The efficiency of ACD/Structure Elucidator has been confirmed over the years by solving a great number of real world problems (almost 1000) related mainly to the structure determination of new natural products. Over 100 examples are presented in this Elucidation of the Month blog.
Trichopsistide A
Using the traditional method of structure elucidation based on analysis of HSQC, HMBC and COSY data, the authors deduced a large part of the molecular structure, but the lack of carbons bearing hydrogen atoms prevented them to assemble the full structure. To alleviate this problem, ACD/Structure Elucidator was utilized in Trichopsistide A, molecular formula C23H29NO5.
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Dichocetide D
Shaker et al. recently reported the isolation of Dichocetide D from the marine fungus Dichotomomyces cejpii under oxygen stress conditions. The structure of Dichocetide D was revised by Elyashberg et al on the basis of chemical considerations and utilization of ACD/Structure Elucidator.
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Vagiallene
E. Ioannou et al have developed an integrated metabolomic platform for the identification of known compounds and detection of new metabolites at the early stages of phytochemical analysis. Vagiallene was isolated through a series of chromatographic separations, molecular formula C15H15Br2O5.
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Spiroaxillarone A
Spirobisnaphthalenes are a relatively new and rare family of secondary metabolites. Their core structure usually consists of two bicyclo[4.4.0]decane units, connected with one another through at least one spiro center. The reported compound is a novel symmetric spirobisnaphthalene with a unique structural feature. Spiroaxillarone A, molecular formula C19H12O6.
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Chloraserrtone A Structure Elucidation
Chloraserrtone A, a new sesquiterpenoid dimer with two lindenane-type sesquiterpenoid monomers bridged by two six-membered rings, was isolated from Chloranthus serratus by Bai et al. It represents the first lindenane-type sesquiterpenoid dimer with an extremely unique skeleton, molecular formula C3H36O9.
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Synthetic product C14H13N3O Structure Elucidation
An unexpected synthetic product coming from Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) in Berlin, from the lab of Dr. Marc Nazaré. The dataset was provided to ACD/Labs as part of our Structure Elucidation Suite Challenge. The product was isolated after a reaction and it was found by HR-MS to have a molecular formula of C14H13N3O.
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Penerpene A Structure Elucidation
The Penicillium sp. KFS28 fungus was isolated from a bivalve mollusk, Meretrix Lusoria, from the Haikou Bay in China. The EtOAc extract of the fermentation broth was processed by the authors who isolated and identified four new paxilline-type indole-terpenoids. Compound 1 has the molecular formula C28H35NO6.
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Ent-Kaurane-Type Diterpenoid Structure Elucidation
Yaouba et al reported the isolation and phytochemical investigation of the constituents of Aspilia pluriseta Schweinf and Aspilia mossambicensis. They isolated, identified and comprehensively investigated compound 1, molecular formula C21H30O3.
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Neosetophomone A Structure Elucidation
El-Elimat et al reported five new and one known meroterpenoids, including the discovery of a novel ioxa[4.3.3]propellane metabolite neosetophomone A that incorporates a 3-methyl-2,3-dihydrofuran bridge into a 5,6 tricyclic 2-hydroxycyclopent-2-en-1-one/tetrahydropyran ring system, molecular formula C24H32O5.
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5α-Cyprinol Structure Elucidation
5α-cyprinol sulfate was isolated from a methanolic extract of fish bile (Cyprinus carpio) after separation by preparative LC. The molecular mass and the presence of a sulfate group were revealed by ESI–MS/MS in the negative mode, and the molecular formula of the compound was determined as C27H48O8S.
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Cycloshermilamine D Structure Elucidation
Investigation of Cystodytes resulted in the isolation of five pyridoacridines, including shermilamines D and E. The structure of another compound, cycloshermilamine D, also isolated from the same tunicate in minute amounts (0.4% of the crude extract) was determined by Koren-Goldshlager et al, molecular formula C21H16N4OS.
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Oroidin Structure Elucidation
Oroidin (C11H10Br2N4O) is a highly proton-deficient bromopyrrole isolated from the sponge Agelas oroides. A CASE solution to this problem was chosen for testing the capability of DFT based NMR chemical shift prediction to distinguish the correct structure when empirical prediction methods fail to suggest the structure reliably.
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Uncarilin A
In the search for novel MT receptor agonists from natural sources, Geng at al used LC-MS to study U. rhynchophylla,, resulting in the isolation of two pairs of dimeric isoechinulin-type enantiomers, (±)-uncarilin A and (±)-uncarilin B. Here we discuss the structure elucidation of uncarilin A (molecular formula C38H42N6O4).
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Matsutakone – Pleurocin A
The ethyl acetate layer of T. matsutake was fractionated and purified by repeated chromatographic methods to yield the white powder matsutakone, molecular formula C28H44O4. The structure of Structure of matsutakone was elucidated from its molecular formula and 1D and 2D NMR data shown in Table 1, which were used by us for challenging ACD/Structure Elucidator.
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Emodacidamide A
During screenings for new secondary metabolites from fungi originating from the South China Sea, Luo and co-workers isolated 10 anthraquinone compounds, including eight new anthraquinones regarded as emodacidamides A−H. Structures of these compounds were elucidated, and the NMR data utilized for the structure elucidation of emodacidamide A (molecular formula C21H19NO8) were used by us to challenge ACD/Structure Elucidator.
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Abyssomicin W
Wang et al. reported the discovery of 12 new analogs of abyssomicin as metabolites of the Streptomyces species. Amongst them Abyssomicin W (molecular formula C20H26O8) has an 8/6/6/6 tetracyclic core. Spectroscopic data of this compound were used to challenge ACD/Structure Elucidator Suite.
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Trichoderpyrone
Chen et al have been looking for novel secondary metabolites from Trichoderma gamsii, a plant endophytic fungus. As a result of this a new polyketide trichoderpyrone (molecular formula C15H17NO5), containing a unique cyclopentenone−pyrone hybrid skeleton was isolated and its structure was determined by detailed analysis of NMR data.
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Spiroschincarin A
Song et al investigated the chemical constituents of the fruit of S. incarnata. They isolated five novel spirocyclic compounds, spiroschincarins A−E, featuring a unique 1-oxaspiro[6.6]tridecane moiety. Their structures, with absolute configurations, were determined by extensive spectroscopic studies. The structure elucidation of spiroschincarin A (molecular formula C31H38O11) from NMR data was used for challenging ACD/Structure Elucidator.
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Sophaline C
Y.-B. Zhang and co-workers reported four novel matrine-based alkaloids, sophalines A-D. Their structures were elucidated using spectroscopic methods and single-crystal X-ray diffraction. We used the Spectroscopic data for Sophaline C (molecular formula C21H26N2O2) to challenge Structure Elucidator.
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4-Bromobenzoic-biscognienyne A
4-Bromobenzoic-biscognienyne A (molecular formula C23H25O4Br) is relatively simple but its elucidation was chosen as a demonstrated approach, using ACD/Structure Elucidator, in situations where several equiprobable user assumptions (“axioms”) should be checked to determine the right structure.
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Alistonitrine A
Monoterpene Indole Alkaloids (MIAs) are found in Alstonia scholaris R. Br. (Apocynaceae) which originates in South Asia. People in the area have been using the bark and leaves as traditional medicines. Zhu and co-workers successfully isolated a new MIA, Alistonitrine A (molecular formula C21H25N3O3), which possesses an unprecedented caged monoterpene indole skeleton.
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Euphorikanin A
Fei and co-workers4 isolated Euphorikanin A (molecular formula C20H26O3), a structurally novel diterpenoid lactone with an unprecedented carbon skeleton featuring a unique tetradecahydrobenzo[cd]-cyclopropa[f ]azulene. Its structure was determined by spectroscopic methods and confirmed by single crystal X-ray analysis.
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Ciliatonoid A
Structures of ciliatonoids A-C, complete with absolute stereochemistry, were characterized by spectroscopic data, X-ray crystallography, and electronic circular dichroism (ECD) analysis. To challenge ACD/Structure Elucidator Suite, Ciliatonoid A (molecular formula C26H32O5) was used. It featured an unprecedented limonoid architecture by way of a very unique cis-fused central motif (in red).
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Pepluacetal
Wan et al isolated and identified three highly modified and biogenetically related diterpenoids including Pepluacetal (molecular formula C22H32O4), which has a novel unprecedented fused-ring skeleton containing cyclopentane and cyclobutane rings which rarely occur in natural compounds.
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Flueggether A
H. Zhang et al observed interesting signals from very minor constituents from F. virosa in their MS analysis. A further fractionation of the fractions returned two extra new alkaloids, one of which, Flueggether A(molecular formula C25H30N2O5), is the first example of Securinega alkaloid oligomers which features an ether bond linkage.
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Astellifadiene
The authors reported the production and structure characterization of the novel sesterterpene Astellifadiene. Analysis of the 1H-1H COSY, HMBC, and NOESY correlations established the planar structure as an unprecedented 6-8-6-5-membered tetracyclic ring system. The use of NMR analyses combined with the crystalline sponge method facilitated the unambiguous determination of the Astellifadiene structure (molecular formula C25H40).
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Mannolide A
Ni et al investigated Cephalotaxus mannii Hook f. which led to the isolation of three new diterpenoids, namely, mannolides A−C, and two new Cephalotaxus troponoids. We used the example of Mannolide A (molecular formula C20H24O5) to challenge our ACD/Structure Elucidator Suite software.
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Sarglaperoxide A
From investigating the constituents of Sarcandra glabra, P. Wang et al isolated a pair of structurally-related terpene lactones, sarglaperoxides A and B. The original experimental data related to Sarglaperoxide A (molecular formula C23H28O5) were used to challenge ACD/Structure Elucidator Suite and determine if the software could reliably elucidate this novel structure.
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Teotihuacanin
Bautista et al reinvestigated the chemical composition of S. amarissima. As a result, Teotihuacanin (molecular formula C20H20O6), an unusual rearranged clerodane diterpene with a new carbon skeleton containing a spiro-10/6 bicyclic system, was isolated from the leaves and flowers of Salvia amarissima.
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Flueggether A
H. Zhang et al observed interesting signals from very minor constituents from F. virosa in their MS analysis. A further fractionation of the fractions showing the interesting MS peaks returned two extra new alkaloids, one of which, Flueggether A (molecular formula C25H30N2O5) is the first example of Securinega alkaloid oligomers which features an ether bond linkage.
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