Journal of magnetic resonance最新文献

{"title":"CTCOSY-JRES: A high-resolution three-dimensional NMR method for unveiling J-couplings","authors":"Xiaoqing Lin,&nbsp;Yulei Chen,&nbsp;Chengda Huang,&nbsp;Xiaozhen Feng,&nbsp;Bo Chen,&nbsp;Yuqing Huang,&nbsp;Zhong Chen","doi":"10.1016/j.jmr.2024.107675","DOIUrl":"https://doi.org/10.1016/j.jmr.2024.107675","url":null,"abstract":"<div><p>Two-dimensional (2D) <em>J</em>-resolved spectroscopy provides valuable information on <em>J</em>-coupling constants for molecular structure analysis by resolving one-dimensional (1D) spectra. However, it is challenging to decipher the <em>J</em>-coupling connectivity in 2D <em>J</em>-resolved spectra because the <em>J</em>-coupling connectivity cannot be directly provided. In addition, 2D homonuclear correlation spectroscopy (COSY) can directly elucidate molecular structures by tracking the <em>J</em>-coupling connectivity between protons. However, this method is limited by the problem of spectral peak crowding and is only suitable for simple sample systems. To fully understand the intuitive coupling relationship and coupling constant information, we propose a three-dimensional (3D) COSY method called CTCOSY-<em>J</em>RES (Constant-Time COrrelation SpectroscopY and <em>J</em>-REsolved Spectroscopy) in this paper. By combining the <em>J</em>-resolved spectrum with the constant-time COSY technique, a doubly decoupled COSY spectrum can be provided while preserving the <em>J</em>-coupling constant along an additional dimension, ensuring high-resolution analysis of <em>J</em>-coupling connectivity and <em>J</em>-coupling information. Moreover, compression sensing and fold-over correction techniques are introduced to accelerate experimental acquisition. The CTCOSY-<em>J</em>RES method has been successfully validated in a variety of sample systems, including industrial, agricultural, and biopharmaceutical samples, revealing complex coupling interactions and providing deeper insights into the resolution of molecular structures.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"362 ","pages":"Article 107675"},"PeriodicalIF":2.2,"publicationDate":"2024-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140558162","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}

{"title":"Clean PDI-1 SQ: Suppression of HSQC artifacts in 2D proton-detected INADEQUATE spectra by pulse sequence redesign","authors":"Justinas Sakas ,&nbsp;Dušan Uhrín ,&nbsp;Ole W. Sørensen","doi":"10.1016/j.jmr.2024.107674","DOIUrl":"https://doi.org/10.1016/j.jmr.2024.107674","url":null,"abstract":"<div><p>Proton-detected INADEQUATE NMR experiments are widely used for structure elucidation of small molecules, in particular the implementations that display ¹³C single-quantum rather than double-quantum frequencies in the indirect dimension of 2D spectra. But unfortunately, such spectra in addition to the desired ¹H–¹³C two-bond correlations also contain HSQC artifacts of comparable magnitude. The redesigned versatile experiment presented in this paper requires no compromise based on different ¹³C multiplicities and suppresses the HSQC artifacts that are a source of possible spectral misinterpretation. Demonstration of the new method is shown by applications to typical small molecules of different complexity.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"362 ","pages":"Article 107674"},"PeriodicalIF":2.2,"publicationDate":"2024-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140539946","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}

{"title":"MaRGE: A graphical environment for MaRCoS","authors":"José M. Algarín ,&nbsp;Teresa Guallart-Naval ,&nbsp;José Borreguero ,&nbsp;Fernando Galve ,&nbsp;Joseba Alonso","doi":"10.1016/j.jmr.2024.107662","DOIUrl":"https://doi.org/10.1016/j.jmr.2024.107662","url":null,"abstract":"<div><p>The open-source console MaRCoS, which stands for “Magnetic Resonance Control System”, combines hardware, firmware and software elements for integral control of Magnetic Resonance Imaging (MRI) scanners. Previous developments have focused on making the system robust and reliable, rather than on users, who have been somewhat overlooked. This work describes a Graphical User Interface (GUI) designed for intuitive control of MaRCoS, as well as compatibility with clinical environments. The GUI is based on an arrangement of tabs and a renewed Application Program Interface (API). Compared to the previous versions, the MaRGE package (“MaRCoS Graphical Environment”) includes new functionalities such as the possibility to export images to standard DICOM formats, create and manage clinical protocols, or display and process image reconstructions, among other features conceived to simplify the operation of MRI scanners. All prototypes in our facilities are commanded by MaRCoS and operated with the new GUI. Here we report on its performance on an experimental 0.2 T scanner designed for hard-tissue, as well as a 72 mT portable scanner presently installed in the radiology department of a large hospital. The possibility to customize, adapt and streamline processes has substantially improved our workflows and overall experience.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"361 ","pages":"Article 107662"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724000466/pdfft?md5=b16f023fb275e84de53d69f4129e9e1c&pid=1-s2.0-S1090780724000466-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140343935","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}

{"title":"NMR measurement of diffusion coefficients by radio-frequency gradients in the case of short relaxation times","authors":"Laouès Guendouz ,&nbsp;Sébastien Leclerc ,&nbsp;Daniel Canet","doi":"10.1016/j.jmr.2024.107668","DOIUrl":"https://doi.org/10.1016/j.jmr.2024.107668","url":null,"abstract":"<div><p>The measurement of translational diffusion coefficients by NMR generally makes use basically of two magnetic field gradient pulses separated by a so-called diffusion interval. The magnetic field gradient arises either from the static magnetic field (denoted by B₀ used for polarizing the nuclear spins) or from the radio-frequency field (denoted by B₁ used for inducing NMR transitions). The B₀ method may be hampered by short effective transverse relaxation times (<span><math><mrow><msubsup><mi>T</mi><mrow><mn>2</mn></mrow><mrow><mo>∗</mo></mrow></msubsup></mrow></math></span>), by important gradient rise and fall times or by eddy currents. This does not occur with B₁ gradients. Moreover, the effect of short transverse relaxation times during the gradient pulses is reduced by at least a factor of two. However, for B₁ gradients, one might face with the limited volume in which the gradient is uniform and with the effect of short relaxation times which imply to reduce the various intervals in the diffusion experiment (this is as well true for the B₀ method). Examples will be given for which the measurement of the diffusion coefficient by B₀ gradients turned out to be impossible while a proper result was obtained with B₁ gradients as far as a correction taking into account the limited volume is applied, together with a correction about the gradient calibration especially when dealing with samples containing paramagnetic species.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"361 ","pages":"Article 107668"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140346900","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}

{"title":"A delayed decoupling methyl-TROSY pulse sequence for atomic resolution studies of folded proteins and RNAs in condensates","authors":"Rashik Ahmed ,&nbsp;Atul K. Rangadurai ,&nbsp;Lisa Ruetz ,&nbsp;Martin Tollinger ,&nbsp;Christoph Kreutz ,&nbsp;Lewis E. Kay","doi":"10.1016/j.jmr.2024.107667","DOIUrl":"10.1016/j.jmr.2024.107667","url":null,"abstract":"<div><p>Solution NMR spectroscopy has tremendous potential for providing atomic resolution insights into the interactions between proteins and nucleic acids partitioned into condensed phases of phase-separated systems. However, the highly viscous nature of the condensed phase challenges applications, and in particular, the extraction of quantitative, site-specific information. Here, we present a delayed decoupling-based HMQC pulse sequence for methyl-TROSY studies of ‘client’ proteins and nucleic acids partitioned into ‘scaffold’ proteinaceous phase-separated solvents. High sensitivity and excellent quality spectra are recorded of a nascent form of superoxide dismutase and of a small RNA fragment partitioned into CAPRIN1 condensates.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"362 ","pages":"Article 107667"},"PeriodicalIF":2.2,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140407964","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}

{"title":"Bayesian NMR petrophysical characterization","authors":"S. Pitawala,&nbsp;P.D. Teal","doi":"10.1016/j.jmr.2024.107663","DOIUrl":"10.1016/j.jmr.2024.107663","url":null,"abstract":"<div><p>Identification of reservoir rock types is necessary for the exploration and recovery of oil and gas. It involves determining the petrophysical properties of rocks such as porosity and permeability which play a significant role in developing reservoir models, estimating the volumes of oil and gas reserves, and planning production methods. Nuclear magnetic resonance (NMR) technology is a fast and accurate tool for petrophysical rock characterization. The distributions of relaxation times (<span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distributions) offer valuable insights into the distribution of pore sizes in rocks, and these distributions are closely linked to important petrophysical parameters like porosity, permeability, and bound fluid volume (BFV).</p><p>This work introduces a Bayesian estimation method for analyzing NMR data. The Bayesian approach uses prior knowledge of <span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distributions in the form of the prior mean and covariance. The Bayesian approach combines prior knowledge with observed data to obtain improved estimation. We use the Bayesian estimation method where prior information regarding the rock sample type, for example shale, is available.</p><p>The estimators were evaluated on decay data simulated from synthesized distributions that replicate the features of experimental <span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distributions of three types of reservoir rocks. We compared the performance of the Bayesian method with two existing methods using porosity, bound fluid volume (BFV) geometric mean (T2LM) and root mean square error (RMSE) of the estimated <span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distribution as evaluation criteria. Additional experiments were carried out using experimental <span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distributions to validate the results.</p><p>The performance of the Bayesian methods was also tested using mismatched priors.</p><p>The experimental results illustrate that the Bayesian estimator outperforms other estimators in estimating the <span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distribution. The Bayesian method also outperforms the ILT method in estimating derived petrophysical properties except in cases where the noise level is below 0.1 and the <span><math><msub><mrow><mi>T</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> distributions are associated with short relaxation times.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"362 ","pages":"Article 107663"},"PeriodicalIF":2.2,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724000478/pdfft?md5=d98572956a2353c56461206f0b46eb2a&pid=1-s2.0-S1090780724000478-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140402257","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}

{"title":"A parallel line probe for spatially selective electrochemical NMR spectroscopy","authors":"Ruipeng Luo,&nbsp;Hans J.W.G. Janssen,&nbsp;Arno P.M. Kentgens,&nbsp;Evan Wenbo Zhao","doi":"10.1016/j.jmr.2024.107666","DOIUrl":"https://doi.org/10.1016/j.jmr.2024.107666","url":null,"abstract":"<div><p><em>In situ</em> NMR is a valuable tool for studying electrochemical devices, including redox flow batteries and electrocatalytic reactors, capable of detecting reaction intermediates, metastable states, time evolution of processes or monitoring stability as a function of electrochemical conditions. Here we report a parallel line detector for spatially selective <em>in situ</em> electrochemical NMR spectroscopy. The detector consists of 17 copper wires and is doubly tuned to ¹H/¹⁹F and X nuclei ranging from ⁶³Cu (106.1 MHz) to ⁷Li (155.5 MHz). The flat geometry of the parallel line detector allows its insertion into a high electrode surface-to-volume electrochemical flow reactor, enabling a detector-in-a-reactor design. This integrated device is named “eReactor NMR probe”. Combined with B₁-selective pulse sequences, selective detection of the nuclei at the electrode-electrolyte interface, that is within a distance of 800 μm from the electrode surface, has been achieved. The selective detection of ⁷Li and ¹⁹F nuclei is demonstrated using two electrolytes, LiCl and LiBF₄ solutions, respectively. A good B₁ homogeneity with an 810° to 90° pulse intensity ratio of 68–72 % was achieved. Using electrochemical plating of lithium metal as a model reaction, we further demonstrated the <em>operando</em> functionality of the probe. The new eReactor NMR probe offers a general method for studying flow electrochemistry, and we envision applications in a wide range of environmentally relevant energy systems, for example, Li metal batteries, electrochemical ammonia synthesis, carbon dioxide capture and reduction, redox flow batteries, fuel cells, water desalination, lignin oxidation etc.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"361 ","pages":"Article 107666"},"PeriodicalIF":2.2,"publicationDate":"2024-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724000508/pdfft?md5=e30a5b4ebb9723fca9772e382799e2a2&pid=1-s2.0-S1090780724000508-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140290817","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}

{"title":"NMRduino: A modular, open-source, low-field magnetic resonance platform","authors":"Michael C.D. Tayler,&nbsp;Sven Bodenstedt","doi":"10.1016/j.jmr.2024.107665","DOIUrl":"10.1016/j.jmr.2024.107665","url":null,"abstract":"<div><p>The NMRduino is a compact, cost-effective, sub-MHz NMR spectrometer that utilizes readily available open-source hardware and software components. One of its aims is to simplify the processes of instrument setup and data acquisition control to make experimental NMR spectroscopy accessible to a broader audience. In this introductory paper, the key features and potential applications of NMRduino are described to highlight its versatility both for research and education.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"362 ","pages":"Article 107665"},"PeriodicalIF":2.2,"publicationDate":"2024-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724000491/pdfft?md5=d80bfceb1f1d7c0d018ee4eed65f6853&pid=1-s2.0-S1090780724000491-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140404966","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}

{"title":"ASAP: An automatic sequential assignment program for congested multidimensional solid state NMR spectra","authors":"Bo Chen","doi":"10.1016/j.jmr.2024.107664","DOIUrl":"https://doi.org/10.1016/j.jmr.2024.107664","url":null,"abstract":"<div><p>Accurate signal assignments can be challenging for congested solid-state NMR (ssNMR) spectra. We describe an automatic sequential assignment program (ASAP) to partially overcome this challenge. ASAP takes three input files: the residue type assignments (RTAs) determined from the better-resolved NCACX spectrum, the full peak list of the NCOCX spectrum, and the protein sequence. It integrates our auto-residue type assignment strategy (ARTIST) with the Monte Carlo simulated annealing (MCSA) algorithm to overcome the hurdle for accurate signal assignments caused by incomplete side-chain resonances and spectral congestion. Combined, ASAP demonstrates robust performance and accelerates signal assignments of large proteins (&gt;200 residues) that lack crystalline order.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"361 ","pages":"Article 107664"},"PeriodicalIF":2.2,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140195528","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}

{"title":"A set of cross-correlated relaxation experiments to probe the correlation time of two different and complementary spin pairs","authors":"Irene Ceccolini ,&nbsp;Clemens Kauffmann ,&nbsp;Julian Holzinger ,&nbsp;Robert Konrat ,&nbsp;Anna Zawadzka-Kazimierczuk","doi":"10.1016/j.jmr.2024.107661","DOIUrl":"10.1016/j.jmr.2024.107661","url":null,"abstract":"<div><p>Intrinsically disordered proteins (IDPs) defy the conventional structure-function paradigm by lacking a well-defined tertiary structure and exhibiting inherent flexibility. This flexibility leads to distinctive spin relaxation modes, reflecting isolated and specific motions within individual peptide planes. In this work, we propose a new pulse sequence to measure the longitudinal ¹³C<span><math><msup><mrow></mrow><mrow><mo>′</mo></mrow></msup></math></span> CSA-¹³C<span><math><msup><mrow></mrow><mrow><mo>′</mo></mrow></msup></math></span>-¹³C<span><math><msup><mrow></mrow><mrow><mi>α</mi></mrow></msup></math></span> DD CCR rate <span><math><msubsup><mrow><mi>Γ</mi></mrow><mrow><mi>z</mi></mrow><mrow><msup><mrow><mi>C</mi></mrow><mrow><mo>′</mo></mrow></msup><mo>/</mo><msup><mrow><mi>C</mi></mrow><mrow><mo>′</mo></mrow></msup><msup><mrow><mi>C</mi></mrow><mrow><mi>α</mi></mrow></msup></mrow></msubsup></math></span> and present a novel 3D version of the transverse <span><math><msubsup><mrow><mi>Γ</mi></mrow><mrow><mi>x</mi><mi>y</mi></mrow><mrow><msup><mrow><mi>C</mi></mrow><mrow><mo>′</mo></mrow></msup><mo>/</mo><msup><mrow><mi>C</mi></mrow><mrow><mo>′</mo></mrow></msup><msup><mrow><mi>C</mi></mrow><mrow><mi>α</mi></mrow></msup></mrow></msubsup></math></span> CCR rate, adopting the symmetrical reconversion approach. We combined these rates with the analogous <span><math><msubsup><mrow><mi>Γ</mi></mrow><mrow><mi>x</mi><mi>y</mi></mrow><mrow><mi>N</mi><mo>/</mo><mi>N</mi><mi>H</mi></mrow></msubsup></math></span> and <span><math><msubsup><mrow><mi>Γ</mi></mrow><mrow><mi>z</mi></mrow><mrow><mi>N</mi><mo>/</mo><mi>N</mi><mi>H</mi></mrow></msubsup></math></span> CCR rates to derive residue-specific correlation times for both spin-pairs within the same peptide plane. The presented approach offers a straightforward and intuitive way to compare the correlation times of two different and complementary spin vectors, anticipated to be a valuable aid to determine IDPs backbone dihedral angles distributions. We performed the proposed experiments on two systems: a folded protein ubiquitin and <em>Coturnix japonica</em> osteopontin, a prototypical IDP. Comparative analyses of the results show that the correlation times of different residues vary more for IDPs than globular proteins, indicating that the dynamics of IDPs is largely heterogeneous and dominated by local fluctuations.</p></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"361 ","pages":"Article 107661"},"PeriodicalIF":2.2,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1090780724000454/pdfft?md5=4e2e55d9d786c2ab1d665523b49c9fdd&pid=1-s2.0-S1090780724000454-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140274127","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}