Pub Date : 2025-03-11DOI: 10.1016/j.jmr.2025.107863
Yishay Manassen , Michael Averbukh , Zion Hazan , Yahel Tzuriel , Pino Boscolo , Alexander Shnirman , Baruch Horovitz
We detect a single spin nuclear magnetic resonance (NMR) by monitoring the intensity modulations of a selected hyperfine line in the electron spin resonance (ESR) spectrum. We analyse the power spectrum of the corresponding hyperfine intensity and obtain the nuclear magnetic resonance (NMR) spectrum. Our process also demonstrates ionization of a molecule with the bias voltage of a Scanning Tunnelling Microscope (STM), allowing detection of NMR even in molecules that are non-radical in their neutral state. We have observed this phenomenon in four types of molecules: toluene, triphenylphosphine, TEMPO and adenosine triphosphate (ATP) showing NMR of H, 13C, 31P and 14N nuclei. The spectra are detailed and show signatures of the chemical environment, i.e. chemical shifts. A theoretical model to account for these data is outlined.
{"title":"NMR of a single nuclear spin detected by a scanning tunnelling microscope","authors":"Yishay Manassen , Michael Averbukh , Zion Hazan , Yahel Tzuriel , Pino Boscolo , Alexander Shnirman , Baruch Horovitz","doi":"10.1016/j.jmr.2025.107863","DOIUrl":"10.1016/j.jmr.2025.107863","url":null,"abstract":"<div><div>We detect a single spin nuclear magnetic resonance (NMR) by monitoring the intensity modulations of a selected hyperfine line in the electron spin resonance (ESR) spectrum. We analyse the power spectrum of the corresponding hyperfine intensity and obtain the nuclear magnetic resonance (NMR) spectrum. Our process also demonstrates ionization of a molecule with the bias voltage of a Scanning Tunnelling Microscope (STM), allowing detection of NMR even in molecules that are non-radical in their neutral state. We have observed this phenomenon in four types of molecules: toluene, triphenylphosphine, TEMPO and adenosine triphosphate (ATP) showing NMR of <span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H, <sup>13</sup>C, <sup>31</sup>P and <sup>14</sup>N nuclei. The spectra are detailed and show signatures of the chemical environment, i.e. chemical shifts. A theoretical model to account for these data is outlined.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"374 ","pages":"Article 107863"},"PeriodicalIF":2.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143628443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
High-field nuclear magnetic resonance (NMR) experiments call for the further development of pulsed magnets with a more practical winding structure and higher magnetic field homogeneity. This study presents the construction method and test results of a high-homogeneity pulsed magnet based on an optimized localized split structure. A winding craft using gap spacers was developed for the precise winding of split-gap transition wires. Magnetic field mapping was achieved in a steady-state low field of 32 mT using a Hall probe, with a measured magnetic field inhomogeneity of 198 ± 19 ppm over 1 cm diameter of spherical volume (DSV). The full-width at half-maximum (FWHM) of NMR spectra was adopted as a means of evaluating the magnetic field homogeneity in the pulsed field. In the optimal position, the measured FWHM is 42.2 ± 2.5 ppm at the low field of 7.7 T over a sample volume of 12.6 mm3. At the high field of 50 T, the FWHM decreases to 16.2 ± 0.8 ppm, which is a superior value achieved in similar reported pulsed magnets.
{"title":"Construction and testing of a high-homogeneity 55 T pulsed magnet for high-field nuclear magnetic resonance measurements","authors":"Wenqi Wei, Luchen Wei, Shunkun Ouyang, Kangjian Luo, Zhuo Wang, Shiyu Liu, Yongkang Luo, Xiaotao Han","doi":"10.1016/j.jmr.2025.107862","DOIUrl":"10.1016/j.jmr.2025.107862","url":null,"abstract":"<div><div>High-field nuclear magnetic resonance (NMR) experiments call for the further development of pulsed magnets with a more practical winding structure and higher magnetic field homogeneity. This study presents the construction method and test results of a high-homogeneity pulsed magnet based on an optimized localized split structure. A winding craft using gap spacers was developed for the precise winding of split-gap transition wires. Magnetic field mapping was achieved in a steady-state low field of 32 mT using a Hall probe, with a measured magnetic field inhomogeneity of 198 ± 19 ppm over 1 cm diameter of spherical volume (DSV). The full-width at half-maximum (FWHM) of NMR spectra was adopted as a means of evaluating the magnetic field homogeneity in the pulsed field. In the optimal position, the measured FWHM is 42.2 ± 2.5 ppm at the low field of 7.7 T over a sample volume of 12.6 mm<sup>3</sup>. At the high field of 50 T, the FWHM decreases to 16.2 ± 0.8 ppm, which is a superior value achieved in similar reported pulsed magnets.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"374 ","pages":"Article 107862"},"PeriodicalIF":2.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143593396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-07DOI: 10.1016/j.jmr.2025.107861
J.W. Zwanziger, A.R. Farrant, U. Werner-Zwanziger
For computing the magnetic shielding in solids, density functional theory as implemented in a plane wave basis has proven to be a reasonably accurate and efficient framework, at least for lighter atoms through the third row of the periodic table. In materials with heavier atoms, terms not usually included in the electronic Hamiltonian can become significant, limiting accuracy. Here we derive and implement the zeroth-order regular approximation (ZORA) relativistic terms in the presence of both external magnetic fields and internal nuclear magnetic dipoles, to derive the ZORA-corrected magnetic shielding in the context of periodic boundary conditions and a plane wave basis. We describe our implementation in an open source code, Abinit, and show how it correctly predicts magnetic shieldings in various scenarios, for example the heavy atom next to light atom cases of the III–V semiconductors such as AlSb.
{"title":"Relativistic effects on the magnetic shielding in solids: First-principles computation in a plane wave code","authors":"J.W. Zwanziger, A.R. Farrant, U. Werner-Zwanziger","doi":"10.1016/j.jmr.2025.107861","DOIUrl":"10.1016/j.jmr.2025.107861","url":null,"abstract":"<div><div>For computing the magnetic shielding in solids, density functional theory as implemented in a plane wave basis has proven to be a reasonably accurate and efficient framework, at least for lighter atoms through the third row of the periodic table. In materials with heavier atoms, terms not usually included in the electronic Hamiltonian can become significant, limiting accuracy. Here we derive and implement the zeroth-order regular approximation (ZORA) relativistic terms in the presence of both external magnetic fields and internal nuclear magnetic dipoles, to derive the ZORA-corrected magnetic shielding in the context of periodic boundary conditions and a plane wave basis. We describe our implementation in an open source code, <span>Abinit</span>, and show how it correctly predicts magnetic shieldings in various scenarios, for example the heavy atom next to light atom cases of the III–V semiconductors such as AlSb.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"374 ","pages":"Article 107861"},"PeriodicalIF":2.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-07DOI: 10.1016/j.jmr.2025.107864
Dominique Lagasca , Rupam Ghosh , Yiling Xiao , Kendra K. Frederick
Dynamic nuclear polarization (DNP) solid-state NMR enables detection of proteins inside cells through sensitivity enhancement from nitroxide biradical polarization agents. AsymPolPOK, a novel water-soluble asymmetric nitroxide biradical, offers superior sensitivity and faster build-up times compared to existing agents like AMUPol. Here, we characterize AsymPolPOK's behavior in mammalian HEK293 cells, examining its cellular distribution, reduction kinetics, and DNP performance. We demonstrate that electroporation achieves uniform cellular delivery of AsymPolPOK, including nuclear permeation, with no cytotoxicity at millimolar concentrations. However, the cellular environment rapidly reduces AsymPolPOK to its monoradical form, with one nitroxide center showing greater reduction resistance than the other. While AsymPolPOK maintains high DNP enhancements and short build-up times in lysates, its performance in intact cells depends critically on delivery method and exposure time to cellular constituents. Electroporation yields higher, more uniform enhancements compared to incubation, but prolonged exposure to the cellular environment diminishes DNP performance in both cases. These findings establish AsymPolPOK's potential for in-cell DNP NMR while highlighting the need for developing more bio-resistant polarization agents to further advance cellular structural biology studies.
{"title":"Stability of the polarization agent AsymPolPOK in intact and lysed mammalian cells","authors":"Dominique Lagasca , Rupam Ghosh , Yiling Xiao , Kendra K. Frederick","doi":"10.1016/j.jmr.2025.107864","DOIUrl":"10.1016/j.jmr.2025.107864","url":null,"abstract":"<div><div>Dynamic nuclear polarization (DNP) solid-state NMR enables detection of proteins inside cells through sensitivity enhancement from nitroxide biradical polarization agents. AsymPolPOK, a novel water-soluble asymmetric nitroxide biradical, offers superior sensitivity and faster build-up times compared to existing agents like AMUPol. Here, we characterize AsymPolPOK's behavior in mammalian HEK293 cells, examining its cellular distribution, reduction kinetics, and DNP performance. We demonstrate that electroporation achieves uniform cellular delivery of AsymPolPOK, including nuclear permeation, with no cytotoxicity at millimolar concentrations. However, the cellular environment rapidly reduces AsymPolPOK to its monoradical form, with one nitroxide center showing greater reduction resistance than the other. While AsymPolPOK maintains high DNP enhancements and short build-up times in lysates, its performance in intact cells depends critically on delivery method and exposure time to cellular constituents. Electroporation yields higher, more uniform enhancements compared to incubation, but prolonged exposure to the cellular environment diminishes DNP performance in both cases. These findings establish AsymPolPOK's potential for in-cell DNP NMR while highlighting the need for developing more bio-resistant polarization agents to further advance cellular structural biology studies.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"374 ","pages":"Article 107864"},"PeriodicalIF":2.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143601469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-06DOI: 10.1016/j.jmr.2025.107865
Ajeak Vigneswaran , Tanner A. Buschmann , Michael P. Latham
Side-chain methyl group NMR spectroscopy provides invaluable insights into macromolecular structure, dynamics, and function, particularly for large biomolecular complexes. Accurate assignment of methyl group resonances in two-dimensional spectra is essential for structural and dynamics studies. Traditional methyl group assignment strategies rely on either transferring assignments from backbone resonance data or NOESY data and high-resolution experimental structures; however, these methods are often limited by molecular size or availability of structural information, respectively. Here, we describe the use of AlphaFold2 structural models as a basis for the manual, distance-based assignment of side-chain methyl group resonances in the folded domains of S. cerevisiae Xrs2. While AlphaFold2 models facilitated initial assignments for the methyl resonances, inaccuracies in the side-chain coordinates highlighted the need for improved structural models. By generating >500 ColabFold-derived models and filtering with methyl residual dipolar couplings (RDCs), we identified structural models with superior agreement to experimental data. These refined models enabled additional methyl group assignments while suggesting an iterative approach to simultaneously improve structure prediction and resonance assignment. Our findings outline a workflow that integrates machine learning-based structural predictions with experimental NMR data, offering a pathway for advancing methyl group assignment in systems lacking high-resolution experimental structures.
{"title":"Leveraging AlphaFold2 and residual dipolar couplings for side-chain methyl group assignment: A case study with S. cerevisiae Xrs2","authors":"Ajeak Vigneswaran , Tanner A. Buschmann , Michael P. Latham","doi":"10.1016/j.jmr.2025.107865","DOIUrl":"10.1016/j.jmr.2025.107865","url":null,"abstract":"<div><div>Side-chain methyl group NMR spectroscopy provides invaluable insights into macromolecular structure, dynamics, and function, particularly for large biomolecular complexes. Accurate assignment of methyl group resonances in two-dimensional spectra is essential for structural and dynamics studies. Traditional methyl group assignment strategies rely on either transferring assignments from backbone resonance data or NOESY data and high-resolution experimental structures; however, these methods are often limited by molecular size or availability of structural information, respectively. Here, we describe the use of AlphaFold2 structural models as a basis for the manual, distance-based assignment of side-chain methyl group resonances in the folded domains of <em>S. cerevisiae</em> Xrs2. While AlphaFold2 models facilitated initial assignments for the methyl resonances, inaccuracies in the side-chain coordinates highlighted the need for improved structural models. By generating >500 ColabFold-derived models and filtering with methyl residual dipolar couplings (RDCs), we identified structural models with superior agreement to experimental data. These refined models enabled additional methyl group assignments while suggesting an iterative approach to simultaneously improve structure prediction and resonance assignment. Our findings outline a workflow that integrates machine learning-based structural predictions with experimental NMR data, offering a pathway for advancing methyl group assignment in systems lacking high-resolution experimental structures.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"374 ","pages":"Article 107865"},"PeriodicalIF":2.0,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-21DOI: 10.1016/j.jmr.2025.107860
Tamar Wolf, Lucio Frydman
Solid-state nuclear magnetic resonance (NMR) can shed light on atomic-level arrangements for most elements in the Periodic Table. This ability hinges on the possibility to overcome NMR's low sensitivity, particularly when dealing with unreceptive nuclei yielding ultra-wideline (>500 kHz) patterns from powdered samples. Herein, we present an experiment capable of enhancing the signals of such static samples, by transferring dipolar order from surrounding, highly polarized protons. The experiment, which we dub Dipolar-Order-based BRoadband Adiabatic INversion Cross-Polarization (DOBRAIN-CP), utilizes a Freeman-Kupče broadband inversion WURST pulse to perform CP over the wideline spectrum of the low receptivity species, while matching the low frequencies associated to 1H1H dipolar fields. We present analytical and numerical analyses of the spin-dynamics of DOBRAIN-CP for spin-½ nuclei, as well as for quadrupolar spins. Experimental results are also presented for spin-½, integer and half-integer quadrupolar spins; these show that although DOBRAIN-CP delivers broadband excitation and sensitivity enhancement compared to direct excitations, it does not exceed the sensitivity enhancement of the BRAIN-CP variant based on Hartmann-Hahn matching. The power requirements for DOBRAIN-CP are extremely low, yet long dipolar-order lifetimes T1D are needed to support the DOBRAIN-CP build-up times.
{"title":"Dipolar-order-based broadband adiabatic inversion as cross- polarization alternative in solid state Wideline NMR","authors":"Tamar Wolf, Lucio Frydman","doi":"10.1016/j.jmr.2025.107860","DOIUrl":"10.1016/j.jmr.2025.107860","url":null,"abstract":"<div><div>Solid-state nuclear magnetic resonance (NMR) can shed light on atomic-level arrangements for most elements in the Periodic Table. This ability hinges on the possibility to overcome NMR's low sensitivity, particularly when dealing with unreceptive nuclei yielding ultra-wideline (>500 kHz) patterns from powdered samples. Herein, we present an experiment capable of enhancing the signals of such static samples, by transferring dipolar order from surrounding, highly polarized protons. The experiment, which we dub Dipolar-Order-based BRoadband Adiabatic INversion Cross-Polarization (DOBRAIN-CP), utilizes a Freeman-Kupče broadband inversion WURST pulse to perform CP over the wideline spectrum of the low receptivity species, while matching the low frequencies associated to <sup>1</sup>H<img><sup>1</sup>H dipolar fields. We present analytical and numerical analyses of the spin-dynamics of DOBRAIN-CP for spin-½ nuclei, as well as for quadrupolar spins. Experimental results are also presented for spin-½, integer and half-integer quadrupolar spins; these show that although DOBRAIN-CP delivers broadband excitation and sensitivity enhancement compared to direct excitations, it does not exceed the sensitivity enhancement of the BRAIN-CP variant based on Hartmann-Hahn matching. The power requirements for DOBRAIN-CP are extremely low, yet long dipolar-order lifetimes T<sub>1D</sub> are needed to support the DOBRAIN-CP build-up times.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"373 ","pages":"Article 107860"},"PeriodicalIF":2.0,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Complete characterization of 13C chemical shift tensor in magnetically oriented microcrystal suspension (MOMS) is demonstrated with an inhouse 1H-13C double resonance probe capable of rotating microcrystals and of tilting the sample temporarily during the period of NMR signal acquisition. The 13C chemical shift tensor in three-dimensional MOMS of l-alanine is determined from 13C rotation patterns around a tilted axis. The present results prove that even for micrometer-sized microcrystals the chemical shift tensor can be fully determined like in the case of a single piece of bulky crystal but without elaborate sample mounting. Two-dimensional experiments correlating chemical shifts for different sample orientations are also demonstrated.
{"title":"Full determination of chemical shift tensor in magnetically oriented microcrystals with modulated rotation and temporal tilt","authors":"Ryosuke Kusumi , Hayate Yasui , Hiroshi Kadoma , Masahisa Wada , Kazuyuki Takeda","doi":"10.1016/j.jmr.2025.107853","DOIUrl":"10.1016/j.jmr.2025.107853","url":null,"abstract":"<div><div>Complete characterization of <sup>13</sup>C chemical shift tensor in magnetically oriented microcrystal suspension (MOMS) is demonstrated with an inhouse <sup>1</sup>H-<sup>13</sup>C double resonance probe capable of rotating microcrystals and of tilting the sample temporarily during the period of NMR signal acquisition. The <sup>13</sup>C chemical shift tensor in three-dimensional MOMS of <span>l</span>-alanine is determined from <sup>13</sup>C rotation patterns around a tilted axis. The present results prove that even for micrometer-sized microcrystals the chemical shift tensor can be fully determined like in the case of a single piece of bulky crystal but without elaborate sample mounting. Two-dimensional experiments correlating chemical shifts for different sample orientations are also demonstrated.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"373 ","pages":"Article 107853"},"PeriodicalIF":2.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143519875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-18DOI: 10.1016/j.jmr.2025.107852
Samuel Perron , Claire S. Tully , Shivam Gupta , Matthew S. Fox , Dmitrij Zagidulin , James J. Noël , Alexei Ouriadov
Although the relaxation time constants of free water are relatively long, the relaxation of water in concrete and other sedimentary materials is significantly shorter. Dissolved ions and porous environments can cause increased magnetic susceptibility effects, leading to the apparent transverse relaxation time T2⁎ of this water to decrease drastically, from seconds to less than a millisecond. The longer T2⁎ of the low field regime (less than 0.5 T) should allow for 2D and even 3D imaging of water content in these types of materials; developing a suitable technique for imaging of short-T2⁎ samples would permit imaging of porous rocks and concrete.
A 12 mL wet bentonite clay sample was placed within a syringe and allowed to absorb increasing volumes of standing water. This progressing absorption was imaged on a 73.5 mT magnetic resonance imaging (MRI) system using the X-Centric pulse sequence. This pulse sequence is a modified version of the common gradient echo (GE) pulse sequence, in which each half of k-space is acquired separately, from the centre outwards in the readout direction, ensuring minimal T2⁎-weighting of the resulting image and allowing for 2D imaging within the short time frame of the shorter T2⁎ of water in the clay. Bulk relaxation measurements of T2⁎ and the longitudinal relaxation time T1 were performed for increasing water content, with a mean T1 of 12.0 ± 1.1 ms and mean T2⁎ of 4.5 ± 0.7 ms; 2D imaging of the clay sample was performed with both GE and X-Centric. In addition, a 2D T2⁎ map was generated from eight X-Centric images taken at different echo times.
The X-Centric pulse sequence was demonstrated to be an effective imaging method for short signal-lifetime samples, such as water trapped in bentonite clay. The ease of implementation, minimal diffusion-weighting and T2⁎ weighting of the k-space centre, and considerable gains in signal-to-noise ratio and imaging efficiency position this pulse sequence as a viable alternative or complement to conventional GE acquisitions. Additionally, the short echo-time of the X-Centric pulse sequence allows it to be used effectively with non-proton MRI, including 23Na and fluorinated gases (e.g., 19F) where the T2⁎-decay is a potentially significant source of signal decay.
{"title":"Implementation of the X-centric pulse sequence at low field for MRI of water penetration in clay","authors":"Samuel Perron , Claire S. Tully , Shivam Gupta , Matthew S. Fox , Dmitrij Zagidulin , James J. Noël , Alexei Ouriadov","doi":"10.1016/j.jmr.2025.107852","DOIUrl":"10.1016/j.jmr.2025.107852","url":null,"abstract":"<div><div>Although the relaxation time constants of free water are relatively long, the relaxation of water in concrete and other sedimentary materials is significantly shorter. Dissolved ions and porous environments can cause increased magnetic susceptibility effects, leading to the apparent transverse relaxation time <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> of this water to decrease drastically, from seconds to less than a millisecond. The longer <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> of the low field regime (less than 0.5 T) should allow for 2D and even 3D imaging of water content in these types of materials; developing a suitable technique for imaging of short-<em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> samples would permit imaging of porous rocks and concrete.</div><div>A 12 mL wet bentonite clay sample was placed within a syringe and allowed to absorb increasing volumes of standing water. This progressing absorption was imaged on a 73.5 mT magnetic resonance imaging (MRI) system using the X-Centric pulse sequence. This pulse sequence is a modified version of the common gradient echo (GE) pulse sequence, in which each half of <em>k</em>-space is acquired separately, from the centre outwards in the readout direction, ensuring minimal <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup>-weighting of the resulting image and allowing for 2D imaging within the short time frame of the shorter <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> of water in the clay. Bulk relaxation measurements of <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> and the longitudinal relaxation time <em>T</em><sub><em>1</em></sub> were performed for increasing water content, with a mean <em>T</em><sub><em>1</em></sub> of 12.0 ± 1.1 ms and mean <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> of 4.5 ± 0.7 ms; 2D imaging of the clay sample was performed with both GE and X-Centric. In addition, a 2D <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> map was generated from eight X-Centric images taken at different echo times.</div><div>The X-Centric pulse sequence was demonstrated to be an effective imaging method for short signal-lifetime samples, such as water trapped in bentonite clay. The ease of implementation, minimal diffusion-weighting and <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup> weighting of the <em>k</em>-space centre, and considerable gains in signal-to-noise ratio and imaging efficiency position this pulse sequence as a viable alternative or complement to conventional GE acquisitions. Additionally, the short echo-time of the X-Centric pulse sequence allows it to be used effectively with non-proton MRI, including <sup>23</sup>Na and fluorinated gases (e.g., <sup>19</sup>F) where the <em>T</em><sub><em>2</em></sub><sup><em>⁎</em></sup>-decay is a potentially significant source of signal decay.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"373 ","pages":"Article 107852"},"PeriodicalIF":2.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143437930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-16DOI: 10.1016/j.jmr.2025.107851
Giulia Fischetti , Nicolas Schmid , Simon Bruderer , Björn Heitmann , Andreas Henrici , Alessandro Scarso , Guido Caldarelli , Dirk Wilhelm
One-dimensional 1H Nuclear Magnetic Resonance (NMR) stands out as the quickest and simplest among various NMR experimental setups. Unfortunately, it suffers from lengthy annotation times and does not always have a clear and unique interpretation. From NMR discovery, efforts have been dedicated to introducing an automated approach to streamline the characterization of chemical compounds while ensuring consistency of the results across the scientific community. Nonetheless, this remains an ongoing challenge that has garnered renewed interest with the emergence of deep learning techniques. Here, we present MuSe Net, a novel supervised probabilistic deep learning framework that can emulate the tasks performed by an expert spectroscopist in annotating one-dimensional NMR spectra generated by small molecules. Considering only the spectrum, MuSe Net detects and classifies multiplets with up to four coupling constants for their splitting phenotype, providing a segmentation of the spectral range. We exploit uncertainty quantification to produce a confidence score to both assess classification reliability and to detect signals that do not fit into any other phenotype class. The results of the evaluation against 48 experimental 1H NMR spectra of small molecules annotated by experts demonstrate that MuSe Net can deal with anomalies and unclear signals while correctly classifying multiplets and detecting overlapping peaks.
{"title":"A deep learning framework for multiplet splitting classification in 1H NMR","authors":"Giulia Fischetti , Nicolas Schmid , Simon Bruderer , Björn Heitmann , Andreas Henrici , Alessandro Scarso , Guido Caldarelli , Dirk Wilhelm","doi":"10.1016/j.jmr.2025.107851","DOIUrl":"10.1016/j.jmr.2025.107851","url":null,"abstract":"<div><div>One-dimensional <sup>1</sup>H Nuclear Magnetic Resonance (NMR) stands out as the quickest and simplest among various NMR experimental setups. Unfortunately, it suffers from lengthy annotation times and does not always have a clear and unique interpretation. From NMR discovery, efforts have been dedicated to introducing an automated approach to streamline the characterization of chemical compounds while ensuring consistency of the results across the scientific community. Nonetheless, this remains an ongoing challenge that has garnered renewed interest with the emergence of deep learning techniques. Here, we present MuSe Net, a novel supervised probabilistic deep learning framework that can emulate the tasks performed by an expert spectroscopist in annotating one-dimensional NMR spectra generated by small molecules. Considering only the spectrum, MuSe Net detects and classifies multiplets with up to four coupling constants for their splitting phenotype, providing a segmentation of the spectral range. We exploit uncertainty quantification to produce a confidence score to both assess classification reliability and to detect signals that do not fit into any other phenotype class. The results of the evaluation against 48 experimental <sup>1</sup>H NMR spectra of small molecules annotated by experts demonstrate that MuSe Net can deal with anomalies and unclear signals while correctly classifying multiplets and detecting overlapping peaks.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"373 ","pages":"Article 107851"},"PeriodicalIF":2.0,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143444601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dynamic nuclear polarization (DNP) is widely used in a wide range of applications in solid-state NMR nowadays due to recent advancements of magic-angle spinning (MAS) DNP. Conventionally, an MAS-DNP system employs a gyrotron as a microwave source and operates at 100 K using nitrogen gas. As an alternative, we present a 400 MHz/263 GHz MAS-DNP system utilizing a compact solid-state microwave source and an ultra-low temperature (ULT) helium MAS probe equipped with a cryogenic preamplifier. Compared to gyrotrons, solid-state microwave sources are compact, cost-effective, and frequency agile. The ULT compensates for the decreased DNP efficiency resulting from the lower microwave power of the solid-state source. Additionally, the large Boltzmann polarization at ULT and the improved signal-to-noise ratio provided by the cryogenic preamplifier enhance the sensitivity of the MAS-DNP system. The system is tested using a DNP standard sample of proline in a mixture of deuterated glycerol and partially deuterated water doped with AMUPol, achieving a DNP enhancement of 85 using a 2 mm-diameter rotor at a sample temperature of 30 K and microwave power of 160 mW. Experimental data show that the Boltzmann polarization and the cryogenic preamplifier contribute an additional sensitivity gain of 11 at 30 K compared to 100 K. Overall, the ULT-DNP related sensitivity gain of this system is estimated to be roughly twice that of a 100 K gyrotron system, although the DNP enhancement factor alone is smaller using a solid-state microwave source.
{"title":"400 MHz/263 GHz ultra-low temperature MAS-DNP using a closed-cycle helium gas cooling system and a solid-state microwave source","authors":"Fumio Hobo , Yusuke Tanimoto , Yuki Endo , Yoh Matsuki , Hiroki Takahashi","doi":"10.1016/j.jmr.2025.107842","DOIUrl":"10.1016/j.jmr.2025.107842","url":null,"abstract":"<div><div>Dynamic nuclear polarization (DNP) is widely used in a wide range of applications in solid-state NMR nowadays due to recent advancements of magic-angle spinning (MAS) DNP. Conventionally, an MAS-DNP system employs a gyrotron as a microwave source and operates at <span><math><mo>∼</mo></math></span>100 K using nitrogen gas. As an alternative, we present a 400 MHz/263 GHz MAS-DNP system utilizing a compact solid-state microwave source and an ultra-low temperature (ULT) helium MAS probe equipped with a cryogenic preamplifier. Compared to gyrotrons, solid-state microwave sources are compact, cost-effective, and frequency agile. The ULT compensates for the decreased DNP efficiency resulting from the lower microwave power of the solid-state source. Additionally, the large Boltzmann polarization at ULT and the improved signal-to-noise ratio provided by the cryogenic preamplifier enhance the sensitivity of the MAS-DNP system. The system is tested using a DNP standard sample of proline in a mixture of deuterated glycerol and partially deuterated water doped with AMUPol, achieving a DNP enhancement of 85 using a 2 mm-diameter rotor at a sample temperature of 30 K and microwave power of 160 mW. Experimental data show that the Boltzmann polarization and the cryogenic preamplifier contribute an additional sensitivity gain of 11<span><math><mo>×</mo></math></span> at 30 K compared to 100 K. Overall, the ULT-DNP related sensitivity gain of this system is estimated to be roughly twice that of a 100 K gyrotron system, although the DNP enhancement factor alone is smaller using a solid-state microwave source.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"373 ","pages":"Article 107842"},"PeriodicalIF":2.0,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143387540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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