Crystalline Sponge Gallery

G075 · Sesquiterpenoid

(−)-Cedrene

C15H24 · 204.36 g mol−1

First crystal structure · Reported for the unmodified analyte in this study → · Read the story ↓

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INTERACTIVE 3D STRUCTURE

Explore (−)-Cedrene in its crystalline sponge

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CHONCagePhenanthrene 2a
2D chemical structure of (−)-Cedrene
(−)-Cedrene · 2D chemical structure
3D crystal structure of (−)-Cedrene determined by the crystalline-sponge method
(−)-Cedrene · crystalline-sponge guest structure
(−)-Cedrene inside a crystalline sponge coordination cage
(−)-Cedrene · coordination-cage host–guest structure

(−)-Cedrene (compound 5) was structurally analyzed using cage 1a and phenanthrene (2a) in the size-compensation strategy for low-polarity small molecules.

Molecular formula
C15H24
Molecular weight
204.36 g mol−1
CCDC accession
2565727 ↗
Host
Pd6L4 cage 1a
Study
Angew. Chem. 2026 · Size compensation
Compound in publication
5

MOLECULAR HISTORY

From a cedar-oil skeleton to the unmodified guest

Cedrene’s structure emerged in stages. First came a carbon skeleton, then a synthesis that put it to the test, and finally stereochemical arguments built from chemical transformations and optical measurements. The 2026 work adds the unmodified molecule’s crystal structure to that chain of evidence.

  1. 1953

    A structure for cedrene

    Stork and Breslow published the structure of cedrene. Their chemical and spectroscopic work connected the structures of cedrol and α-cedrene, giving later synthetic studies a defined carbon framework to construct and test.1, 3

  2. 1955

    The skeleton is made in the laboratory

    Stork and Clarke reported the total synthesis of cedrol and cedrene. This short communication turned the assigned framework into a synthetic target that could be reached experimentally; its fuller stereochemical account followed in 1961.2, 3

  3. 1961

    Stereochemistry through chemical correlation

    The detailed cedrol study established stereochemistry through synthesis and chemical relationships. Its absolute-configuration argument used a cedrol-derived cedrene isomer, conversion to norcedranone, and the product’s Cotton effect—evidence obtained through transformations and optical measurements.3

  4. 2026

    Cedrene itself enters the crystal record

    Cedrene now reaches the crystal without a chemical change to the analyte. Paired with phenanthrene in cage 1a, its framework is resolved directly; a second measurement in chiral cage 1b strengthens absolute-configuration assignment. The published study reports the unmodified molecule’s first crystal structure.4

WHY THIS STRUCTURE MATTERS

Chemical correlations and synthesis had established cedrene’s structure. The 2026 measurements add direct crystallographic evidence for the unmodified hydrocarbon and strengthen its absolute-configuration assignment using a chiral host.

References

  1. G. Stork; R. Breslow. “The Structure of Cedrene.” J. Am. Chem. Soc. 1953, 75, 3291. DOI 10.1021/ja01109a524 ↗
  2. G. Stork; F. H. Clarke, Jr. “The Total Synthesis of Cedrol and Cedrene.” J. Am. Chem. Soc. 1955, 77, 1072–1073. DOI 10.1021/ja01609a104 ↗
  3. G. Stork; F. H. Clarke, Jr. “Cedrol: Stereochemistry and Total Synthesis.” J. Am. Chem. Soc. 1961, 83, 3114–3125. DOI 10.1021/ja01475a030 ↗
  4. W. He; L. Soliman; H. Takezawa; M. Fujita. “Expanding the Chemical Space of Analytes in the 2G Crystalline Sponge Method: Size-Compensation Strategy for the Structural Analysis of Low-Polarity Small Molecules.” Angew. Chem. Int. Ed. 2026, e4748505. DOI 10.1002/anie.4748505 ↗

Crystal records in this study

HostModulatorCCDCSI table
Standard cage 1aPhenanthrene 2a2565727S2

SOURCE PUBLICATION

Expanding the Chemical Space of Analytes in the 2G Crystalline Sponge Method: Size-Compensation Strategy for the Structural Analysis of Low-Polarity Small Molecules

W. He, L. Soliman, H. Takezawa, M. Fujita

Angew. Chem. Int. Ed. 2026, e4748505.

First published: 20 October 2026 · Early View

DOI 10.1002/anie.4748505 ↗

Enhanced absolute-configuration determination

The known absolute configuration of the chiral diamine ligand at each Pd center of the cage serves as an internal stereochemical reference for comparison with the guest. Introducing chirality into the host framework also improves absolute-structure discrimination by anomalous scattering, as assessed by the Flack parameter below.

Chiral cage 1b · CCDC 2565758 ↗

Flack x = 0.080(8) (Parsons; CIF)

(−)-Cedrene · Chiral cage 1b · Measured guest structure
Measured guest structure
(−)-Cedrene · Chiral cage 1b · Host–guest structure
Host–guest structure