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168 results for “NMR Data”
MS and NMR data of in situ Captured Marine Exometabolites
<p>This folder contains the raw data pertaining to the article <i><strong>In Situ</strong></i> <strong>Capture and Real Time Enrichment of Marine Chemical Diversity </strong></p><p><a href="https://doi.org/10.1021/acscentsci.3c00661">https://doi.org/10.1021/acscentsci.3c00661</a></p><p>Data are organized in folders corresponding to each figure. Briefly, this folder contains the raw mass spectrometry (MS) data, the cytoscape files of the full molecular network (Fig3), the xcel spreadsheets of annotated MS spectra related to each investigated specialized exometabolites from the Mediterranean sponges <i>Aplysina cavernicola </i>(AC, Fig4), <i>Spongia officinalis </i>(SO, Fig5)<i>, </i>and <i>Agelas oroides </i>(AO, Fig6)<i>, </i>the raw 1H NMR data from each sponge exometabolite (EM) extract with their corresponding crude extract (CR).</p><ul><li>All MS2 data were acquired on a Bruker Impact II qTOF (ESI positive, collision energy 20-40eV) also deposited here : MSV000091465</li><li>SIRIUS software and CANOPUS were used to further annotate the chemodiversity of captured marine EMs</li><li>All NMR data were acquired on a BRUKER avance II+ instrument (600 MHz, cryoprobe) in CD<i>3</i>OD</li></ul><p>-------------------------</p><p><strong>References related to in silico MS annotation tools:</strong></p><ul><li>Kai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A. Hoffmann, Daniel Petras, William H. Gerwick, Juho Rousu, Pieter C. Dorrestein and Sebastian Böcker <i>Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra</i>. Nature Biotechnology, 2020. https://doi.org/10.1038/s41587-020-0740-8</li><li>Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart <i>ClassyFire: automated chemical classification with a comprehensive, computable taxonomy </i>J Cheminf, 8, 2016. https://doi.org/10.1186/s13321-016-0174-y</li><li>Kim, Hyun Woo and Wang, Mingxun and Leber, Christopher A. and Nothias, Louis-Félix and Reher, Raphael and Kang, Kyo Bin and van der Hooft, Justin J. J. and Dorrestein, Pieter C. and Gerwick, William H. and Cottrell, Garrison W. NPClassifier:<i> A Deep Neural Network-Based Structural Classification Tool for Natural Products. </i>Journal of Natural Products, 84, 2021. https://doi.org/10.1021/acs.jnatprod.1c00399</li></ul>
NMR and MS data of identified bromotyrosine alkaloids produced and released by Aplysina cavernicola
<p>This folder contains NMR and MS datasets of each identified bromotyrosine spiroisoxazoline pertaining to the publication<em> </em>entitled:</p> <p><strong>Diving into the molecular diversity of <em>Aplysina cavernicola’s </em>exo-metabolites: contribution of bromo-spiroisoxazoline alkaloids.</strong> <em>ACS Omega</em> 2022 <strong> <a href="https://pubs.acs.org/doi/10.1021/acsomega.2c05415"> </a></strong><a href="https://pubs.acs.org/doi/10.1021/acsomega.2c05415">https://doi.org/10.1021/acsomega.2c05415</a></p> <ul> <li>All NMR data were acquired in CD<sub>3</sub>OD at 600 MHz (Bruker Avance III, cryosonde TCI) using 2 mm NMR tubes</li> <li>All MS<sup>2</sup> data were acquired on a Bruker Impact II qTOF (ESI positive, collision energy 20-40eV)</li> </ul> <p>The compressed folder of the newly described Aplysine1 contains also raw data related to circular dichroism (CD) and infrared (IR) analyses, as well as quantum mechanical calculations of <sup>13</sup>C NMR shifts using GIAO NMR and DP4+ analyses.</p> <p>The Excel spreadsheet for DP4+ analyses were obtained from: Grimblat N et al. “Beyond DP4: An Improved Probability for the Stereochemical Assignment of Isomeric Compounds Using Quantum Chemical Calculations of NMR Shifts.” <em>The Journal of Organic Chemistry</em> 80, no. 24 (December 18, 2015): 12526–34. <a href="https://doi.org/10.1021/acs.joc.5b02396">https://doi.org/10.1021/acs.joc.5b02396</a>.</p> <p>All MS data are also made Freely available at the UCSD Center for Computational Mass Spectrometry database with the MassIVE identifier <a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=4f6d3c00539a412a9c6d7fac0f7f2a81">MSV000089502</a> .</p> <p>NOTE: 3,5 dibromotyrosine was not identified neither in<em> Aplysina cavernicola </em>crude extract nor as exo-metabolites but was used for MS dereplication purposes.</p>
NMR data for "Rapid and simple 13C-hyperpolarization by 1H dissolution dynamic nuclear polarization followed by an in-line magnetic field inversion"
<p>Liquid-state and solid-state NMR data for "Rapid and simple 13C-hyperpolarization by 1H dissolution dynamic nuclear polarization followed by an in-line magnetic field inversion".</p> <p>The data enclosed are NMR data generated by the software Topspin by Burker Biospin. The experiments are dDNP runs that come in two parts: a solid-state and a liquid-state part.</p> <ul> <li>Experiments from 1 to 9 are reference experiments used to quantify polarization in other experiments</li> <li>Experiments 11-19, 21-29, 31-39, ... 61-69 correspond to 6 dDNP runs performed a different samples from the same batch. The numbers correspond between solid and liquid-state datasets</li> </ul> <p>The codes used to analyze the data are available at in a next upload.</p> <p>Refer to the main text of the paper and its supplementary material at 10.26434/chemrxiv-2023-6gd0l for more information.</p>
Data for "Dynamic of binary molecular systems – advantages and limitations of NMR relaxometry"
<p>Raw data for "Dynamic of binary molecular systems – advantages and limitations of NMR relaxometry". DOI of article: https://doi.org/10.1063/5.0188257</p>
Data for "Detection of metabolite-protein interactions in complex biological samples by high-resolution relaxometry: towards interactomics by NMR"
<p>Raw NMR data for relaxometry experiments, divided by donor sample. For every donor sample 2 or 3 different samples were used in order to record data at 19 different magnetic fields.</p> <p>Data from fast field-cycling relaxometry. All the data is in one xlsx file, divided by donor sample.</p> <p>Relaxometry results for alanine, lactate, creatinine and glutamine, obtained from the fitting of their relaxation decays recorded at 19 different fields, divided by donor sample.</p>
NMR Data for "Unveiling a Key Catalytic Pocket for the Ruthenium NHC-Catalysed Asymmetric Heteroarene Hydrogenation" (DOI: 10.1039/D1SC06409F)
<p># NMR Data for "Unveiling a Key Catalytic Pocket for the Ruthenium NHC-Catalysed Asymmetric Heteroarene Hydrogenation" (DOI: 10.1039/D1SC06409F)</p> <p>In the following, the original NMR Data for the publication "Unveiling a Key Catalytic Pocket for the Ruthenium NHC-Catalysed Asymmetric Heteroarene Hydrogenation" (DOI: 10.1039/D1SC06409F) is provided. </p> <p>## Experimental methodology and associated data</p> <p>### Dataset 200113.40a</p> <p>Inside an argon filled glovebox, 4.6 mg of **1-A** (5.4 µmol) was dissolved in 0.65 mL THF-d<sub>8</sub> (distilled over sodium/benzophenone and stored over 3 Å molecular sieves), yielding a clear, dark yellow solution. The solution was then transferred into a medium pressure J Young NMR tube and sealed. Subsequently, initial NMR spectra under argon atmosphere were recorded (t = 0 h).</p> <p>Afterwards, 2 bar of H2 pressure were applied to the J Young NMR tube, resulting in a partial H<sub>2</sub> pressure of 1 bar (due to the presence of 1 bar argon). After shaking to dissolve the added H<sub>2</sub>, a slow color change to orange could be observed. The reaction was monitored using 1H NMR (Bruker AV 400, 400 MHz), showing consumption of dissolved H<sub>2</sub> as evidenced by a decrease in intensity for the H<sub>2</sub> signal at δ(1H) = 4.55 ppm. Six hours after the first addition of H<sub>2</sub>, the J Young NMR tube was re-pressurized with 2 bar H<sub>2</sub>, and again after 36 h, shaking the NMR tube regularly to dissolve H<sub>2</sub>. After the third pressurization, no further decrease of dissolved H<sub>2</sub> could be observed.</p> <p>#### NMR experiments and timestamps</p> <p>File name | NMR Experiment | Time stamp / h (relative to H<sub>2</sub> addition)<br> --- | --- | ---<br> 200113.40a.1 | 1H | 0<br> 200113.40a.2 | 1H | 0<br> 200113.40a.3 | 1H | 0.5<br> 200113.40a.4 | 1H | 1<br> 200113.40a.5 | 1H | 2.5<br> 200113.40a.6 | 1H | 2.5<br> 200113.40a.7 | 1H | 5 <br> 200113.40a.8 | 1H COSY-45 | 5<br> 200113.40a.9 | 1H | 6.5<br> 200113.40a.10 | 1H | 22.5<br> 200113.40a.11 | 1H | 30<br> 200113.40a.12 | 1H | 31<br> 200113.40a.13 | 29Si-inept | 31<br> 200113.40a.14 | 1H-29Si HMBC | 31<br> 200113.40a.15 | 1H | 45.5<br> 200113.40a.16 | 1H-29Si HMBC | 45.5<br> 200113.40a.17 | 1H | 55<br> 200113.40a.18 | 1H | 69.5<br> 200113.40a.110 | 1H (larger measurement window) | 22.5<br> 200113.40a.111 | 1H (larger measurement window) | 30<br> 200113.40a.115 | 1H (larger measurement window) | 45.5<br> 200113.40a.117 | 1H (larger measurement window) | 55<br> 200113.40a.118 | 1H (larger measurement window) | 69.5</p> <p>### Dataset 200117.40a</p> <p>69.5 h after the first addition of H<sub>2</sub> no significant changes could be observed in the 1H NMR spectra anymore. At this point, 0.15 mL of a 0.052 M solution of benzofuran in THF-d<sub>8</sub> (7.8 µmol benzofuran, ca. 1.5 equivalents relative to **1-A**) were added to the NMR tube while applying 2 bar of H<sub>2</sub> pressure. No significant color change was observed upon addition of the substrate. Subsequently, the NMR tube was sealed and the reaction was monitored using 1H NMR for an additional 119 h, especially following the hydride signals at δ(1H) = −3.7 ppm and δ(1H) = −3.8 ppm as well as the signals of 2,3-dihydrobenzofuran at δ(1H) = 4.48 ppm and δ(1H) = 3.15 ppm. After 119 h of reaction time, the color of the reaction solution had changed to light orange.</p> <p>#### NMR experiments and timestamps</p> <p>File name | NMR Experiment | Time stamp / h (relative to substrate addition)<br> --- | --- | ---<br> 200117.40a.1 | 1H | 0.5<br> 200117.40a.2 | 1H | 1.5<br> 200117.40a.3 | 1H | 7<br> 200117.40a.4 | 1H | 24<br> 200117.40a.5 | 1H | 24.5 <br> 200117.40a.6 | 1H | 72 <br> 200117.40a.7 | 1H COSY-45 | 72<br> 200117.40a.101 | 1H (larger measurement window) | 0.5<br> 200117.40a.103 | 1H (larger measurement window) | 7<br> 200117.40a.104 | 1H (larger measurement window) | 24</p>
Glucosinolate and Desulfoglucosinolate NMR Data and Structures
<p><sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N NMR spectra, NMR parameters, and structures of a set of 31 glucosinolates or desulfoglucosinolates</p>
Titration_DB: NMR-monitored protein pH titration chemical shift data.
<p>This archive contains a backup of the NMR titration_db database raw chemical shift data.<br> Reference: D. Farrell et al., “Titration_DB: Storage and analysis of NMR-monitored protein pH titration curves.,” Proteins, vol. 78, no. 4, pp. 843–857, 2009.</p> <p>This data was formerly hosted on an interactive website which is no longer active. The files are stored as csv format, one per protein. They are also split into three folders according to the nuclei whose chemical shifts were used to detect the measurement (1H,13C or 15 N). Much of this data was obtained from literature. A table in the zip file (titration_dataset_info.csv) associates the protein name with the original paper. </p> <p>Note that the database stored the pka values fit using a model to each residue dataset. This is not stored here.</p> <p>Also present is a file titdb.fs. This is a binary file that can only be opened using the PEATDB software. PEATDB (Protein Engineering Analysis Tool - Database) was an application for sharing, analysing and storing experimental and theoretical data from Protein Engineering experiments.<br> This is now legacy software and no longer maintained. It was used to allow interactive fitting of the titration data using the Ekin module.<br> It is still possible to install this software if you really need to. It is stored on github at https://github.com/dmnfarrell/peat.</p> <p>D. Farrell May 2019</p>
NMR data - Mechanism and regioselectivity of the anionic oxidative rearrangement of 1,3-diketones towards all-carbon quaternary carboxylates
<p>NMR characterisation raw data for the publication:</p> <p>Mechanism and regioselectivity of the anionic oxidative rearrangement of 1,3-diketones towards all-carbon quaternary carboxylates</p>
NMR data of all compounds appearing in the study "Visible Light-Mediated Formal Alkylation and [4+1]-Cycloaddition Strategies of Silyl Enol Ethers with Aryldiazoacetates"
<p>FID files of NMR data (<em>e.g.</em> 1H, 13C{1H}, 19F{1H}, COSY, HSQC, DEPT135 and HMBC) associated with all compounds synthesized during the study entitled "Visible Light-Mediated Reactions of Silyl Enol Ethers with Aryldiazoacetates: Formal Alkylation and [4+1]-Cycloaddition Strategies" (a research project in organic synthesis)</p>
An assessment of acd_lotus for the structural dereplication of natural products using 13C NMR spectroscopy data.
<p> A method that relies on carbon-13 nuclear magnetic resonance (NMR) spectroscopy, elaborated in earlier works of the author's research group, requires the availability of a dedicated database that establishes relationships between chemical structures, biological and chemical taxonomy, and spectroscopy. The construction of such a database, called <a href="https://doi.org/10.5281/zenodo.6621129">acd_lotus</a>, was reported earlier and its usefulness was only illustrated by <a href="https://doi.org/10.1002/cmtd.202200054">three examples</a>. This dataset provides the results of structure searches carried out starting from 58 carbon-13 NMR data sets recorded on compounds selected in the metabolomics section of BMRB, the biological magnetic resonance bank.</p> <p>Correction in the JSON file of ascochitine.</p> <p>Addition of a CSV file according to <a href="https://doi.org/10.1186/s13321-021-00520-4">Schymanski and Bolton</a> for the description of the selected compounds.</p> <p>Better PNG drawings for compounds 28, 38, 46, and 57.</p> <p>Better PNG drawing for compounds 7 and 26.</p>
Raw NMR FID data of cryptoporic acid derivatives isolated from Cryptoporus volvatus fruiting bodies
<p>This is a NMR FID data of cryptoporic acid derivatives isolated from fruiting bodies of <em>Cryptoporus volvatus</em> (Polyporaceae).</p> <p>Isolation and structural elucidation of these compounds will be reported in the article titled "Species prioritization based on spectral dissimilarity: A case study of polyporoid fungi species", which is currently under revision.</p>
MD Data for Patterns in protein flexibility: a comparison of NMR "ensembles", MD trajectories and crystallographic B-factors
<p>This data set comprises five zipped directories that contain the scripts and intermediate molecular dynamics (MD) results used in (initially as of April 24, 2017, updated with additional directories on December 15, 2020) a soon to be submitted paper, "Patterns in protein flexibility: a comparison of NMR 'ensembles', MD trajectories and crystallographic B-factors" written by the authors of this entry. An earlier version of this paper is available via BioRxiv, DOI: https://doi.org/10.1101/240655.</p> <p>This paper explores patterns in coordinate variance and coordinate uncertainty in MD trajectories and in protein structures derived from NMR and compares coordinate variances/uncertainties with those crystallographic B-factors. The files, MD_data.zip and MD_data2.zip, each unzip to contain input files and scripts for reproducing the MD trajectories used in this paper (using DESMOND): MD_data.zip contains input files/scripts for the MD trajectories used in the preprint; MD_data2.zip contains input files/scripts for trajectories ran following publication of the preprint. The file btab_analysis_scripts.zip contains key scripts for analyzing those trajectories (following file conversion with VMD and superimposition with THESEUS) in MATLAB (this analysis assumes the presence of the FindCore Toolbox, written by David Snyder and available via the MATLAB Central File Exchange, as well as the MATLAB Statistics and Machine Learning Toolbox). And the files, superimposed_MD_trajectories.zip and superimposed_MD_trajectories2.zip, each unzip to yield the trajectories (superimposed using THESEUS and in PDB multimodel file format) analyzed in the soon to be submitted paper: superimposed_MD_trajectories.zip contains trajectories reported in the preprint and superimposed_MD_trajectories2.zip contains the results of subsequent simulations. </p>
Megalocarpoidolide_I NMR data
<p>Megalocarpoidolide_I, raw and processed NMR data; LSD (Logic for Structure Determination) software input file and result.</p>
Primary NMR Data Supporting the Article "Synthetic approach to 2-alkyl-4-quinolones and 2-alkyl-4-quinolone-3-carboxamides based on common β-keto amide precursors"
<p>This archive contains raw 1H/13C FIDs and associated data in Bruker-specific format that can be viewed with Bruker’s TopSpin or other appropriate NMR processing software. The subfolders are named in accordance with the compound numbering in the associated research paper (Synthetic Approach to 2-Alkyl-4-quinolones and 2-Alkyl-4-quinolone-3-carboxamides Based on Common β-Keto Amide Precursors).</p> <p>Correspondence: angelov@uni-plovdiv.bg</p> <p> </p>
Data for: Making 1H-1H couplings more accessible and accurate with selective 2DJ NMR experiments aided by 13C satellites
<p><sup>1</sup>H-<sup>1</sup>H coupling constants are one of the primary sources of information for NMR structural analysis. Several selective 2DJ experiments have been proposed that allow their individual measurement at pure shift resolution. However, all these experiments fail in the not uncommon case when coupled protons have very close chemical shifts. Firstly, the coupling between protons with overlapping multiplets is inaccessible due to the inability of a frequency-selective pulse to invert just one of them. Secondly, the strong coupling condition affects the accuracy of coupling measurements involving third spins. These shortcomings impose a limit on the effectiveness of state-of-the-art experiments, such as G-SERF or PSYCHEDELIC. Here, we introduce two new and complementary selective 2DJ experiments that we coin SERFBIRD and SATASERF. These experiments overcome the aforementioned issues by utilizing the <sup>13</sup>C satellite signals at natural isotope abundance, which resolve the chemical shift degeneracy. We demonstrate the utility of these experiments on the tetrasaccharide stachyose and the challenging case of norcamphor, for the latter achieving measurement of all <em>J</em><sub>HH</sub> couplings while only few were accessible with PSYCHEDELIC. The new experiments are applicable to any organic compound and will prove valuable for configurational and conformational analyses.</p> <p>This deposit contains Bruker pulse sequences of the SERFBIRD and SATASERF experiments, and the Bruker NMR experimental data. See the readme.pdf file for an overview of the latter.</p>
NMR data for Bis(ethanol) bis(4-benzoyl-1-(4-methoxybenzyl)-1H-pyrazol-5-olate)magnesium (17). 1H, 13C, HSQC
<p>NMP FAIRSpec example collection</p>
Amines-NMR data
<p>Raw NMR data for the article "A General Catalyst for the Base-Free Mono-N-Alkylation of Aromatic and Aliphatic Amines with Alcohols " published in Cell Reports Physical Science.</p> <p>The raw NMR data files for all compounds reported in the article are included. The numbering corresponds to those in the article.</p> <p>Each parent folder contains subfolders with different files. In order to process this data, the full parent folder must be dragged into either Mestrenova or Topspin and then the data is automatically processed. If the name of the raw data files are renamed, the software (<a href="https://mestrelab.com/">Mestrenova</a> or <a href="https://www.bruker.com/en/products-and-solutions/mr/nmr-software/topspin.html">Topspin</a>) will not be able to process the files. </p>
Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
<h1><strong>Changes applied to V2</strong></h1> <p>In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.</p> <p>The <strong>S2RCI</strong> and <strong>MD</strong> datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: </p> <ul> <li><strong>AlphaFold2 Models</strong>: Both original and truncated structures. </li> <li><strong>WEBnma Modes</strong>: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. </li> <li><strong>Root-Mean-Square-Fluctuations (RMSF)</strong>: Profiles calculated before and after truncation of AF2 models. </li> <li><strong>NMR Data: Normal Mode Analysis (NMA)</strong>: Performed on corresponding NMR ensembles (see below). </li> </ul> <p> </p> <p>The <strong>NMR Data</strong> of NMA in these datasets includes: </p> <ul> <li>NMR ensembles </li> <li>Individual NMR models extracted from each ensemble </li> <li>STRIDE secondary structure calculations per-individual NMR models</li> <li>RMSF profiles per-individual NMR models</li> </ul> <p>For detailed information, please refer to the `Readme.txt` file within each corresponding folder. </p> <p>The <strong>S2 dataset</strong> includes all the features listed above, except for the NMR analysis.</p>
NMR data for (NPA)6Zn3(H2O)2 in Synthesis, structural analysis, and docking studies with SARS-CoV-2 of a trinuclear zinc complex with N-phenylanthranilic acid ligands
<p><sup>1</sup>H, <sup>13</sup>C, COSY, HMBC, and HSQC NMR data in fid format for (NPA)<sub>6</sub>Zn<sub>3</sub>(H<sub>2</sub>O)<sub>2</sub> (NPA = 2-(phenylamino) benzoate) in DMSO-<em>d</em><sub>6.</sub></p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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