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Lin Q, Meng C, Liu J, Liu F, Zhou Q, Liu J, Peng C, Xiong L. An Optimized Two-Dimensional Quantitative Nuclear Magnetic Resonance Strategy for the Rapid Quantitation of Diester-Type C 19-Diterpenoid Alkaloids from Aconitum carmichaelii. Anal Chem 2023. [PMID: 37209123 DOI: 10.1021/acs.analchem.2c05109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
With the development of nuclear magnetic resonance (NMR) spectrometers and probes, two-dimensional quantitative nuclear magnetic resonance (2D qNMR) technology with a high signal resolution and great application potential has become increasingly accessible for the quantitation of complex mixtures. However, the requirement that the relaxation recovery time be equal to at least five times T1 (longitudinal relaxation time) makes it difficult for 2D qNMR to simultaneously achieve high quantitative accuracy and high data acquisition efficiency. By comprehensively using relaxation optimization and nonuniform sampling, we successfully established an optimized 2D qNMR strategy for HSQC experiments at the half-hour level and then accurately quantified the diester-type C19-diterpenoid alkaloids in Aconitum carmichaelii. The optimized strategy had the advantages of high efficiency, high accuracy, good reproducibility, and low cost and thus could serve as a reference to optimize 2D qNMR experiments for quantitative analysis of natural products, metabolites, and other complex mixtures.
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Affiliation(s)
- Qiao Lin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Chunwang Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jie Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Fei Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qinmei Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Juan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Liang Xiong
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Innovative Medicine Ingredients of Southwest Specialty Medicinal Materials, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Hyberts SG, Wagner G. High fidelity sampling schedules for NMR spectra of high dynamic range. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 339:107228. [PMID: 35550910 PMCID: PMC10675079 DOI: 10.1016/j.jmr.2022.107228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
The ability to reconstruct non-uniformly sampled (NUS) NMR spectra has mostly been accepted. Still a concern is lingering regarding artifacts from sampling non-uniformly. As experienced, some sampling schedules yield better results than others. Finding a useful schedule is relatively trivial for a low dynamic range spectrum and a conservative sparsity, but not so when the dynamic range is large and/or when extreme sparsity is used. High dynamic range is typically found in NOESY and spectra of metabolites, where quantification of peak heights is desired at high fidelity. Extreme sparsity is desired when high throughput is a goal. In all cases, selecting a poor sampling schedule can create unnecessary artifacts. Effectively, it is important to select a sampling schedule that provides a signal-to-artifact apex ratio (SAAR) value in par or better than the signal-to-noise ratio (SNR) value. Notably, by signal-to-artifact apex ratio we consider reconstruction fidelity as the apex intensity likeness, i.e., as the true signal to the tallest artifact. We show that the quality of reconstruction depends on the particular sampling schedule. We evaluate the reconstruction quality in the frequency domain following a matched Lorentz-to-Gauss transform plus common apodization and Fourier Transform. As the Lorentz-to-Gauss transform improves resolution and reduces ridges we include this when defining the Signal-to-Artifact Apex Ratio (SAAR) metric. This metric measures the ratio of simulated reconstructed peak height to the tallest artifact of reconstruction in a spectrum without noise. Once a NUS schedule is found with an optimal SAAR it will be satisfactory for all spectra recorded with the same parameter set. Tables with good seed values are provided in the supplement.
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Affiliation(s)
- Sven G Hyberts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
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Speciale I, Notaro A, Garcia-Vello P, Di Lorenzo F, Armiento S, Molinaro A, Marchetti R, Silipo A, De Castro C. Liquid-state NMR spectroscopy for complex carbohydrate structural analysis: A hitchhiker's guide. Carbohydr Polym 2022; 277:118885. [PMID: 34893288 DOI: 10.1016/j.carbpol.2021.118885] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 11/19/2022]
Abstract
Structural determination of carbohydrates is mostly performed by liquid-state NMR, and it is a demanding task because the NMR signals of these biomolecules explore a rather narrow range of chemical shifts, with the result that the resonances of each monosaccharide unit heavily overlap with those of others, thus muddling their punctual identification. However, the full attribution of the NMR chemical shifts brings great advantages: it discloses the nature of the constituents, the way they are interconnected, in some cases their absolute configuration, and it paves the way to other and more sophisticated analyses. The purpose of this review is to provide a practical guide into this challenging subject. It will drive through the strategy used to assign the NMR data, pinpointing the core information disclosed from each NMR experiment, and suggesting useful tricks for their interpretation, along with other resources pivotal during the study of these biomolecules.
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Affiliation(s)
- Immacolata Speciale
- Department of Agricultural Sciences, University of Naples, 80055 Portici, Italy.
| | - Anna Notaro
- Department of Agricultural Sciences, University of Naples, 80055 Portici, Italy.
| | - Pilar Garcia-Vello
- Department of Chemical Sciences, University of Naples, 80126 Naples, Italy.
| | - Flaviana Di Lorenzo
- Department of Agricultural Sciences, University of Naples, 80055 Portici, Italy.
| | - Samantha Armiento
- Department of Chemical Sciences, University of Naples, 80126 Naples, Italy.
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples, 80126 Naples, Italy.
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples, 80126 Naples, Italy.
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples, 80126 Naples, Italy.
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Naples, 80055 Portici, Italy.
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Pustovalova Y, Delaglio F, Craft D, Arthanari H, Bax A, Billeter M, Bostock M, Dashti H, Hansen D, Hyberts S, Johnson B, Kazimierczuk K, Lu H, Maciejewski M, Miljenović T, Mobli M, Nietlispach D, Orekhov V, Powers R, Qu X, Robson S, Rovnyak D, Wagner G, Ying J, Zambrello M, Hoch J, Donoho D, Schuyler A. NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:843-861. [PMID: 37905225 PMCID: PMC10583271 DOI: 10.5194/mr-2-843-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/10/2021] [Indexed: 11/02/2023]
Abstract
Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago , it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., "resolution") or peaks of weak intensity (i.e., "sensitivity"). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the "Nonuniform Sampling Contest" (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.
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Affiliation(s)
- Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - D. Levi Craft
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin Billeter
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, Gothenburg 405 30, Sweden
| | - Mark J. Bostock
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Hesam Dashti
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - D. Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Sven G. Hyberts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce A. Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Hengfa Lu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China
| | - Mark Maciejewski
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Tomas M. Miljenović
- Centre for Advanced Imaging, The University of Queensland, 4072 St Lucia, Queensland, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, 4072 St Lucia, Queensland, Australia
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, Gothenburg 405 30, Sweden
| | - Robert Powers
- Department of Chemistry and Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Xiaobo Qu
- Department of Electronic Science, Biomedical Intelligent Cloud R&D Center, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Scott Anthony Robson
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - David Rovnyak
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Zambrello
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - David L. Donoho
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Adam D. Schuyler
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
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Namyslo JC, Drafz MHH, Kaufmann DE. Durable Modification of Wood by Benzoylation-Proof of Covalent Bonding by Solution State NMR and DOSY NMR Quick-Test. Polymers (Basel) 2021; 13:2164. [PMID: 34208957 PMCID: PMC8271922 DOI: 10.3390/polym13132164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
A convenient, broadly applicable and durable wood protection was recently published by Kaufmann and Namyslo. This procedure efficiently allows for esterification of wood hydroxyl groups with (1H-benzotriazolyl)-activated functionalized benzoic acids. The result of such wood-modifying reactions is usually monitored by an increase in mass of the wood material (weight percent gain value, WPG) and by infrared spectroscopy (IR). However, diagnostic IR bands suffer from overlap with naturally occurring ester groups, mainly in the hemicellulose part of unmodified wood. In contrast to known NMR spectroscopy approaches that use the non-commonly available solid state techniques, herein we present solution state NMR proof of the covalent attachment of our organic precursors to wood. The finding is based on a time-efficient, non-uniformly sampled (NUS) solution state 1H,13C-HMBC experiment that only needs a tenth of the regular recording time. The appropriate NMR sample of thoroughly dissolved modified wood was prepared by a mild and non-destructive method. The 2D-HMBC shows a specific cross-signal caused by spin-spin coupling over three bonds from the ester carbonyl carbon atom to the α-protons of the esterified wood hydroxyl groups. This specific coupling pathway requires a covalent bonding as a conditio sine qua non. An even more rapid test to monitor the covalent bonding was achieved with an up-to-date diffusion-ordered spectroscopy sequence (Oneshot-DOSY) based on 1H or 19F as the sensitive nucleus. The control experiment in a series of DOSY spectra gave a by far higher D value of (1.22 ± 0.06)∙10-10 m2∙s-1, which is in accordance with fast diffusion of the "free" and thus rapidly moving small precursor molecule provided as its methyl ester. In the case of a covalent attachment to wood, a significantly smaller D value of (0.12 ± 0.01)∙10-10 m2∙s-1 was obtained.
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Affiliation(s)
| | | | - Dieter E. Kaufmann
- Institute of Organic Chemistry, Clausthal University of Technology, Leibnizstr. 6, 38678 Clausthal-Zellerfeld, Germany; (J.C.N.); (M.H.H.D.)
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