An integrated approach for mixture analysis using MS and NMR techniques

Kühn, Stefan; Colreavy‐Donnelly, Simon; Souza, Juliana Santana de; Borges, Ricardo Moreira

doi:10.1039/c8fd00227d

Cited by 26 publications

(40 citation statements)

References 22 publications

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“…Experimental validation of computational models can be accomplished through comparison with products detected using chemical analysis [172,173], for example by using integrated NMR and mass spectral approaches [174][175][176], which provide complementary information regarding chemical diversity and bonding. Van Krevelen diagrams are used by geochemists to characterize large sets of chemical species by plotting the atomic ratios of certain elements.…”

Section: Experimental Vetting Of the Computational Methodsmentioning

confidence: 99%

Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Sharma

Arya

Cruz

et al. 2021

Life

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Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models.

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Section: Experimental Vetting Of the Computational Methodsmentioning

confidence: 99%

Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Sharma

Arya

Cruz

et al. 2021

Life

View full text Add to dashboard Cite

show abstract

“…Both chemical shifts and J couplings can be computed and could be used in matching experimental data. Several types of NMR experiments can be used to measure homo- and heteronuclear scalar coupling constants through one or more bonds, 488 and if the data could be effectively used, then it could be more routinely measured in a metabolomics workflow. Currently, unknown identification of molecules perhaps relies too much on the chemical shift alone.…”

Section: Outlook For Role In Metabolomicsmentioning

confidence: 99%

Quantum Chemistry Calculations for Metabolomics

et al. 2021

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A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e. , in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

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“…A set of NMR and of MS n spectra constitute a better way to identify a known compound than a fusion temperature and an optical rotation value, even though the two latter may suffice to rule out an incorrect structure hypothesis. Dereplication by MS-based methods has earned a high level of interest with the advent of MS 2 -driven molecular network analysis [19,20]. Alternatively, a molecular (elemental) formula deduced from high-resolution MS (HRMS) associated to 1D and 2D NMR spectra may suffice to identify a known compound with a high level of confidence if reference data are available.…”

Section: Spectroscopymentioning

confidence: 99%

The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case

et al. 2021

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The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from Urceolina peruviana, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources.

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An integrated approach for mixture analysis using MS and NMR techniques

Abstract: We suggest an improved software pipeline for mixture analysis.

Cited by 26 publications

References 22 publications

Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Quantum Chemistry Calculations for Metabolomics

The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case

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