Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems

Elyashberg, Mikhail E.; Williams, Antony J.; Blinov, Kirill A.

doi:10.1039/c002332a

Cited by 99 publications

(93 citation statements)

References 84 publications

(364 reference statements)

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“…Such a task can be performed, for example, by the newer version of CHEMDRAW program, initially aimed at chemical graphics. There are also more advanced specialized programs which search through large databases looking for molecular environments being the closest to the environment of a given atom whose chemical shift is to be predicted (28)(29)(30)(31)(32). In order to facilitate evaluation of similarity of substructures in an objective manner the special structure coding methods (e.g., HOSE code (33)) have been elaborated.…”

Section: Predicting Nmr Spectra Basing On Empirical Knowledgementioning

confidence: 99%

Theoretical modeling of ¹³C NMR chemical shifts—How to use the calculation results

Gryff‐Keller¹

2011

Concepts Magnetic Resonance

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Owing to wide accessibility of the general utility quantum chemistry programs, theoretical calculations of spectral parameters defining NMR spectra have become relatively easy for medium size molecules. This new and powerful tool allows investigators to perform much deeper interpretation of the NMR data and gain new information valuable for structural chemistry studies. It is usually realized and well understood that theoretical calculations of NMR parameters, as for any quantum mechanical calculations, have several limitations, difficult to overcome, and that the accuracy of calculation results is strongly dependent on the theoretical method applied. On the other hand, it is less commonly recognized that the effectiveness of all the combined calculational/spectroscopic approach depends meaningfully on the method of comparison of the experimental and theoretical data as well. This article is addressed primarily to experimental chemists who use in their everyday work 13 C NMR spectroscopy to solve various structural and physicochemical problems. After recalling some basic concepts concerning NMR parameters and their calculations, some suggestions concerning the rational choice of the calculational method and the experiment/theory comparison method are formulated. To support these recommendations and convince the reader of their utility, several practical examples are presented in the text. All these concepts reflect the author's beliefs which, albeit well-grounded, by no means should be treated as indispensable truths; they are rather worth considering as hints about how to solve various practical dilemmas.

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Section: Predicting Nmr Spectra Basing On Empirical Knowledgementioning

confidence: 99%

Theoretical modeling of ¹³C NMR chemical shifts—How to use the calculation results

Gryff‐Keller¹

2011

Concepts Magnetic Resonance

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“…The results of doing this were stark: in 0.06s only four possible structures were generated; the revised structure of acremolin was ranked highest, while the original structure (1) was not generated at all.…”

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confidence: 99%

The case for CASE

2015

Chemistry & Industry

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“…One among these is Logic Structure Determination (LSD) software. So far, previous studies have shown that LSD successfully elucidates flavonoid, alkaloid, and steroid compounds (Mulholland et al, 2006;Elyashberg et al, 2010;Hubert et al, 2015). However, none of those studies had been applied to cembranoid class.…”

Section: Introductionmentioning

confidence: 99%

“…This program aims to generate all possible structures that are consistent with a particular set of spectroscopic data with minimum amount of human intervention (Jaspars, 1999) as there are evidences of incorrect natural products structures in several publications (Elyashberg et al, 2010). Furthermore, CASE may serves as a solution for limited connectivity of 2D NMR information that may not be able to be solved through manual elucidation (Blinov et al, 2003a).…”

Section: Introductionmentioning

confidence: 99%

“…The correct structure can be selected among 2-4 possible structures by searching in the open natural products database, such as chemspider (http://www.chemspider.com) or NCBI (National Center for Biotechnology Information) database (https://pubchem.ncbi.nlm.nih.gov). Other studies have also shown that LSD may be applied on other types of compounds, such as flavonoid, steroids, and alkaloids (Mulholland et al, 2006;Elyashberg et al, 2010;Hubert et al, 2015), and that the application of LSD with direct 2 bond NMR experimental data is a reliable CASE technique to identify small molecule bioprospecting compounds in natural products studies. …”

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confidence: 99%

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Logic Structure Determination (LSD) as a Computer Assisted Structure Elucidation (Case) for Molecular Structure Determination of Cytotoxic Cembranoids from Soft Coral

Januar

Zamani

Soedharma

et al. 2016

Squalen Bull. Marine Fisheries Postharvest Biotech.

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Indonesian tropical soft corals are valuable resources that produce pharmacological cytotoxic cembranoids. However, the manual structure determination in these compounds requires adequate knowledge of organic chemistry. This study presents the application of Logic Structure Determination (LSD) as a freeware Computer Assisted Structure Elucidation (CASE) for automatic molecular structure determination of cembranoid compounds from soft corals species. 12 Nuclear Magnetic Resonance (NMR) datasets of cytotoxic cembranoids were used to evaluate the accuracy of LSD in generating the possible structures. The results of this study shows that LSD generated numerous possible molecular structures as the data input files were only derived from 2D-NMR HMQC (Heteronuclear MultipleQuantum Correlation), COSY (Homonuclear Correlation Spectroscopy), and HMBC (Heteronuclear Multiple Bond Correlation). The accuracy was significantly enhanced (only 2-4 possible cembranoid structures from each NMR dataset) with the addition of H2BC (Heteronuclear 2 Bond Correlation) experimental data. This may indicate that VLRC (Very Long-Range Correlations) significantly affects LSD capability. Furthermore, LSD with direct 2 bond NMR experimental data is a reliable CASE technique for cembranoid compounds identification. In general, this freeware-CASE has the potential to be applied on other types of small molecule compounds and may serves as a solution for elucidation bottleneck step in studies on Indonesian natural products.

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Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems

Cited by 99 publications

References 84 publications

Theoretical modeling of ¹³C NMR chemical shifts—How to use the calculation results

Theoretical modeling of ¹³C NMR chemical shifts—How to use the calculation results

The case for CASE

Logic Structure Determination (LSD) as a Computer Assisted Structure Elucidation (Case) for Molecular Structure Determination of Cytotoxic Cembranoids from Soft Coral

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Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems

Cited by 99 publications

References 84 publications

Theoretical modeling of 13C NMR chemical shifts—How to use the calculation results

Theoretical modeling of 13C NMR chemical shifts—How to use the calculation results

The case for CASE

Logic Structure Determination (LSD) as a Computer Assisted Structure Elucidation (Case) for Molecular Structure Determination of Cytotoxic Cembranoids from Soft Coral

Contact Info

Product

Resources

About

Theoretical modeling of ¹³C NMR chemical shifts—How to use the calculation results

Theoretical modeling of ¹³C NMR chemical shifts—How to use the calculation results