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26 results for “macrocycles”
Tuning the Thermal Stability and Photoisomerization of Azoheteroarenes through Macrocycle Strain
<p>Azobenzene and its derivatives are one of the most-widespread molecular scaffolds in a range of modern applications, as well as in fundamental research. After photoexcitation, azo-based photoswitches revert back to the most stable isomer in a timescale ( ) that determines the range of potential applications. Attempts to bring to extreme values prompted to the development of azobenzene and azoheteroarene derivatives that either rebalance the E- and Z- isomer stabilities, or exploit unconventional thermal isomerization mechanisms. In the former case, one successful strategy has been the creation of macrocycle strain, which tends to impact the E/Z stability asymmetrically, and thus significantly modify . On the bright side, bridged derivatives have shown an improved optical switching owing to the higher quantum yields and absence of degradation. However, in most (if not all) cases, bridged derivatives display a <em>reversed</em> thermal stability (more stable Z-isomer), and smaller than the acyclic counterparts, which restricts their potential interest to applications requiring a fast forward and backwards switch. In this paper, we investigate the impact of alkyl bridges to the thermal stability of phenyl-azoheteroarenes using computational methods, and we reveal that is indeed possible to combine such improved photo-switching characteristics while preserving the <em>regular</em> thermal stability (more stable E-isomer), and increased values under the appropriate connectivity and bridge length.</p>
Xanthene[n]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly
<p>Data underlying the figures in the publication “Xanthene[<em>n</em>]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly”, published in <em>J</em><em>ACS Au</em> 2021, 1, 11, 1885–1891. <a href="https://doi.org/10.1021/jacsau.1c00343">https://doi.org/10.1021/jacsau.1c00343</a></p>
CREMP-CycPeptMPDB: Conformer-rotamer ensembles of macrocyclic peptides for machine learning with permeability annotations
<p>CREMP-CycPeptMPDB: A resource generated for the rapid development and evaluation of machine learning models for permeable macrocyclic peptides. CREMP-CycPeptMPDB contains 3,258 unique macrocyclic peptides and their high-quality structural ensembles generated using the Conformer-Rotamer Ensemble Sampling Tool (CREST). Altogether, this dataset contains nearly 8.7 million unique macrocycle geometries, each annotated with energies derived from semi-empirical tight-binding DFT calculations and with experimental membrane permeability measurements obtained from the <a href="http://cycpeptmpdb.com/" target="_blank" rel="noopener">CycPeptMPDB</a> database. We anticipate that this dataset will enable the development of machine learning models that can improve peptide design and optimization for novel therapeutics.</p> <p>This dataset complements the <a title="CREMP" href="../doi/10.5281/zenodo.7931444" target="_blank" rel="noopener">CREMP dataset</a>, which contains a larger selection of conformer ensembles for homodetic macrocyclic peptides.</p> <p>We provide the data in two available formats, either as Python pickle files, which provide quick read access with RDKit version 2022.09.5 or later, and as text-based SDF files with associated metadata in JSON format. Each file is named based on its amino acid sequence, with residues separated by periods, using standard one-letter codes with lowercase letters representing D-amino acids and "Me" prefixes representing <em>N</em>-methylated amino acids. The sequences are in no particular order, e.g., "C.R.E.M.P" and "R.E.M.P.C" correspond to the same peptide macrocycle. The filename extensions are ".pickle", ".sdf", and ".json".</p> <p>Each file in the “pickle” folder contains a Python dictionary with amino acid sequence, SMILES, CREST metadata, and a single RDKit molecule object containing all conformers. All files in the folder were compressed into a single “pickle.tar.gz” archive. In the “sdf_and_json” folder, each individual SDF file contains all conformers, each associated with its own JSON file that contains CREST metadata. Similarly, all are compressed into another single archive, “sdf_and_json.tar.bz2”. A single summary CSV file is also provided containing ”sequence”, “smiles”, “num_monomers”, “num_atoms”, “num_heavy_atoms”, along with the CREST metadata “totalconfs”, “uniqueconfs”, “lowestenergy”, “poplowestpct”, “temperature”, “ensembleenergy”, “ensembleentropy”, and “ensemblefreeenergy”. The number of unique conformers with different 3D structures is given by “uniqueconfs”, while “totalconfs” includes the number of rotamers in addition.</p> <p>The unzipped sizes of the archives are approximately 13 GB for "pickle.tar.gz" and 84 GB for "sdf_and_json.tar.bz2". If you encounter errors when trying to load the pickle files, please make sure your RDKit version is at least 2022.09.5. If that doesn't work, try other Python versions.</p>
CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning
<p>CREMP: A resource generated for the rapid development and evaluation of machine learning models for macrocyclic peptides. CREMP contains 36,198 unique macrocyclic peptides and their high-quality structural ensembles generated using the Conformer-Rotamer Ensemble Sampling Tool (CREST). Altogether, this dataset contains nearly 31.3 million unique macrocycle geometries, each annotated with energies derived from semi-empirical tight-binding DFT calculations. We anticipate that this dataset will enable the development of machine learning models that can improve peptide design and optimization for novel therapeutics.</p> <p>We provide the data in two available formats, either as Python pickle files, which provide quick read access with RDKit version 2022.09.5 or later, and as text-based SDF files with associated metadata in JSON format. Each file is named based on its amino acid sequence, with residues separated by periods, using standard one-letter codes with lowercase letters representing D-amino acids and "Me" prefixes representing <em>N</em>-methylated amino acids. The sequences are in no particular order, e.g., "C.R.E.M.P" and "R.E.M.P.C" correspond to the same peptide macrocycle. The filename extensions are ".pickle", ".sdf", and ".json".</p> <p>Each file in the “pickle” folder contains a Python dictionary with amino acid sequence, SMILES, CREST metadata, and a single RDKit molecule object containing all conformers. All files in the folder were compressed into a single “pickle.tar.gz” archive. In the “sdf_and_json” folder, each individual SDF file contains all conformers, each associated with its own JSON file that contains CREST metadata. Similarly, all are compressed into another single archive, “sdf_and_json.tar.bz2”. A single summary CSV file is also provided containing ”sequence”, “smiles”, “num_monomers”, “num_atoms”, “num_heavy_atoms”, along with the CREST metadata “totalconfs”, “uniqueconfs”, “lowestenergy”, “poplowestpct”, “temperature”, “ensembleenergy”, “ensembleentropy”, and “ensemblefreeenergy”. The number of unique conformers with different 3D structures is given by “uniqueconfs”, while “totalconfs” includes the number of rotamers in addition.</p> <p>The unzipped sizes of the archives are approximately 32 GB for "pickle.tar.gz" and 210 GB for "sdf_and_json.tar.bz2". If you encounter errors when trying to load the pickle files, please make sure your RDKit version is at least 2022.09.5. If that doesn't work, try other Python versions.</p>
Window[1]resorcin[3]arenes: A novel macrocycle able to self-assemble to a catalytically active hexameric cage
<p>open data for paper Window[1]resorcin[3]arenes: A novel macrocycle able to self-assemble to a catalytically active hexameric cage</p>
Raw data for the article "Synthesis of Fluorescent Cyclic Peptides via Gold(I)-Catalyzed Macrocyclization"
<p>Raw NMR, IR, MS fluorescence and imaging data for the article "Synthesis of Fluorescent Cyclic Peptides via Gold(I)-Catalyzed Macrocyclization" published in the Journal of the American Chemical Society, DOI: </p><p><a href="https://doi.org/10.1021/jacs.3c09261">https://doi.org/10.1021/jacs.3c09261</a></p><p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
Simulation Reveals the Chameleonic Behavior of Macrocycles
<p>Supporting Information for article titled "Simulation Reveals the Chameleonic Behavior of Macrocycles"</p>
Initial structures of macrocyclic Gαq protein inhibitors bound to the Gq heterotrimer
<p>Initial PDB structures of the Gq heterotrimer in its apo form or bound to either ym2 or fr9 inhibitors. These structures were used in the molecular dynamics simulations described in the manuscript below: </p> <p><strong>Unraveling binding mechanism and kinetics of macrocyclic Gαq protein inhibitors</strong> (under review)<br> <em>Jan H. Voss<sup>1</sup>, Jessica Nagel<sup>1</sup>, Muhammad Rafehi<sup>1</sup>, Ramon Guixà-González<sup>2,5</sup>, Davide Malfacini<sup>3</sup>, Julian Patt<sup>3</sup>, Stefan Kehraus<sup>3</sup>, Asuka Inoue<sup>4</sup>, Gabriele M. König<sup>3</sup>, Evi Kostenis<sup>3</sup>, Xavier Deupi<sup>2,5</sup>, Vigneshwaran Namasivayam<sup>1</sup>, and Christa E. Müller<sup>1</sup></em></p> <p><em><sup>1</sup>PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany<br> <sup>2</sup>Condensed Matter Theory Group, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland<br> <sup>3</sup>Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53113 Bonn, Germany<br> <sup>4</sup>Tohoku University, Graduate School of Pharmaceutical Sciences, Sendai, Miyagi, 980-8578 Japan<br> <sup>5</sup>Laboratory of Biomolecular Research, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland</em></p>
Raw data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization"
<p>Raw NMR, HPLC and MS data for the article "Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization" published in Angewandte Chemie, DOI: </p> <p><a href="https://doi.org/10.1002/anie.202306036">https://doi.org/10.1002/anie.202306036</a> </p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Data for: On-resin synthesis and late-stage functionalization of macrocyclic atosiban mimetics via 5-iodo-1,4-triazoles
Open the record for dataset details and reuse information.
Raw data for the article "Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization"
<p>Raw NMR, HPLC and MS data for the article "Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization" published in Angewandte Chemie, DOI: </p> <p><a href="https://doi.org/10.1002/anie.202404747">https://doi.org/10.1002/anie.202404747</a> </p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
Fig. 3 in New tricks for old dogs: Two new macrocyclic trichothecene epimers and absolute configuration of 16-hydroxyverrucarin B
Fig. 3. Determination of the absolute configuration of compound 1 using Mosher's esters: ΔδH values [ΔδH (in ppm) = δS – δR].
Fig. 4 in New tricks for old dogs: Two new macrocyclic trichothecene epimers and absolute configuration of 16-hydroxyverrucarin B
Fig. 4. Comparison of the ECD data in millidegrees between compounds 1 and 2 recorded in MeOH at 0.05 mg/mL; the ECD data reported in molar ellipticity are in the supplement (Fig. S23).
Fig. 6 in New tricks for old dogs: Two new macrocyclic trichothecene epimers and absolute configuration of 16-hydroxyverrucarin B
Fig. 6. Determination of the absolute configuration of compound 3 using Mosher's esters: ΔδH values [ΔδH (in ppm) = δS – δR].
Schrock molybdenum alkylidene catalyst enables selective formation of macrocyclic unsaturated lactones by ring-closing metathesis at high-concentration
<p>Data supporting findings described in Green Chemistry, 2023, 25, 2299-2304. <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D2GC02988J">https://doi.org/10.1039/D2GC02988J</a></p> <p>The research was performed within OPUS project and was funded by National Science Centre, Poland, grant number DEC-2019/33/B/ST4/00874.</p>
Supplementary dataset for Expanded sequence space of radical S-adenosylmethionine-dependent enzyme involved in post-translational macrocyclization
<p>Supplementary dataset for <a href="https://www.researchsquare.com/article/rs-1789925/v1">Expanded sequence space of radical S-adenosylmethionine-dependent enzyme involved in post-translational macrocyclization</a></p> <p>Supporting Information Dataset 1: Logo sequences of 500 clusters in precursor SSN.</p> <p>Supporting Information Dataset 2: 199 cyclophane precursor from actinobacteria</p> <p>Supporting Information Dataset 3: Distribution of different enzymes adjacent to small peptides</p> <p>Supporting Information Dataset 4: Cross-comparison analysis of antiSMASH and PRISM-RiPP-predicted rSAM maturase</p> <p>Supporting Information Dataset 5: mmseq2 output of all identified precursors.</p>
Catalyst-Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides
<p>Data underlying the figures in the publication “Catalyst-Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides”, published in <em>Angew. Chem. Int. Ed.,</em> <strong>2020</strong>, 59, 18390–18394. <a href="https://onlinelibrary.wiley.com/doi/10.1002/anie.202005733">https://onlinelibrary.wiley.com/doi/10.1002/anie.202005733</a></p> <p>Table of contents:</p> <p><strong>1. Dataset</strong>; Word file containing: synthesis, experimental data, general procedures for the preparation of the catalyst, overview and methodology for nonreduced transannular polyketide cyclizations, selectivity, methodology and overview of transannular polyketide cyclization cascades (partially reduced), and NMR & X-ray data of the compounds in the publication.</p>
Fig. 7. Key COSY and NOSEY correlations for compound 3 in New tricks for old dogs: Two new macrocyclic trichothecene epimers and absolute configuration of 16-hydroxyverrucarin B
Fig. 7. Key COSY and NOSEY correlations for compound 3.
Fig. 2. Key COSY and NOSEY correlations for compound 1 in New tricks for old dogs: Two new macrocyclic trichothecene epimers and absolute configuration of 16-hydroxyverrucarin B
Fig. 2. Key COSY and NOSEY correlations for compound 1.
Computational data on "Proton Affinity and Conformational Integrity in a 24-atom Triazine Macrocycle Across Physiologically-relevant pH"
<p>The archive contains 5 different folders:<br><br>1. mdp_files, that contains all the input files for the minimization, equilibration and molecular dynamics run (in gromacs format);<br>2. topologies, that contains the equilibrated configurations and topology of the 2 systems studied -protonated and deprotonated macrocycles- (in gromacs format);<br>3. trajectories, that contains the coordinates of the macrocycles during the metadynamics calculations and the relevant metadynamics output files (hills file and energy file);<br>4. plumed_input, that contains the input file for the metadynamics calculations.<br>5. gaussian, that contains input and output for the single-point charge calculations.</p>
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