Rhodimer Structure Elucidation

July 22, 2021

by Mikhail Elyashberg, Leading Researcher, ACD/Labs

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Rhodimer

Atilaw et al [1] have been studying the roots of Tephrosia rhodesica, a member of the tropical and subtropical Tephrosia genus consisting of more than 400 species. A new variety of flavonoids has been found in them with promising biological activities (antiplasmodial). They isolated five new compounds including rhodimer 1. Its structure was determined by NMR spectroscopic, mass spectrometric, and single-crystal X-ray diffractometric analyses.

Compound 1 was isolated as white crystals from a CH₂Cl₂−CH₃OH (1:1) solution. Its molecular formula was determined as C₄₂H₄₄O₇ based on HR-EI-MS ([M]⁺ m/z 660.3095, calcd

660.3087) and NMR data analysis. The total number of heavy atoms in the molecule is 49, the RDBE value is equal to 21.

The 1D and 2D NMR spectroscopic data of compound 1 presented in [1] were used for challenging ACD/Structure Elucidator (ACD/SE).

Table 1. 1D and 2D NMR spectroscopic data of compound 1

The data presented in Table 1 were entered into ACD/SE and a Molecular Connectivity Diagram (MCD) was automatically created by the program. The slightly edited MCD is shown in  Figure 1.

MCD overview. The carbon atoms colored in magenta are set by the program  as sp² hybridized,  while the two light blue carbons CH 88.4 and C 100.40 can be of either sp² or sp³ hybridization. As the carbons C 159.3 and C 162.8 are connected to OH groups based on the observed HMBC correlations, a label “ob” was set for these atoms, which means that neighborhood with a heteroatom is obligatory. The evident carbonyl bond was manually drawn for carbon C 196.3.

The MCD was checked by the program for contradictions from the 2D NMR data and none was found. Fuzzy Structure Generation was initiated with the automatically set options. This means that an unknown number of NSCs (non-standard HMBC correlations) of unknown lengths are allowed. Structure  generation, followed by ¹³C chemical shift prediction using the incremental approach was initiated.

Results: k = 50 → (structural filtering) → 9 → (duplicate removing) → 9, t_g = 15 m. 2 (from 61) connectivities have been extended during generation.

After predicting the ¹³C chemical shifts using HOSE code based and neural networks approaches, all structures were ranked in ascending order of the average deviations of the experimental chemical shifts from the calculated ones. The two first structures of the ranked output file are presented in Figure 2.

The first ranked structure #1 is identical to compound 1 in [1]. This means that ACD/Structure Elucidator determined the structure of rhodimer correctly (and vice-versa!).  In the process of Fuzzy Structure Generation the program automatically detected the presence of two NSCs in HMBC data and determined their lengths and positions. The chemical shift prediction for structure #1 was performed with good accuracy as is see from the number of green atoms in structure #1. The validity of structure #1 was further confirmed by the calculation of an empirical DP4 probability which was found to be 100 for structure #1. The structure of the rhodimer together with the assigned ¹³C chemical shifts is shown below.

References

1. Y. Atilaw, L. Muiva-Mutisya, J. Bogaerts, S. Duffy, A. Valkonen, M. Heydenreich, V. M. Avery, K. Rissanen, M. Erdélyi, A. Yenesew. (2020). Prenylated Flavonoids from the Roots of Tephrosia rhodesica.J. Nat. Prod. 83: 2390−2398.

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