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Rhodimer Structure Elucidation

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Complete list of elucidations:

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.

Rhodimer
1

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

C/X Label δC δC сalc  (HOSE) XHn δH M H to C HMBC
C 1 78.600 79.100 CH 5.430 u C 11, C 10, C 9, C 3
C 2 43.700 43.230 CH2 2.840 u C 1, C 4, C 10, C 3
C 2 43.700 43.230 CH2 3.070 u  
C 3 196.300 198.540 C      
C 4 100.400 102.380 C      
C 5 159.300 160.170 C      
C 6 109.800 109.870 C      
C 7 162.800 163.720 C      
C 8 108.100 107.650 C      
C 9 157.600 159.150 C      
C 10 139.100 138.700 C      
C 11 125.900 125.760 CH 7.470 u C 1, C 12
C 12 128.700 128.340 CH 7.430 u C 10
C 13 128.500 128.770 CH 7.390 u C 11
C 14 21.800 22.440 CH2 3.180 u C 8, C 15, C 16, C 9, C 7
C 15 122.500 122.640 CH 5.150 u C 17, C 14, C 18
C 16 131.600 133.270 C      
C 17 17.800 17.930 CH3 1.570 u C 18, C 15, C 16
C 18 25.800 25.810 CH3 1.650 u C 17, C 15, C 16
C 19 75.400 76.740 CH 5.060 u C 21, C 29, C 28
C 20 36.900 31.850 CH2 2.180 u C 21, C 22, C 6, C 28
C 20 36.900 31.850 CH2 2.310 u  
C 21 26.800 26.760 CH 4.660 u C 20, C 19, C 22, C 6, C 27, C 23, C 5, C 7
C 22 102.800 108.690 C      
C 23 157.500 156.050 C      
C 24 88.400 93.470 CH 6.170 s C 32, C 21, C 22, C 26, C 23, C 25
C 25 158.600 157.160 C      
C 26 110.500 114.150 C      
C 27 154.300 154.790 C      
C 28 141.400 139.700 C      
C 29 126.000 126.920 CH 7.380 u C 19, C 30
C 30 128.300 127.250 CH 7.340 u C 28
C 31 127.600 127.850 CH 7.290 u C 29
C 32 21.900 22.820 CH2 3.350 u C 26, C 33, C 34, C 27, C 25
C 33 123.200 123.320 CH 5.240 u C 35, C 32, C 36
C 34 130.800 131.350 C      
C 35 17.800 17.870 CH3 1.660 s C 36, C 33, C 34
C 36 25.900 25.860 CH3 1.680 s C 35, C 33, C 34
C 37 55.900 56.490 CH3 3.730 s C 23
C 38 55.800 55.630 CH3 3.870 s C 25
O 1     OH 12.610 s C 4, C 6, C 5
O 2     OH 6.800 s C 8, C 6, C 7

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. 

Rhodimer
Figure 1. Molecular connectivity diagram (MCD)

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, tg = 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.

Rhodimer
Figure 2. Two top ranked structures of the output file. Green circles mark atoms for which D=|dexp - dclc| carbon chemical shift is between 0 and 3 ppm, yellow 3-15 ppm and red  > 15 ppm. The red arrows show nonstandard HMBC correlations (NSCs) whose lengths are of four chemical bonds that were defined during Fuzzy Structure Generation.

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.    

Rhodimer

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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.

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 www.acdlabs.com/TeachingSE.

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