.

    • Crossref
    • Export Citation
  • 8.

    Mahmudov, K. T.; Kopylovich, M. N.; Guedes da Silva, M. F. C.; Pombeiro, A. J. L.: Non-covalent interactions in the synthesis of coordination compounds: recent advances. Coord. Chem. Rev. 345 (2017) 54–72.

    • Crossref
    • Export Citation
  • 9.

    Hazra, S.; Martins, N. M. R.; Mahmudov, K. T.; Zubkov, F. I.; Guedes da Silva, M. F. C.; Pombeiro, A. J. L.: A tetranuclear diphenyltin(IV) complex and its catalytic activity in the aerobic BaeyerVilliger oxidation of cyclohexanone. J. Organomet. Chem. 867 (2018) 193–200.

    • Crossref
    • Export Citation
  • 10.

    Borisova, K. K.; Kvyatkovskaya, E. A.; Nikitina, E. V.; Aysin, R. R.; Novikov, R. A.; Zubkov, F. I.: Classical example of total kinetic and thermodynamic control: the Diels–Alder reaction between DMAD and bis-furyl dienes. J. Org. Chem. 83 (2018) 4840–4850.

    • Crossref
    • PubMed
    • Export Citation
  • 11.

    Borisova, K. K.; Nikitina, E. V.; Novikov, R. A.; Khrustalev, V. N.; Dorovatovskii, P. V.; Zubavichus, Y. V.; Kuznetsov, M. L.; Zaytsev, V. P.; Varlamov, A. V.; Zubkov, F. I.: Diels–Alder reactions between hexafluoro-2-butyne and bis-furyl dienes: kinetic versus thermodynamic control. Chem. Commun. 54 (2018) 2850–2853.

    • Crossref
    • Export Citation
  • 12.

    Cremer, D.; Pople, J. A.: General definition of ring puckering coordinates. J. Am. Chem. Soc. 97 (1975) 1354–1358.

    • Crossref
    • Export Citation
  • 13.

    Bernstein, J.; Davis, R. E.; Shimoni, L.; Chang, N.-L.: Patterns in hydrogen bonding: functionality and graph set analysis in crystals. Angew. Chem. Int. Ed. Engl. 34 (1995) 1555–1573.

    • Crossref
    • Export Citation
  • 14.

    Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H.: OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 42 (2009) 339–341.

    • Crossref
    • Export Citation

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  • 1.

    Kvyatkovskaya, E. A.; Zaytsev,V.; Zubkov, F. I.; Dorovatovskii, P. V.; Zubavichus, Y. V.; Khrustalev, V. N.: Interaction between maleic acid andN-R-furfurylamines: crystal structure of 2-methyl-N-[(5-phenylfuran-2-yl)methyl]propan-2-aminium (2Z)-3-carboxyacrylate andN-[(5-iodofuran-2-yl)methyl]-2-methylpropan-2-aminium (2Z)-3-carboxyprop-2-enoate. Acta Crystallogr. E73 (2017) 515–519.

  • 2.

    Shixaliyev, N. Q.; Ahmadova, N. E.; Gurbanov, A. V.; Maharramov, A. M.; Mammadova, G. Z.; Nenajdenko, V. G.; Zubkov, F. I.; Mahmudov, K. T.; Pombeiro, A. J. L.: Tetrel, halogen and hydrogen bonds in bis(4-((E)-(2,2-dichloro-1-(4-substitutedphenyl)vinyl)diazenyl)phenyl)methane dyes. Dyes Pigments 150 (2018) 377–381.

    • Crossref
    • Export Citation
  • 3.

    Nasirova, D. K.; Malkova, A. V.; Polyanskii, K. B.; Yankina, K. Y.; Amoyaw, P. N.-A.; Kolesnik, I. A.; Kletskov, A. V.; Godovikov, I. A.; Nikitina, E. V.; Zubkov, F. I.: Rearrangement of 2-azanorbornenes to tetrahydrocyclopenta [c]pyridines under the action of activated alkynes – a short pathway for construction of the altemicidin core. Tetrahedron Lett. 58 (2017) 4384–4387.

    • Crossref
    • Export Citation
  • 4.

    Vandyshev, D. Y.; Shikhaliev, K. S.; Potapov, A. Y.; Krysin, M. Y.; Zubkov, F. I.; Sapronova, L. V.: A novel synthetic approach to hydroimidazo[1,5-b]pyridazines by the recyclization of itaconimides and HPLC–HRMS monitoring of the reaction pathway. Beilstein J. Org. Chem. 13 (2017) 2561–2568.

    • Crossref
    • PubMed
    • Export Citation
  • 5.

    Shetne, V. A. A.; Zubkov, F. I.: The latest advances in chemistry of 1,2,4-oxadiazines. Chem. Heterocyclic Compd. 53 (2017) 495–497.

    • Crossref
    • Export Citation
  • 6.

    Desiraju, G. R.: Supramolecular synthons in crystal engineering—a new organic synthesis. Angew. Chem. Int. Ed. 34 (1995) 2311–2327.

    • Crossref
    • Export Citation
  • 7.

    Mahmudov, K. T.; Pombeiro, A. J. L.: Resonance–assisted hydrogen bonding as a driving force in synthesis and a synthon in the design of materials. Chem. Eur. J. 22 (2016) 16356–16398.

    • Crossref
    • Export Citation
  • 8.

    Mahmudov, K. T.; Kopylovich, M. N.; Guedes da Silva, M. F. C.; Pombeiro, A. J. L.: Non-covalent interactions in the synthesis of coordination compounds: recent advances. Coord. Chem. Rev. 345 (2017) 54–72.

    • Crossref
    • Export Citation
  • 9.

    Hazra, S.; Martins, N. M. R.; Mahmudov, K. T.; Zubkov, F. I.; Guedes da Silva, M. F. C.; Pombeiro, A. J. L.: A tetranuclear diphenyltin(IV) complex and its catalytic activity in the aerobic BaeyerVilliger oxidation of cyclohexanone. J. Organomet. Chem. 867 (2018) 193–200.

    • Crossref
    • Export Citation
  • 10.

    Borisova, K. K.; Kvyatkovskaya, E. A.; Nikitina, E. V.; Aysin, R. R.; Novikov, R. A.; Zubkov, F. I.: Classical example of total kinetic and thermodynamic control: the Diels–Alder reaction between DMAD and bis-furyl dienes. J. Org. Chem. 83 (2018) 4840–4850.

    • Crossref
    • PubMed
    • Export Citation
  • 11.

    Borisova, K. K.; Nikitina, E. V.; Novikov, R. A.; Khrustalev, V. N.; Dorovatovskii, P. V.; Zubavichus, Y. V.; Kuznetsov, M. L.; Zaytsev, V. P.; Varlamov, A. V.; Zubkov, F. I.: Diels–Alder reactions between hexafluoro-2-butyne and bis-furyl dienes: kinetic versus thermodynamic control. Chem. Commun. 54 (2018) 2850–2853.

    • Crossref
    • Export Citation
  • 12.

    Cremer, D.; Pople, J. A.: General definition of ring puckering coordinates. J. Am. Chem. Soc. 97 (1975) 1354–1358.

    • Crossref
    • Export Citation
  • 13.

    Bernstein, J.; Davis, R. E.; Shimoni, L.; Chang, N.-L.: Patterns in hydrogen bonding: functionality and graph set analysis in crystals. Angew. Chem. Int. Ed. Engl. 34 (1995) 1555–1573.

    • Crossref
    • Export Citation
  • 14.

    Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H.: OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 42 (2009) 339–341.

    • Crossref
    • Export Citation
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