Home Physical Sciences Crystal structure of (−)-flavesine H, C15H22N2O2
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Crystal structure of (−)-flavesine H, C15H22N2O2

  • Kai Peng , Ding Luo ORCID logo EMAIL logo and Guang-cun Wang EMAIL logo
Published/Copyright: October 30, 2024

Abstract

C15H22N2O2, monoclinic, P21 (no. 4), a = 8.4853(2) Å, b = 19.5759(4) Å, c = 9.0640(2) Å, β = 106.845(2)°, V = 1441.00(6) Å3, Z = 4, R gt (F) = 0.00374, wR ref (F 2) = 0.0991, T = 150 K.

CCDC no.: 2392013

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: 0.12 × 0.11 × 0.10 mm
Wavelength:

μ:
Cu Kα radiation (1.54184 Å)

0.73 mm−1
Diffractometer, scan mode:

θ max, completeness:
SuperNova, ω

74.0°, >99 %
N(hkl)measured, N(hkl)unique, R int: 13135, 5610, 0.034
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 5461
N(param)refined: 367
Programs: Olex2, 1 SHELX 2 , 3
Table 2:

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

Atom x y z U iso*/U eq
O1 0.0677 (2) 0.64406 (9) 0.4676 (2) 0.0312 (4)
O2 −0.0398 (2) 0.54071 (10) 0.3946 (2) 0.0325 (4)
N1 0.2342 (2) 0.88293 (10) 1.0100 (2) 0.0250 (4)
N2 0.0937 (3) 0.68675 (10) 1.0753 (2) 0.0253 (4)
H2 0.080730 0.642775 1.088276 0.030*
C2 0.2620 (3) 0.93510 (12) 1.1325 (3) 0.0284 (5)
H2A 0.201969 0.977264 1.088893 0.034*
H2B 0.380828 0.946217 1.168477 0.034*
C3 0.2061 (3) 0.91228 (13) 1.2692 (3) 0.0302 (5)
H3A 0.084373 0.913547 1.241358 0.036*
H3B 0.249871 0.944057 1.356499 0.036*
C4 0.2662 (3) 0.84011 (12) 1.3181 (3) 0.0273 (5)
H4A 0.387929 0.839547 1.357058 0.033*
H4B 0.221542 0.824367 1.401708 0.033*
C5 0.2091 (3) 0.79350 (12) 1.1809 (3) 0.0227 (4)
C6 0.2021 (3) 0.81839 (12) 1.0334 (3) 0.0221 (4)
C7 0.1687 (3) 0.76709 (12) 0.9019 (3) 0.0228 (4)
H7 0.272091 0.740381 0.913726 0.027*
C8 0.1234 (3) 0.80092 (13) 0.7436 (3) 0.0312 (5)
H8A 0.124652 0.766616 0.663669 0.037*
H8B 0.011184 0.820487 0.719391 0.037*
C9 0.2471 (4) 0.85701 (14) 0.7445 (3) 0.0357 (6)
H9A 0.359563 0.837566 0.771992 0.043*
H9B 0.223177 0.877524 0.640453 0.043*
C10 0.2374 (4) 0.91131 (13) 0.8601 (3) 0.0349 (6)
H10A 0.333400 0.942130 0.876549 0.042*
H10B 0.136731 0.938913 0.817096 0.042*
C11 0.0367 (3) 0.71732 (12) 0.9208 (3) 0.0238 (5)
H11 −0.064506 0.744516 0.915694 0.029*
C12 −0.0116 (3) 0.66129 (13) 0.7994 (3) 0.0268 (5)
H12A −0.060624 0.683013 0.697835 0.032*
H12B −0.097998 0.632781 0.822312 0.032*
C13 0.1278 (3) 0.61467 (12) 0.7872 (3) 0.0261 (5)
H13A 0.176239 0.591787 0.887508 0.031*
H13B 0.215004 0.642584 0.764062 0.031*
C14 0.0691 (3) 0.56065 (12) 0.6621 (3) 0.0273 (5)
H14A −0.030474 0.538626 0.676404 0.033*
H14B 0.155336 0.525083 0.677879 0.033*
C15 0.0285 (3) 0.58544 (12) 0.4953 (3) 0.0246 (5)
C17 0.1647 (3) 0.72619 (12) 1.1945 (3) 0.0240 (5)
H17 0.186370 0.707345 1.294986 0.029*
O1A 0.2960 (3) 0.33844 (11) 0.1245 (2) 0.0472 (5)
O2A 0.2134 (4) 0.44442 (12) 0.1513 (3) 0.0557 (7)
N1A 0.4754 (3) 0.10655 (10) −0.3462 (3) 0.0285 (4)
N2A 0.2809 (2) 0.29788 (10) −0.4760 (2) 0.0249 (4)
H2AA 0.254774 0.341081 −0.496205 0.030*
C2A 0.5439 (4) 0.06458 (14) −0.4479 (3) 0.0368 (6)
H2AB 0.516018 0.016033 −0.437788 0.044*
H2AC 0.665415 0.068760 −0.414701 0.044*
C3A 0.4784 (4) 0.08591 (14) −0.6156 (3) 0.0370 (6)
H3AA 0.359780 0.074700 −0.654741 0.044*
H3AB 0.537190 0.060645 −0.678211 0.044*
C4A 0.5031 (3) 0.16262 (15) −0.6300 (3) 0.0331 (5)
H4AA 0.622136 0.173228 −0.602999 0.040*
H4AB 0.450926 0.177527 −0.737429 0.040*
C5A 0.4265 (3) 0.19960 (12) −0.5227 (3) 0.0248 (5)
C6A 0.4203 (3) 0.16933 (12) −0.3843 (3) 0.0230 (4)
C7A 0.3672 (3) 0.21316 (12) −0.2689 (3) 0.0234 (5)
H7A 0.464891 0.240971 −0.212318 0.028*
C8A 0.3144 (3) 0.17164 (14) −0.1485 (3) 0.0313 (5)
H8AA 0.303139 0.202139 −0.064982 0.038*
H8AB 0.206226 0.150008 −0.196675 0.038*
C9A 0.4423 (4) 0.11699 (15) −0.0821 (3) 0.0368 (6)
H9AA 0.549619 0.138795 −0.031290 0.044*
H9AB 0.408731 0.090203 −0.003620 0.044*
C10A 0.4600 (4) 0.06985 (14) −0.2091 (3) 0.0366 (6)
H10C 0.558543 0.040806 −0.168267 0.044*
H10D 0.362777 0.039426 −0.240138 0.044*
C11A 0.2329 (3) 0.26319 (12) −0.3523 (3) 0.0231 (4)
H11A 0.130395 0.236452 −0.400269 0.028*
C12A 0.1919 (3) 0.31801 (13) −0.2476 (3) 0.0278 (5)
H12C 0.101107 0.346790 −0.310269 0.033*
H12D 0.152132 0.295109 −0.167830 0.033*
C13A 0.3365 (3) 0.36402 (14) −0.1682 (3) 0.0324 (6)
H13C 0.380657 0.385045 −0.247381 0.039*
H13D 0.424956 0.335786 −0.100272 0.039*
C14A 0.2900 (3) 0.42046 (13) −0.0726 (3) 0.0288 (5)
H14C 0.377674 0.455573 −0.050405 0.035*
H14D 0.187392 0.442392 −0.135672 0.035*
C15A 0.2640 (3) 0.39783 (13) 0.0797 (3) 0.0305 (5)
C17A 0.3626 (3) 0.26502 (12) −0.5568 (3) 0.0247 (5)
H17A 0.379115 0.287390 −0.644186 0.030*
O3 0.0057 (3) 0.55455 (9) 0.1139 (2) 0.0358 (4)
H3D 0.070130 0.521348 0.113187 0.054*
H3C −0.005520 0.554018 0.204122 0.054*
O4 0.1809 (3) 0.42944 (10) 0.4334 (2) 0.0386 (5)
H4C 0.190543 0.433391 0.343010 0.058*
H4D 0.110787 0.459768 0.438147 0.058*

1 Source of material

The dried roots of Sophora flavescens (25.0 kg) were sourced from Xi’an, Shanxi Province, China. After three extractions with 95 % ethanol, the combined extracts were concentrated under vacuum to yield 1.6 kg of residue. This was suspended in water, adjusted to pH 4 with HCl, and partitioned with chloroform. The aqueous phase was then adjusted to pH 9 with ammonium hydroxide and re-extracted with chloroform, yielding 464 g of chloroform-soluble fraction. Chromatography on macroporous resin produced several fractions, with the title compound isolated from the EtOH/H2O (10:90) fraction and crystallized from methanol.

2 Experimental details

Using Olex2, 1 the structure was solved with the ShelXT 2 structure solution program and refined with the ShelXL 3 refinement package.

3 Comment

Matrine-type alkaloids are a class of naturally occurring compounds predominantly found in plants of the Sophora genus. These alkaloids are characterized by their tetracyclic quinolizidine core structure. 4 Recent advancements in pharmacological research have highlighted the diverse biological activities. 5 , 6 Due to their intricate stereostructure and diverse biological activities, matrine-type alkaloids have garnered significant interest as promising targets for both pharmacological studies and synthetic chemistry endeavors.

The title compound was identified as (−)-flavesine H, the enantiomer of the previously reported (+)-flavesine H. 6  It belongs to the matrine-type alkaloids, distinguished by an open-loop ring D. Notably, the single-crystal structure of (+-)-flavesine H has not yet been reported. The C=O bond lengths 1.236(3)–1.277(3) Å, C–N bond lengths 1.314(3)–1.476(3) Å, C=C bond lengths 1.386(3)–1.408(3) Å and C–C bond lengths 1.507(3)–1.547(2) Å, which were derived from the title structure are within normal ranges. 7


Corresponding authors: Ding Luo and Guang-cun Wang, Department of Anesthesiology, The Fifth Affiliated Hospital of Jinan University, Heyuan 517000, P.R. China, E-mail: (D. Luo), (G.-c. Wang)

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

  2. Conflict of interests: The authors declare no conflicts of interest regarding this article.

  3. Research funding: National Natural Science Foundation of China (No. 82304320).

References

1. 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. 2009, 42, 339–341; https://doi.org/10.1107/s0021889808042726.Search in Google Scholar

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5. Zhang, Y. B.; Zhan, L. Q.; Li, G. Q.; Wang, F.; Wang, Y.; Li, Y. L.; Ye, W. C.; Wang, G. C. Dimeric Matrine-type Alkaloids from the Roots of Sophora flavescens and their anti–Hepatitis B Virus Activities. J. Org. Chem. 2016, 81, 6273–6280; https://doi.org/10.1021/acs.joc.6b00804.Search in Google Scholar PubMed

6. Zhang, Y. B.; Luo, D.; Yang, L.; Cheng, W.; He, L. J.; Kuang, G. K.; Li, M. M.; Li, Y. L.; Wang, G. C. Matrine-type Alkaloids from the Roots of Sophora flavescens and their Antiviral Activities against the Hepatitis B Virus. J. Nat. Prod. 2018, 81, 2259–2265; https://doi.org/10.1021/acs.jnatprod.8b00576.Search in Google Scholar PubMed

7. Li, W. Z.; Xu, L. H.; Liang, C. B.; Wang, H. B. Crystal Structure of (E)-N′-(4-((E)-3-(dimethylamino)acryloyl)-3-hydroxyphenyl)-N, N-Dimethylformimidamide, C14H19N3O2. Z. Kristallogr. N. Cryst. Struct. 2024, 239, 399–400; https://doi.org/10.1515/ncrs-2024-0017.Search in Google Scholar

Received: 2024-09-11
Accepted: 2024-10-18
Published Online: 2024-10-30
Published in Print: 2025-02-25

© 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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