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Trichoderpyrone Structure Elucidation

July 1, 2017
by Mikhail Elyashberg, Leading Researcher, ACD/Labs


A large number of gene clusters is known to exist in filamentous fungi. These are responsible for producing many structurally diverse secondary metabolite compounds. These include polyketides (PKs), non-ribosomal peptides (NRPs), polyketides and non-ribosomal peptides hybrids (PK-NRPs), terpenes and indole-alkaloids. Chen et al [1] have been looking for novel secondary metabolites from Trichoderma gamsii, a plant endophytic fungus. As a result of this a new polyketide trichoderpyrone, (1) containing a unique cyclopentenone−pyrone hybrid skeleton was isolated and its structure was determined by detailed analysis of NMR data (1H, 13C, HSQC, COSY and HMBC).


Trichoderpyrone (1) was isolated as an orange colored oil, and its molecular formula was determined using HR-ESI-MS to be C15H17NO5. Structure 1 was confirmed by comparison with structures and chemical shifts of known compounds shown in Figure 1.

Figure 1. Trichoderpyrone.  Comparison of 13C NMR chemical shift values of 1 with those of other compounds containing similar fragments.

The NMR spectroscopic data presented in [1] are summarized in Table 1. These were entered into ACD/Structure Elucidator.

Table 1. Trichoderpyrone NMR spectroscopic data.

C/X Label δC δCcalc* XHn δH H to C HMBC
C 1 165.8 168.67 C
C 2 105 106.09 C
C 3 167.1 166.11 C
C 4 102.4 103.15 CH 5.92 C 2, C 3, C 5
C 5 159.5 160.28 C
C 6 19.4 19.67 CH3 2.11 C 3, C 4, C 5
C 7 15.7 19.87 CH3 1.32 C 2, C 8, C 9
C 8 22.6 26.97 CH 4.1 C 1, C 2, C 3, C 9, C
10, C 13
C 9 111.5 108.34 C
C 10 202.1 206.33 C
C 11 76.8 74.78 C
C 12 42.8 39.74 CH2 2.5 C 9, C 10, C 11, C 13, C
C 12 42.8 39.74 CH2 2.67
C 13 172.5 173.99 C
C 14 140.8 139.56 CH 5.77
C 15 113.1 111.97 CH2 5.04
C 15 113.1 111.97 CH2 5.22
N 1 NH2 8.08 C 9
N 1 NH2 7.39
O 1 OH 13.16 C 3
O 2 O
O 3 OH 5.41 C 10, C 11, C 12, C 14

*13C NMR chemical shift prediction was performed using HOSE code based approach.

The Molecular Connectivity Diagram (MCD) created by the program is shown in Figure 2.

Figure 2. Trichoderpyrone Molecular Connectivity Diagram. Carbon atoms hybridized as sp3 and sp2 were marked by dark blue and pink colors respectively. Other hybridizations are marked by a light blue color. Labels ob and fb denote the possibility of heteroatom neighboring for a given carbon atom: ob – obligatory, fb – forbidden.  HMBC connectivities are denoted by green arrows and all are assumed to be 2-3 bonds.

No MCD edits were made. Checking MCD for consistency of HMBC data showed that no contradictions were detected and so Strict Structure Generation was initiated. No structures were generated during this, which can happen when there are Non-Standard Correlations (NSC’s) of more than 3 bonds that were not entered as such and not detected by the MCD checking procedure. Therefore Structure Generation was run again using the Fuzzy Structure Generation option, then followed by 13C chemical shift prediction and structure filtering (a threshold for average chemical shift deviations of calculated chemical shifts from the experimental ones was set at 5 ppm). This delivered the following result: k=1014 → 3 → 1, tg =10 s. The program reported that one connectivity has been extended during generation. The single structure suggested by the program, along with average chemical shift deviations, is shown in Figure 3.

Figure 3. The structure of trichoderpyrone suggested by ACD/Structure Elucidator.  Carbon chemical shift prediction was performed using Incremental, Neural Networks and Hierarchical Organization of Spherical Environments (HOSE) based code. Average chemical shift deviations of predicted chemical shifts from experimental ones dI(13C), dN(13C) and dA(13C),  along with a maximum deviation max_dA(13C), are shown.

We see that the structure, which was automatically elucidated fully, coincides with the structure 1 while the chemical shifts are the same as those assigned by the authors [1]. Values of average deviations are in the limits typical for best structures distinguished by the ranking procedure used in ACD/Structure Elucidator[2].  A red arrow denotes the HMBC correlation of 4 bond lengths discovered by the program during Fuzzy Structure Generation. Inspection of the HMBC spectrum available from the Supporting Information of [1] (Figure 4) shows a very weak peak for this correlation (in a red circle) which agrees with it originating from a 4-bond correlation.

Figure 4. Trichoderpyrone. Part of the HMBC spectrum published in SI of [1].

In conclusion the structure of a new polyketide trichoderpyrone, with an unusual hybrid skeleton, was elucidated in just 10 seconds using only the NMR data published.


  1. L. Chen, S.-B. Niu, L. Li,  G. Ding, M. Yu, G.-s. Zhang, M.-h. Wang, L.-y. Li, T. Zhang, H.-M. Jia, H.-w. Zhang, H. Shang, X.-z. Liu, Z.-m. Zou. Trichoderpyrone, a Unique Polyketide Hybrid with a Cyclopentenone−Pyrone Skeleton from the Plant Endophytic Fungus Trichoderma gamsii.J. Nat. Prod., ASAP, DOI: 10.1021/acs.jnatprod.7b00190
  2. M.E. Elyashberg, A.J. Williams. (2015). Computer-based Structure Elucidation from Spectral Data (p. 454). Springer-Verlag Berlin, Heidelberg.

For more hands-on experience in the methods of Computer-Assisted Structure Elucidation, using ACD/Structure Elucidator, we recommend the textbook Computer–Based Structure Elucidation from Spectral Data from Springer, by M.E. Elyashberg and A.J. Williams.

The special version of ACD/Structure Elucidator and 100 problems (in electronic format) which were discussed in the book are available at

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