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New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 13383

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Special Issue Editors

Prof. Dr. Ioannis P. Gerothanassis

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Guest Editor

Department of Chemistry, Panepistimion Ioanninon, Ioannina, Greece
Interests: NMR spectroscopy; natural products

Prof. Dr. Teobald Kupka

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Guest Editor

Institute of Chemistry, University of Opole, 48, Oleska Street, 45-052 Opole, Poland
Interests: nuclear magnetic shielding tensor; GIAO NMR; indirect spin-spin coupling constants; ZPV corrections to nuclear magnetic shielding; temperature correction (TC); solvent effect; relativistic corrections (RC); bioactive compounds; natural products
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Special Issue Information

Dear Colleagues,

NMR spectroscopy has played a central role in the development of several research fields in chemistry, biology and material sciences, by providing information at an atomic resolution. This Special Issue will provide a platform for publishing original research papers, short communications, feature articles and reviews in the following contemporary applications of NMR:

Advanced NMR techniques in solution;
Hyperpolarized NMR techniques;
Solid-state NMR techniques;
New tools for processing complex NMR data;
NMR techniques and current trends in the analysis of complex mixtures;
NMR hyphenated techniques;
NMR high-throughput screening applications;
Applications of residual dipolar couplings to structural determination;
NMR structures of proteins, nucleic acids and carbohydrates;
NMR studies of ligand–biomolecular interactions;
Membrane proteins and lipids;
Biomolecular dynamics;
Paramagnetic NMR;
Quantum chemical calculations of NMR parameters for structure determination (nuclear magnetic shielding tensor, GIAO NMR, indirect spin-spin coupling constants, ZPV corrections to nuclear magnetic shielding, temperature correction, solvent effect, relativistic corrections);
NMR metabolomics and foodomics;
NMR repositories for structure elucidation;
Data mining and computer-assisted structural elucidation;
In-cell NMR.

Prof. Dr. Ioannis P. Gerothanassis
Prof. Dr. Teobald Kupka
Guest Editors

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Keywords

NMR spectroscopy
NMR pulse sequences
hyperpolarized NMR
metabolomics
high-throughput methods
hyphenated techniques
quantum chemical calculations of NMR parameters for structure determination
nuclear magnetic shielding tensor
GIAO NMR
indirect spin-spin coupling constants
in-cell NMR

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Published Papers (9 papers)

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Research

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24 pages, 4125 KiB

Open AccessArticle

Can Graph Machines Accurately Estimate ¹³C NMR Chemical Shifts of Benzenic Compounds?

by François Duprat, Jean-Luc Ploix and Gérard Dreyfus

Molecules 2024, 29(13), 3137; https://doi.org/10.3390/molecules29133137 - 1 Jul 2024

Viewed by 1472

Abstract

In the organic laboratory, the ¹³C nuclear magnetic resonance (NMR) spectrum of a newly synthesized compound remains an essential step in elucidating its structure. For the chemist, the interpretation of such a spectrum, which is a set of chemical-shift values, is made easier if he/she has a tool capable of predicting with sufficient accuracy the carbon-shift values from the structure he/she intends to prepare. As there are few open-source methods for accurately estimating this property, we applied our graph-machine approach to build models capable of predicting the chemical shifts of carbons. For this study, we focused on benzene compounds, building an optimized model derived from training a database of 10,577 chemical shifts originating from 2026 structures that contain up to ten types of non-carbon atoms, namely H, O, N, S, P, Si, and halogens. It provides a training root-mean-squared relative error (RMSRE) of 0.5%, i.e., a root-mean-squared error (RMSE) of 0.6 ppm, and a mean absolute error (MAE) of 0.4 ppm for estimating the chemical shifts of the 10k carbons. The predictive capability of the graph-machine model is also compared with that of three commercial packages on a dataset of 171 original benzenic structures (1012 chemical shifts). The graph-machine model proves to be very efficient in predicting chemical shifts, with an RMSE of 0.9 ppm, and compares favorably with the RMSEs of 3.4, 1.8, and 1.9 ppm computed with the ChemDraw v. 23.1.1.3, ACD v. 11.01, and MestReNova v. 15.0.1-35756 packages respectively. Finally, a Docker-based tool is proposed to predict the carbon chemical shifts of benzenic compounds solely from their SMILES codes. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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18 pages, 3448 KiB

Open AccessArticle

Spectral Assignment in the [3 + 2] Cycloadditions of Methyl (2E)-3-(Acridin-4-yl)-prop-2-enoate and 4-[(E)-2-Phenylethenyl]acridin with Unstable Nitrile N-Oxides

by Lucia Ungvarská Maľučká and Mária Vilková

Molecules 2024, 29(12), 2756; https://doi.org/10.3390/molecules29122756 - 9 Jun 2024

Viewed by 721

Abstract

The investigation of cycloaddition reactions involving acridine-based dipolarophiles revealed distinct regioselectivity patterns influenced mainly by the electronic factor. Specifically, the reactions of methyl-(2E)-3-(acridin-4-yl)-prop-2-enoate and 4-[(1E)-2-phenylethenyl]acridine with unstable benzonitrile N-oxides were studied. For methyl-(2E)-3-(acridin-4-yl)-prop-2-enoate, the formation of two regioisomers favoured the 5-(acridin-4-yl)-4,5-dihydro-1,2-oxazole-4-carboxylates, with remarkable exclusivity in the case of 4-methoxybenzonitrile oxide. Conversely, 4-[(1E)-2-phenylethenyl]acridine displayed reversed regioselectivity, favouring products 4-[3-(substituted phenyl)-5-phenyl-4,5-dihydro-1,2-oxazol-4-yl]acridine. Subsequent hydrolysis of isolated methyl 5-(acridin-4-yl)-3-phenyl-4,5-dihydro-1,2-oxazole-4-carboxylates resulted in the production of carboxylic acids, with nearly complete conversion. During NMR measurements of carboxylic acids in CDCl₃, decarboxylation was observed, indicating the formation of a new prochiral carbon centre C-4, further confirmed by a noticeable colour change. Overall, this investigation provides valuable insights into regioselectivity in cycloaddition reactions and subsequent transformations, suggesting potential applications across diverse scientific domains. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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16 pages, 2858 KiB

Open AccessArticle

Metabolic Characteristics and Discriminative Diagnosis of Growth Hormone Deficiency and Idiopathic Short Stature in Preadolescents and Adolescents

by Yajie Chang, Jing Chen, Hongwei Zhu, Rong Huang, Jinxia Wu, Yanyan Lin, Quanquan Li, Guiping Shen and Jianghua Feng

Molecules 2024, 29(7), 1661; https://doi.org/10.3390/molecules29071661 - 7 Apr 2024

Viewed by 1016

Abstract

Growth hormone deficiency (GHD) and idiopathic short stature (ISS) are the most common types of short stature (SS), but little is known about their pathogenesis, and even less is known about the study of adolescent SS. In this study, nuclear magnetic resonance (NMR)-based metabolomic analysis combined with least absolute shrinkage and selection operator (LASSO) were performed to identify the biomarkers of different types of SS (including 94 preadolescent GHD (PAG), 61 preadolescent ISS (PAI), 43 adolescent GHD (ADG), and 19 adolescent ISS (ADI)), and the receiver operating characteristic curve (ROC) was further used to evaluate the predictive power of potential biomarkers. The results showed that fourteen, eleven, nine, and fifteen metabolites were identified as the potential biomarkers of PAG, PAI, ADG, and ADI compared with their corresponding controls, respectively. The disturbed metabolic pathways in preadolescent SS were mainly carbohydrate metabolism and lipid metabolism, while disorders of amino acid metabolism played an important role in adolescent SS. The combination of aspartate, ethanolamine, phosphocholine, and trimethylamine was screened out to identify PAI from PAG, and alanine, histidine, isobutyrate, methanol, and phosphocholine gave a high classification accuracy for ADI and ADC. The differences in metabolic characteristics between GHD and ISS in preadolescents and adolescents will contribute to the development of individualized clinical treatments in short stature. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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20 pages, 5089 KiB

Open AccessArticle

A Versatile Broadband Attached Proton Test Experiment for Routine ¹³C Nuclear Magnetic Resonance Spectroscopy

by Peter Bigler, Ilche Gjuroski, Dib Chakif and Julien Furrer

Molecules 2024, 29(4), 809; https://doi.org/10.3390/molecules29040809 - 9 Feb 2024

Viewed by 950

Abstract

The proposed broadband attached proton test sequence allows the user to easily record ¹³C nuclear magnetic resonance multiplicity-edited and quaternary-carbon-only spectra. Compared to earlier attached proton test experiments, it preserves both a tolerance for wide ranges of one-bond-coupling constant values and the effective suppression of residual CHn signals in the quaternary-carbon-only spectra. The recording of edited spectra or quaternary-carbon-only spectra is made easy by a single, user-controllable constant. These attributes make the broadband attached proton test experiment attractive for the ¹³C analysis of small molecules, including spectral editing, particularly in high-throughput analysis laboratories. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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11 pages, 1198 KiB

Open AccessArticle

Molecular Melodies: Unraveling the Hidden Harmonies of NMR Spectroscopy

by Iria Pérez Varela, Gavin Shear and Carlos Cobas

Molecules 2024, 29(4), 762; https://doi.org/10.3390/molecules29040762 - 7 Feb 2024

Viewed by 1274

Abstract

This work explores the evolution of auditory analysis in NMR spectroscopy, tracing its journey from a supplementary tool to visual methods such as oscilloscopes, to a technique sidelined due to technological advancements. Despite its renaissance in the late 1990s with artistic and scientific applications, widespread adoption was hindered by the necessity for hardware modifications and reliance on specialized software. Addressing these barriers, this paper introduces a new feature in Mnova NMR software that facilitates the easy auditory interpretation of NMR signals. We discuss new applications of this tool, emphasizing its utility in aiding the identification of specific functional groups by auditory analysis of the spectrum’s multiplets, such as distinguishing between aromatic, olefinic, or aliphatic protons, thereby enriching the interpretative capabilities of NMR data. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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16 pages, 6589 KiB

Open AccessArticle

The Synergy between Nuclear Magnetic Resonance and Density Functional Theory Calculations

by Poul Erik Hansen

Molecules 2024, 29(2), 336; https://doi.org/10.3390/molecules29020336 - 9 Jan 2024

Cited by 1 | Viewed by 1270

Abstract

This paper deals with the synergy between Nuclear Magnetic Resonance (NMR) spectroscopic investigations and DFT calculations, mainly of NMR parameters. Both the liquid and the solid states are discussed here. This text is a mix of published results supplemented with new findings. This paper deals with examples in which useful results could not have been obtained without combining NMR measurements and DFT calculations. Examples of such cases are tautomeric systems in which NMR data are calculated for the tautomers; hydrogen-bonded systems in which better XH bond lengths can be determined; cage compounds for which assignment cannot be made based on NMR data alone; revison of already published structures; ionic compounds for which reference data are not available; assignment of solid-state spectra and crystal forms; and the creation of libraries for biological molecules. In addition to these literature cases, a revision of a cage structure and substituent effects on pyrroles is also discussed. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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16 pages, 3142 KiB

Open AccessArticle

Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT Calculations—Comparison with the Liquid State

by Themistoklis Venianakis, Michael G. Siskos, George Papamokos and Ioannis P. Gerothanassis

Molecules 2023, 28(16), 6144; https://doi.org/10.3390/molecules28166144 - 20 Aug 2023

Cited by 4 | Viewed by 1262

Abstract

Molecular structures, in chloroform and DMSO solution, of the free fatty acids (FFAs) caproleic acid, oleic acid, α-linolenic acid, eicosapentanoic acid (EPA) and docosahexaenoic acid (DHA) are reported with the combined use of NMR and DFT calculations. Variable temperature and concentration chemical shifts of the COOH protons, transient 1D NOE experiments and DFT calculations demonstrate the major contribution of low molecular weight aggregates of dimerized fatty acids through intermolecular hydrogen bond interactions of the carboxylic groups, with parallel and antiparallel interdigitated structures even at the low concentration of 20 mM in CDCl₃. For the dimeric DHA, a structural model of an intermolecular hydrogen bond through carboxylic groups and an intermolecular hydrogen bond between the carboxylic group of one molecule and the ω-3 double bond of a second molecule is shown to play a role. In DMSO-d₆ solution, NMR and DFT studies show that the carboxylic groups form strong intermolecular hydrogen bond interactions with a single discrete solvation molecule of DMSO. These solvation species form parallel and antiparallel interdigitated structures of low molecular weight, as in chloroform solution. This structural motif, therefore, is an intrinsic property of the FFAs, which is not strongly affected by the length and degree of unsaturation of the chain and the hydrogen bond ability of the solvent. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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17 pages, 3935 KiB

Open AccessArticle

Molecular Basis for the Selectivity of DHA and EPA in Sudlow’s Drug Binding Sites in Human Serum Albumin with the Combined Use of NMR and Docking Calculations

by Eleni Alexandri, Themistoklis Venianakis, Alexandra Primikyri, Georgios Papamokos and Ioannis P. Gerothanassis

Molecules 2023, 28(9), 3724; https://doi.org/10.3390/molecules28093724 - 26 Apr 2023

Cited by 8 | Viewed by 2030

Abstract

Medium- and long-chain saturated and unsaturated free fatty acids (FFAs) are known to bind to human serum albumin (HSA), the main plasma carrier protein. Atomic-level structural data regarding the binding mode in Sudlow’s sites I (FA7) and II (FA4, FA3) of the polyunsaturated ω-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), however, are largely unknown. Herein, we report the combined use of saturation transfer difference (STD) and Interligand NOEs for Pharmacophore Mapping (INPHARMA) NMR techniques and molecular docking calculations to investigate the binding mode of DHA and EPA in Sudlow’s sites Ι and ΙΙ of HSA. The docking calculations and the significant number of interligand NOEs between DHA and EPA and the drugs warfarin and ibuprofen, which are stereotypical ligands for Sudlow’s sites I and II, respectively, were interpreted in terms of competitive binding modes and the presence of two orientations of DHA and EPA at the binding sites FA7 and FA4. The exceptional flexibility of the long-chain DHA and EPA and the formation of strongly folded structural motives are the key properties of HSA–PUFA complexes. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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Review

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23 pages, 1247 KiB

Open AccessReview

On the Use of Deuterated Organic Solvents without TMS to Report ¹H/¹³C NMR Spectral Data of Organic Compounds: Current State of the Method, Its Pitfalls and Benefits, and Related Issues

by Ryszard B. Nazarski

Molecules 2023, 28(11), 4369; https://doi.org/10.3390/molecules28114369 - 26 May 2023

Cited by 2 | Viewed by 2134

Abstract

The quite popular, simple but imperfect method of referencing NMR spectra to residual ¹H and ¹³C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δ_H and δ_C values that exist in the literature. Taking into account the most reliable data, it was possible to recommend ‘best’ δ_X values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual ¹H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl₃). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δ_X values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δ_C reported for CDCl₃, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two ‘instrumental’ schemes in which Method A is often implicitly applied, that is, the default Method C using ²H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for ¹H/¹³C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δ_X data applied for the reference ¹H/¹³C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases. Full article

(This article belongs to the Special Issue New Insights into Nuclear Magnetic Resonance (NMR) Spectroscopy)

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