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NMR Spectroscopy in Natural Product Structure Elucidation

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (31 October 2019) | Viewed by 20856

Special Issue Editor


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Guest Editor
Department of Organic Chemistry, University of Vienna, Vienna, Austria
Interests: NMR-Spectroscopy; computer-assisted structure elucidation; spectrum prediction; software development; structure verification

Special Issue Information

Dear Colleagues,

NMR-Spectroscopy is the most important technique used in the process of structure elucidation of organic natural products. The tremendous development of sophisticated 1D and 2D-pulse techniques over the past three decades allows deep insights into the constitution, configuration, and conformation of complex organic molecules on a routine basis. The earlier bottleneck of low sensitivity and long measuring times resulting thereof has been eliminated by cryo-probes, higher field strengths, and fast acquisition techniques. In parallel, the availability of sample changers has also dramatically increased the amount of experimental data. The bottleneck nowadays can be found in the interpretation of the measured spectra despite the fact that sophisticated spectrum prediction and structure verification software is around.

The aim of this Special Issue is to highlight the recent advances in the combined application of sophisticated NMR-techniques together with computer-assisted structure elucidation tools to actual challenges in the field of organic natural products. The authors are invited to make use of programs of their choice performing, e.g., spectrum prediction, structure verification, and isomer generation applied to their structure elucidation problems based on high-level NMR-techniques. In order to accelerate the reviewing process of the original research manuscripts, all authors are encouraged on a volunteer basis to use the “CSEARCH-Robot-Referee” (https://nmrpredict.orc.univie.ac.at/molecules/robot.php) as well as the “13C Spectral Similarity Search” (https://nmrpredict.orc.univie.ac.at/molecules/eval.php). The resulting reports should be attached as SIs to the manuscript; furthermore, the experimental raw NMR-data can be also deposited using the NMReData-format, which is already supported by many software-vendors (see http://nmredata.org/).

Prof. Dr. Wolfgang Robien
Guest Editor

Manuscript Submission Information

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Keywords

  • New natural products
  • Structure elucidation
  • NMR-spectroscopy
  • Computer-assisted structure elucidation
  • Spectrum prediction
  • Isomer generation
  • Structure verification
  • Combined application of NMR-spectroscopy and software tools

Published Papers (5 papers)

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Research

25 pages, 4581 KiB  
Article
Conformational Investigations in Flexible Molecules Using Orientational NMR Constraints in Combination with 3J-Couplings and NOE Distances
by Christophe Farès, Julia B. Lingnau, Cornelia Wirtz and Ulrich Sternberg
Molecules 2019, 24(23), 4417; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24234417 - 03 Dec 2019
Cited by 11 | Viewed by 4586
Abstract
The downscaling of NMR tensorial interactions, such as dipolar couplings, from tens of kilohertz to a few hertz in low-order media is the result of dynamics spanning several orders of magnitudes, including vibrational modes (~ns-fs), whole-molecule reorientation (~ns) and higher barrier internal conformational [...] Read more.
The downscaling of NMR tensorial interactions, such as dipolar couplings, from tens of kilohertz to a few hertz in low-order media is the result of dynamics spanning several orders of magnitudes, including vibrational modes (~ns-fs), whole-molecule reorientation (~ns) and higher barrier internal conformational exchange (<ms). In this work, we propose to employ these dynamically averaged interactions to drive an “alignment-tensor-free” molecular dynamic simulation with orientation constraints (MDOC) in order to efficiently access the conformational space sampled by flexible small molecules such as natural products. Key to this approach is the application of tensorial pseudo-force restraints which simultaneously guide the overall reorientation and conformational fluctuations based on defined memory function over the running trajectory. With the molecular mechanics force-field, which includes bond polarization theory (BPT), and complemented with other available NMR parameters such as NOEs and scalar J-couplings, MDOC efficiently arrives at dynamic ensembles that reproduce the entire NMR dataset with exquisite accuracy and theoretically reveal the systems conformational space and equilibrium. The method as well as its potential towards configurational elucidation is presented on diastereomeric pairs of flexible molecules: a small 1,4-diketone 1 with a single rotatable bond as well as a 24-ring macrolide related to the natural product mandelalide A 2. Full article
(This article belongs to the Special Issue NMR Spectroscopy in Natural Product Structure Elucidation)
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24 pages, 4747 KiB  
Article
Yuccalechins A–C from the Yucca schidigera Roezl ex Ortgies Bark: Elucidation of the Relative and Absolute Configurations of Three New Spirobiflavonoids and Their Cholinesterase Inhibitory Activities
by Łukasz Pecio, Mostafa Alilou, Solomiia Kozachok, Ilkay Erdogan Orhan, Gokcen Eren, Fatma Sezer Senol Deniz, Hermann Stuppner and Wiesław Oleszek
Molecules 2019, 24(22), 4162; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24224162 - 16 Nov 2019
Cited by 9 | Viewed by 3731
Abstract
The ethyl acetate fraction of the methanolic extract of Yucca schidigera Roezl ex Ortgies bark exhibited moderate acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory activity (IC50 47.44 and 47.40 µg mL−1, respectively). Gel filtration on Sephadex LH-20 and further RP-C18 [...] Read more.
The ethyl acetate fraction of the methanolic extract of Yucca schidigera Roezl ex Ortgies bark exhibited moderate acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory activity (IC50 47.44 and 47.40 µg mL−1, respectively). Gel filtration on Sephadex LH-20 and further RP-C18 preparative HPLC of EtOAc fraction afforded 15 known and 3 new compounds, stereoisomers of larixinol. The structures of the isolated spirobiflavonoids 15, 26, and 29 were elucidated using 1D and 2D NMR and MS spectroscopic techniques. The relative configuration of isolated compounds was assigned based on coupling constants and ROESY (rotating-frame Overhauser spectroscopy) correlations along with applying the DP4+ probability method in case of ambiguous chiral centers. Determination of absolute configuration was performed by comparing calculated electronic circular dichroism (ECD) spectra with experimental ones. Compounds 26 and 29, obtained in sufficient amounts, were evaluated for activities against AChE and BChE, and they showed a weak inhibition only towards AChE (IC50 294.18 µM for 26, and 655.18 µM for 29). Furthermore, molecular docking simulations were performed to investigate the possible binding modes of 26 and 29 with AChE. Full article
(This article belongs to the Special Issue NMR Spectroscopy in Natural Product Structure Elucidation)
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12 pages, 1853 KiB  
Article
Characterization of Eight Novel Spiroleptosphols from Fusarium avenaceum
by Klaus Ringsborg Westphal, Manuela Ilse Helga Werner, Katrine Amalie Hamborg Nielsen, Jens Laurids Sørensen, Valery Andrushchenko, Jacob Winde, Morten Hertz, Mikkel Astrup Jensen, Mathilde Lauge Mortensen, Petr Bouř, Teis Esben Sondergaard and Reinhard Wimmer
Molecules 2019, 24(19), 3498; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24193498 - 26 Sep 2019
Cited by 5 | Viewed by 3060
Abstract
Chemical analyses of Fusarium avenaceum grown on banana medium resulted in eight novel spiroleptosphols, T1, T2 and U–Z (18). The structures were elucidated by a combination of high-resolution mass spectrometric data and 1- and 2-D NMR experiments. The relative [...] Read more.
Chemical analyses of Fusarium avenaceum grown on banana medium resulted in eight novel spiroleptosphols, T1, T2 and U–Z (18). The structures were elucidated by a combination of high-resolution mass spectrometric data and 1- and 2-D NMR experiments. The relative stereochemistry was assigned by 1H coupling and NOESY/ROESY experiments. Absolute stereochemistry established for 7 by vibrational circular dichroism was found analogous to that of the putative polyketide spiroleptosphol from Leptosphaeria doliolum. Full article
(This article belongs to the Special Issue NMR Spectroscopy in Natural Product Structure Elucidation)
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11 pages, 746 KiB  
Article
Phytochemical Study of Aerial Parts of Leea asiatica
by Hyun Woo Kil, Taewoong Rho and Kee Dong Yoon
Molecules 2019, 24(9), 1733; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24091733 - 04 May 2019
Cited by 25 | Viewed by 3313
Abstract
Leea asiatica (L.) Ridsdale (Leeaceae) is found in tropical and subtropical countries and has historically been used as a traditional medicine in local healthcare systems. Although L. asiatica extracts have been found to possess anthelmintic and antioxidant-related nephroprotective and hepatoprotective effects, [...] Read more.
Leea asiatica (L.) Ridsdale (Leeaceae) is found in tropical and subtropical countries and has historically been used as a traditional medicine in local healthcare systems. Although L. asiatica extracts have been found to possess anthelmintic and antioxidant-related nephroprotective and hepatoprotective effects, little attention has been paid toward the investigation of phytochemical constituents of this plant. In the current study, phytochemical analysis of isolates from L. asiatica led to the identification of 24 compounds, including a novel phenolic glucoside, seven triterpenoids, eight flavonoids, two phenolic glycosides, four diglycosidic compounds, and two miscellaneous compounds. The phytochemical structures of the isolates from L. asiatica were elucidated using spectroscopic analyses including 1D- and 2D-NMR and ESI-Q-TOF-MS. The presence of triterpenoids and flavonoids supports the evidence for anthelmintic and antioxidative effects of L. asiatica. Full article
(This article belongs to the Special Issue NMR Spectroscopy in Natural Product Structure Elucidation)
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9 pages, 571 KiB  
Article
DP4-Assisted Structure Elucidation of Isodemethylchodatin, a New Norlichexanthone Derivative Meager in H-Atoms, from the Lichen Parmotrema tsavoense
by Thuc-Huy Duong, Mehdi A. Beniddir, Joël Boustie, Kim-Phi-Phung Nguyen, Warinthorn Chavasiri, Guillaume Bernadat and Pierre Le Pogam
Molecules 2019, 24(8), 1527; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24081527 - 18 Apr 2019
Cited by 6 | Viewed by 3312
Abstract
A phytochemical investigation of the foliose lichen Parmotrema tsavoense (Krog and Swinscow) Krog and Swinscow (Parmeliaceae) resulted in the isolation of a new trichlorinated xanthone, isodemethylchodatin. The structure elucidation of this new norlichexanthone derivative proved tricky owing to proton deficiency, and to the [...] Read more.
A phytochemical investigation of the foliose lichen Parmotrema tsavoense (Krog and Swinscow) Krog and Swinscow (Parmeliaceae) resulted in the isolation of a new trichlorinated xanthone, isodemethylchodatin. The structure elucidation of this new norlichexanthone derivative proved tricky owing to proton deficiency, and to the lack of NMR data of closely related analogues. The structure of this compound was determined based on an integrated interpretation of 13C-NMR chemical shifts, MS spectra, and DP4-based computational chemistry was also performed to provide an independent and unambiguous validation of the determined structure. Isodemethylchodatin represents the first chlorinated lichexanthone/norlichexanthone derivative bearing a methoxy group at C-5. Full article
(This article belongs to the Special Issue NMR Spectroscopy in Natural Product Structure Elucidation)
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