ACD/Structure Elucidator Featured Solution

For more than a decade, ACD/Structure Elucidator has been used by industry and academic experts to help solve some of the toughest structure problems. Using data from various analytical techniques (NMR, MS, UV, and IR) Structure Elucidator can propose chemical structures that are consistent with ALL available analytical data. The computer-assisted structure elucidation (CASE) software is used time and time again to help solve unknown structures and to correct erroneous proposed structures.

Read on to see our featured story highlighting the use of Structure Elucidator and be sure to return to this page every month where we will highlight a new compound of interest.

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The Initial Challenge (or click each heading to read in sections)

Botryococcus braunii is a colonial green microalga that is known for producing various types of hydrocarbons and other types of oils. In a 1998 publication, Okada and co-workers1 isolated and identified two new carotenoids in their efforts to better understand the relationship between colony color and hydrocarbon production (color being a key element to distinguish different types of colonies).

The Evidence

  • The molecular formula of α-botryoxanthin A was determined to be C74H112O2
  • The following data were acquired:
    • 1D 1H NMR and 13C NMR
    • 2D 1H-1H COSY (4 correlations), 1H-13C HMBC (224 correlations)

The CASE (Computer Assisted Structure Elucidation) Investigation



The Molecular Connectivity Diagram produced by Structure Elucidator
  • ACD/Structure Elucidator produced a Molecular Connectivity Diagram (MCD) from the experimental data.
  • A built-in algorithm, specifically designed to check the consistency of all the experimental data, reported one issue with a non-standard connectivity.
  • The reported issues enabled the software to run the elucidation in Fuzzy Generation mode with parameters m=1 (the number of connectivities with non-standard lengths) and a=1 (the connectivity augmentation).2
  • Applying all possible combinations of connectivities, the Fuzzy Generation mode generated two candidate structures in less than 6 hours. Structure 1 ranked in the first position based on the lower dA value; the average deviation (dA) is a comparison between the experimental and predicted chemical shifts.
  • If the single NSC was corrected by hand, it was unnecessary to use the Fuzzy Generation mode, and the software generated a single structure in less than 1 second.


  • Structure 1
  • Structure 1 matches the structure published by the original authors who solved it by traditional means.

Conclusions

For this example, Fuzzy Generation mode is successfully applied to solve for a large molecule (> 1000 Da) with a large number of NMR connectivities. The Fuzzy Generation mode offers the user the capability to automatically scrutinize NMR data and provide a solution which is not available with other CASE systems. ACD/Structure Elucidator is a complete elucidation package offering tools to speed up the elucidation process and ensure that no candidate is overlooked.

1S. Okada, I.Tonegawa, H. Matsuda, M.Murakami, K. Yamaguchi Phytochem., 47:1111–1115, 1998.
2Mikhail E. Elyashberg, Kirill A. Blinov, Sergey G. Molodtsov, Antony J. Williams, and Gary E. Martin J. Chem. Inf. Model., 47 (3):1053–1066, 2007.