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Nawrocka EK, Jadwiszczak M, Leszczyński PJ, Kazimierczuk K. Supporting the assignment of NMR spectra with variable-temperature experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:479-485. [PMID: 38303612 DOI: 10.1002/mrc.5433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful tools in analytical chemistry. An important step in the analysis of NMR data is the assignment of resonance frequencies to the corresponding atoms in the molecule being investigated. The traditional approach considers the spectrum's characteristic parameters: chemical shift values, internuclear couplings, and peak intensities. In this paper, we show how to support the process of assigning a series of spectra of similar organic compounds by using temperature coefficients, that is, the rates of change in chemical shift values associated with given changes in temperature.
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Affiliation(s)
- Ewa K Nawrocka
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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Mailhiot S, Mankinen O, Li J, Kharbanda Y, Telkki VV, Urbańczyk M. CAT on MOUSE: Control and automation of temperature for single-sided NMR instruments such as NMR-MOUSE. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:252-258. [PMID: 37344254 DOI: 10.1002/mrc.5376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
Temperature-dependent experiments are a rapidly growing area of interest for low-field NMR. In this work, we present a new device for wide-range temperature control for single-sided NMR instruments. The presented device, called CAT, is simple to build, inexpensive, and easy to modify to accommodate different samples. We present the capabilities of the device using a freezing temperature study of acetic acid/water mixtures. Additionally, we present the stability of the device over long measurement times. We believe that by introducing such a device with an open-source design, we allow researchers to use it in a wide range of applications and to fully incorporate variable-temperature studies in the world of single-sided instruments.
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Affiliation(s)
| | - Otto Mankinen
- NMR Research Unit, University of Oulu, Oulu, Finland
| | - Jing Li
- NMR Research Unit, University of Oulu, Oulu, Finland
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, Gif-sur-Yvette, France
| | - Yashu Kharbanda
- NMR Research Unit, University of Oulu, Oulu, Finland
- Laboratoire Navier (Ecole des Ponts ParisTech-Université Gustave Eiffel), Champs-sur-Marne, France
| | | | - Mateusz Urbańczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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Romero JA, Kazimierczuk K, Kasprzak P. Optimizing measurements of linear changes of NMR signal parameters. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 360:107632. [PMID: 38382405 DOI: 10.1016/j.jmr.2024.107632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Serial NMR experiments are commonly applied in variable-temperature studies, reaction monitoring, and other tasks. The resonance frequencies often shift linearly over the series, and the shift rates help to characterize the studied system. They can be determined using a classical fitting of peak positions or a more advanced method of Radon transform. However, the optimal procedure for data collection remains to be determined. In this paper, we discuss how to invest experimental time, i.e., whether to measure more scans at the expense of the number of spectra or vice versa. The results indicate that classical fitting provides slightly less error than the Radon transform, although the latter can be the method of choice for a low signal-to-noise ratio. We demonstrate this fact through theoretical consideration, simulations, and an experiment. Finally, we extend our considerations to the linear fitting of peak amplitudes. Interestingly, the optimal setup for measuring peak height changes differs from the one for resonance frequency changes - fewer spectra with more scans provide better results.
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Affiliation(s)
- Javier Agustin Romero
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-097, Poland
| | | | - Paweł Kasprzak
- Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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Sahoo GR, Roy AS, Srivastava M. Time-Frequency Analysis of Two-Dimensional Electron Spin Resonance Signals. J Phys Chem A 2023; 127:7793-7801. [PMID: 37699569 PMCID: PMC10529365 DOI: 10.1021/acs.jpca.3c02708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Two-dimensional electron spin resonance (2D ESR) spectroscopy is a unique experimental technique for probing protein structure and dynamics, including processes that occur at the microsecond time scale. While it provides significant resolution enhancement over the one-dimensional experimental setup, spectral broadening and noise make extraction of spectral information highly challenging. Traditionally, two-dimensional Fourier transform (2D FT) is applied for the analysis of 2D ESR signals, although its efficiency is limited to stationary signals. In addition, it often fails to resolve overlapping peaks in 2D ESR. In this work, we propose a time-frequency analysis of 2D time-domain signals, which identifies all frequency peaks by decoupling a signal into its distinct constituent components via projection on the time-frequency plane. The method utilizes 2D undecimated discrete wavelet transform (2D UDWT) as an intermediate step in the analysis, followed by signal reconstruction and 2D FT. We have applied the method to a simulated 2D double quantum coherence (DQC) signal for validation and a set of experimental 2D ESR signals, demonstrating its efficiency in resolving overlapping peaks in the frequency domain, while displaying frequency evolution with time in case of non-stationary data.
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Affiliation(s)
- Gyana Ranjan Sahoo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Aritro Sinha Roy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- National Biomedical Resources for Advanced ESR Technologies (ACERT), Ithaca, New York 14853, United States
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- National Biomedical Resources for Advanced ESR Technologies (ACERT), Ithaca, New York 14853, United States
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Shchukina A, Schwarz TC, Nowakowski M, Konrat R, Kazimierczuk K. Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes. JOURNAL OF BIOMOLECULAR NMR 2023; 77:149-163. [PMID: 37237169 PMCID: PMC10406685 DOI: 10.1007/s10858-023-00418-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to "conventional" compressed sensing. We exemplify the concept of "difference CS" with one such case-the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.
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Affiliation(s)
- Alexandra Shchukina
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas C Schwarz
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
| | - Michał Nowakowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter Campus 5, 1030, Vienna, Austria
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Bruno F, Fiorucci L, Ravera E. Sensitivity considerations on denoising series of spectra by singular value decomposition. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:373-379. [PMID: 36840610 DOI: 10.1002/mrc.5338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 05/11/2023]
Abstract
When acquiring series of spectra ( T 1 , T 2 , CP buildup curves, etc.) on samples with poor SNR, we are usually faced with choosing between taking a few points with a large number of scans to maximize the SNR or more points with a smaller number of scans to maximize the information content. In this Letter, we show how low-rank decomposition can be used to denoise a series of spectra, reducing the trade-off between the number of scans and the number of experiments.
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Affiliation(s)
- Francesco Bruno
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
| | - Letizia Fiorucci
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
| | - Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, 50019, Italy
- Florence Data Science, University of Florence, Firenze, 50134, Italy
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Nawrocka EK, Urbańczyk M, Koziński K, Kazimierczuk K. Variable-temperature NMR spectroscopy for metabolite identification in biological materials. RSC Adv 2021; 11:35321-35325. [PMID: 35493175 PMCID: PMC9043013 DOI: 10.1039/d1ra05626c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/21/2021] [Indexed: 01/28/2023] Open
Abstract
Nuclear magnetic resonance is a "workhorse technique" used in metabolomics, complementary to mass spectrometry. Unfortunately, only the most basic NMR methods are sensitive enough to allow fast medical screening. The most common of them, a simple 1H NMR, suffers from low dispersion of resonance frequencies, which often hampers the identification of metabolites. In this article we show that 1H NMR spectra contain previously overlooked parameters potentially helpful in metabolite identification, namely the rates of temperature-induced changes of chemical shifts. We prove that they are reproducible between various metabolite mixtures and can be determined quickly when Radon transform is used to process the data.
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Affiliation(s)
- Ewa K Nawrocka
- Centre of New Technologies, University of Warsaw ul. Banacha 2C 02-097 Warsaw Poland
- Faculty of Chemistry, University of Warsaw ul. Pasteura 1 02-093 Warsaw Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw ul. Banacha 2C 02-097 Warsaw Poland
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Kamil Koziński
- Centre of New Technologies, University of Warsaw ul. Banacha 2C 02-097 Warsaw Poland
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