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Afzeliindanone Structure Elucidation

August 15, 2022
by Mikhail Elyashberg, Leading Researcher, ACD/Labs


The shrub Uvaria afzelii Scot Elliot, grows in the Wes African sub-region, and belongs to the Annonaceae family. It has long be used for traditional medicines. It has been reported that there is antibacterial activity in the ethanolic extract of its stems. Several compounds were isolated from this extract.

Okpekon et al [1] isolated an unusual new indanone, named afzeliindanone 1.


It was the first 1-indanone derivative isolated from a plant. Its structure was determined  using 1D and 2D NMR spectra (HSQC, HMBC and COSY) and confirmed by NOESY correlations. However recently Rita et al [2] synthesized the proposed structure of afzeliindanone using the steps shown in Figure 1.

Figure 1. Synthesis of the proposed structure of afzeliindanone.

There were significant differences observed between the 1H NMR and 13C NMR spectra of the synthetic material and those reported for the natural prioduct. The signals associated with the CH2CH2 moiety and the methoxy group were in good agreement, but the correlation of the signals of the aromatic rings was poor. Therefore, it was concluded that structure 1 of the natural product had been misassigned. The true structure of afzeliindanone was determined just now in the work published by Elyashberg at al [3].

In this work, the molecular formula C16H14O3 and the NMR spectra presented by Okpekon et al [1] were entered into the ACD/Structure Elucidator (ACD/SE) program. The spectral data are presented in Table 1.

Table 1. NMR spectroscopic data of afzeliindanone obtained in work [1].

Label dC dC calc (HOSE) CHn dH 1H( M) COSY H to C HMBC
C 1 202.000 206.630 C
C 2 42.200 36.310 CH2 2.640 u 3.220 C 3, C 4, C 1
C 3 22.700 25.990 CH2 3.220 u C 2, C 9, C 10, C 4, C 1
C 4 137.900 149.790 C
C 5 131.100 137.490 C
C 6 125.400 131.680 CH 7.410 d 7.110 C 9, C 10
C 7 127.900 126.260 CH 7.110 u C 5, C 8
C 8 144.400 123.810 CH 7.090 u
C 9 126.200 135.250 C
C 10 130.000 131.180 C
C 11 102.700 113.640 CH 7.260 u C 5, C 4, C 13
C 12 148.100 146.450 C
C 13 146.800 144.710 C
C 14 110.300 114.610 CH 7.090 u 6.070 C 7, C 4, C 12, C 1
C 15 128.400 123.810 CH 6.070 d C 10
C 16 56.000 55.920 CH3 3.910 u C 12

Structure 1 together with 13C chemical shift assignments was entered into the program and 13C chemical shift prediction was performed using the three methods common for ACD/SE (incremental, neural networks and HOSE code based approaches). Figure 2 shows the results of these calculations.

Figure 2. Structure of afzeliindanone (1) proposed by Okpekon et al [1]. 13C chemical shift prediction was performed using the HOSE code-based method, neural networks, and the incremental approach. The average deviations of 13C chemical shifts determined by these methods  are denoted as dA, dN and dI correspondingly. Each atom is colored to mark a difference between its experimental and calculated 13C chemical shifts. The green color represents a difference between 0 to 3 ppm, yellow was >3 to 15 ppm, and red was >15 ppm. Red arrows indicate nonstandard HMBC correlations (NSC) – those whose lengths exceeds three chemical bonds (nJCH, n>3).
Figure 2 shows that the average and maximum deviations of calculated chemical shifts from the experimental ones are very large, which is evidence of inappropriateness of the structure proposed by the authors [1]. If the authors [1] had calculated the 13C chemical shits by at least one of the fast empirical methods implemented into ACD/SE they would had immediately realized that the structure is wrong. In addition, to suggest structure 1, it was necessary to allow for three NSCs of four bond length in the HMBC spectrum (see Figure 2), something rather unlikely for such a structure.

To  determine the true structure of afzeliindanone the common funtions of ACD/SE were utilized. Using the data presented in Table 1, the Molecular Connectivity Diagram (MCD) was created (see Figure 3).

Figure 3. Molecular connectivity diagram (MCD) of afzeliindanone.  Hybridizations of carbon atoms are marked by corresponding colors: sp2 – violet, sp3 – blue. Labels “ob” and “fb” are set by the program to carbon atoms for which neighboring with heteroatom is either obligatory (ob) or forbidden (fb).  HMBC connectivities are marked by green arrows, while COSY connectivities – with blue ones. Ambiguous connectivities are marked by dotted lines.

MCD analysis was performed which indicated absence of any contradictions in the 2D NMR data. Therefore, Strict Structure Generation followed by 13C chemical shift prediction by the incremental approach and artificial neural networks was initiated. All produced structures were filtered through the spectral and structural filter standard in ACD/SE. Results: k=25 → (filtering) → 3 → (removal of duplicates) → 3, tg = 1 s, where k is number of structures, tg – processor time.

The output structural file ranked in descending order of average deviations is shown in Figure 4.

Figure 4. The output file ranked in descending order of δA(13C) values.

We see that structure #1 is characterized by minimum deviations and should be declared as the most probable structure. Its validity is confirmed by DP4 probabilities calculated for all three methods of 13C chemical shift prediction. The proposed structure 1 could not be generated because it contains three NSC HMBC correlations (see Figure 2).

To further support structure #1 as the top solution and reject 1, Fuzzy Structure Generation (FSG) was run using options which allowed for the presence of three NSCs. Results: k=63,139 → (structure filtering) → 1,016 → (duplicate removal) → 363, tg = 9 min. It turned out that structure #1 was again obtained as the first ranked structure, while 1 was at the 113th(!) position in the file ranked by dN(13C) values.

According to the methodology suggested in [4], a final confirmation of the best structure was performed in article [3] by DFT-based  calculations of 13C chemical shifts both for structures 1 and #1. The DFT option  DU8+ was used for this.  The calculations gave the following results:

Structure #1: RMSD = 1.19 ppm, MAE = 0.89 ppm.

Structure 1: RMSD =5.92 ppm, MAE = 5.26 ppm.

Thus, the correct structure of afzeliindanone was unambiguously determined by the combined application of CASE and DFT methods of NMR chemical shift prediction.

The correct structure with assigned 13C chemical shifts is shown below.


  1. T. Okpekon, M. Millot, P. Champy, C. Gleye, S. Yolou, C. Bories, P. Loiseau, Laurens, R. Hocquemille. (2009). A novel 1-indanone isolated from Uvaria afzelii roots. Nat. Prod. Res., 23(10), 909–915. 10.1080/14786410802497240
  2. R. Rita, M. H. bin Abdul Rahman, S. S. M. Chong, R. W. Bates. (2020). Synthesis of the Proposed Structure of Afzeliindanone, Synlett, 31, 1479–1481. 10.1055/s-0040-1707470
  3. M. Elyashberg, I. M. Novitskiy, R. W Bates, A. G. Kutateladze, C. M. Williams. (2022). Reassignment of Improbable Natural Products Identified through Chemical Principle Screening. European J. Org. Chem., e202200572,
  4. A.V. Buevich, M. E. Elyashberg. (2018). Towards unbiased and more versatile NMR-based structure elucidation: A powerful combination of CASE algorithms and DFT calculations. Magn. Reson. Chem., 56, 493–504.

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