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Application of Nuclear Magnetic Resonance (NMR) Spectroscopy in Bioorganic Chemistry
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Application of Nuclear Magnetic Resonance (NMR) Spectroscopy in Bioorganic Chemistry

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 30 July 2024 | Viewed by 2026

Special Issue Editor

Prof. Dr. Cristina Airoldi

E-Mail Website
Guest Editor
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
Interests: ligand–receptor interaction studies; metabolomics; natural products; amyloid protein inhibition; anti-virulence compounds, anti-tumour compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nuclear magnetic resonance (NMR) spectroscopy is one of the techniques of choice employed by bioorganic chemists. Indeed, it finds application in the study of the structure and conformation of bioorganic molecules and their molecular interactions. Notably, it can be used for the characterization of both large and small biomolecules, as well as for the structural resolution of large supramolecular complexes. Furthermore, its intrinsically quantitative nature can be exploited to determine the purity of the organic molecules present in a sample, as well as for the identification and quantification of metabolites present in complex mixtures, such as biofluids, cells, tissues and natural extracts. Finally, NMR spectroscopy makes it possible to elucidate the mechanisms of organic reactions, also monitoring them in real time, including those involving enzymatic catalysis.

Original research articles and review papers elucidating how NMR spectroscopy can provide new insights and/or original methodological approaches to the study of bioorganic chemistry are very welcome from outstanding experts of the topic. 

Prof. Dr. Cristina Airoldi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular recognition
  • ligand–receptor interaction studies
  • structural and conformational studies of bioorganic molecules and bioconjugates
  • natural and synthetic bioactive compounds
  • reaction monitoring and reaction mechanism elucidation
  • NMR-based metabolomics
  • qNMR (quantitative NMR) of bioorganic compounds

Published Papers (3 papers)

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Research

23 pages, 15079 KiB  
Article
Optoelectronic Response to the Fluor Ion Bond on 4-(4,4,5,5-Tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde
by Ulises J. Guevara, Jesús Núñez, Laura M. Pérez, Anton Tiutiunnyk, Neudo Urdaneta, Eduardo Cisternas and David Laroze
Int. J. Mol. Sci. 2024, 25(9), 5000; https://doi.org/10.3390/ijms25095000 - 03 May 2024
Viewed by 198
Abstract
Boronate esters are a class of compounds containing a boron atom bonded to two oxygen atoms in an ester group, often being used as precursors in the synthesis of other materials. The characterization of the structure and properties of esters is usually carried [...] Read more.
Boronate esters are a class of compounds containing a boron atom bonded to two oxygen atoms in an ester group, often being used as precursors in the synthesis of other materials. The characterization of the structure and properties of esters is usually carried out by UV-visible, infrared, and nuclear magnetic resonance (NMR) spectroscopic techniques. With the aim to better understand our experimental data, in this article, the density functional theory (DFT) is used to analyze the UV-visible and infrared spectra, as well as the isotropic shielding and chemical shifts of the hydrogen atoms 1H, carbon 13C and boron 11B in the compound 4-(4,4,5,5-tetramethyl-1,3,2-dioxoborolan-2-yl)benzaldehyde. Furthermore, this study considers the change in its electronic and spectroscopic properties of this particular ester, when its boron atom is coordinated with a fluoride anion. The calculations were carried out using the LSDA and B3LYP functionals in Gaussian-16, and PBE in CASTEP. The results show that the B3LYP functional gives the best approximation to the experimental data. The formation of a coordinated covalent B–F bond highlights the remarkable sensitivity of the NMR chemical shifts of carbon, oxygen, and boron atoms and their surroundings. Furthermore, this bond also highlights the changes in the electron transitions bands n→π* and π→π* during the absorption and emission of a photon in the UV-vis, and in the stretching bands of the C=C bonds, and bending of BO2 in the infrared spectrum. This study not only contributes to the understanding of the properties of boronate esters but also provides important information on the interactions and responses optoelectronic of the compound when is bonded to a fluorine atom. Full article
(This article belongs to the Special Issue Application of Nuclear Magnetic Resonance (NMR) Spectroscopy in Bioorganic Chemistry)
19 pages, 3608 KiB  
Article
Differential Solvent DEEP-STD NMR and MD Simulations Enable the Determinants of the Molecular Recognition of Heparin Oligosaccharides by Antithrombin to Be Disentangled
by Michela Parafioriti, Stefano Elli, Juan C. Muñoz-García, Jonathan Ramírez-Cárdenas, Edwin A. Yates, Jesús Angulo and Marco Guerrini
Int. J. Mol. Sci. 2024, 25(9), 4669; https://doi.org/10.3390/ijms25094669 - 25 Apr 2024
Viewed by 437
Abstract
The interaction of heparin with antithrombin (AT) involves a specific sequence corresponding to the pentasaccharide GlcNAc/NS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA). Recent studies have revealed that two AGA*IA-containing hexasaccharides, which differ in the sulfation degree of the iduronic acid unit, exhibit similar binding to AT, albeit with [...] Read more.
The interaction of heparin with antithrombin (AT) involves a specific sequence corresponding to the pentasaccharide GlcNAc/NS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA). Recent studies have revealed that two AGA*IA-containing hexasaccharides, which differ in the sulfation degree of the iduronic acid unit, exhibit similar binding to AT, albeit with different affinities. However, the lack of experimental data concerning the molecular contacts between these ligands and the amino acids within the protein-binding site prevents a detailed description of the complexes. Differential epitope mapping (DEEP)-STD NMR, in combination with MD simulations, enables the experimental observation and comparison of two heparin pentasaccharides interacting with AT, revealing slightly different bound orientations and distinct affinities of both glycans for AT. We demonstrate the effectiveness of the differential solvent DEEP-STD NMR approach in determining the presence of polar residues in the recognition sites of glycosaminoglycan-binding proteins. Full article
(This article belongs to the Special Issue Application of Nuclear Magnetic Resonance (NMR) Spectroscopy in Bioorganic Chemistry)
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20 pages, 2716 KiB  
Article
Antarctic Soil Metabolomics: A Pilot Study
by Carlotta Ciaramelli, Alessandro Palmioli, Maura Brioschi, Simona Viglio, Maura D’Amato, Paolo Iadarola, Solveig Tosi, Laura Zucconi and Cristina Airoldi
Int. J. Mol. Sci. 2023, 24(15), 12340; https://doi.org/10.3390/ijms241512340 - 02 Aug 2023
Viewed by 1010
Abstract
In Antarctica, ice-free areas can be found along the coast, on mountain peaks, and in the McMurdo Dry Valleys, where microorganisms well-adapted to harsh conditions can survive and reproduce. Metabolic analyses can shed light on the survival mechanisms of Antarctic soil communities from [...] Read more.
In Antarctica, ice-free areas can be found along the coast, on mountain peaks, and in the McMurdo Dry Valleys, where microorganisms well-adapted to harsh conditions can survive and reproduce. Metabolic analyses can shed light on the survival mechanisms of Antarctic soil communities from both coastal sites, under different plant coverage stages, and inner sites where slow-growing or dormant microorganisms, low water availability, salt accumulation, and a limited number of primary producers make metabolomic profiling difficult. Here, we report, for the first time, an efficient protocol for the extraction and the metabolic profiling of Antarctic soils based on the combination of NMR spectroscopy and mass spectrometry (MS). This approach was set up on samples harvested along different localities of Victoria Land, in continental Antarctica, devoid of or covered by differently developed biological crusts. NMR allowed for the identification of thirty metabolites (mainly sugars, amino acids, and organic acids) and the quantification of just over twenty of them. UPLC-MS analysis identified more than twenty other metabolites, in particular flavonoids, medium- and long-chain fatty acids, benzoic acid derivatives, anthracenes, and quinones. Our results highlighted the complementarity of the two analytical techniques. Moreover, we demonstrated that their combined use represents the “gold standard” for the qualitative and quantitative analysis of little-explored samples, such as those collected from Antarctic soils. Full article
(This article belongs to the Special Issue Application of Nuclear Magnetic Resonance (NMR) Spectroscopy in Bioorganic Chemistry)
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