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48 results for “Organic synthesis”
Synthesis data for manuscript: Global stocks and capacity of mineral-associated soil organic carbon
<p>Supporting synthesis data for manuscript: Georgiou K., Jackson R. B., Vindušková O., Abramoff R. Z., Ahlström A., Feng W., Harden J. W., Pellegrini A. F. A., Polley H. W., Soong J. L., Riley W. J., Torn M. S. Global stocks and capacity of mineral-associated soil organic carbon. <em>Nature Communications</em>, 2022.</p> <p>We performed an observational synthesis of soil fractionation data constituting 1,144 globally-distributed soil profiles from 78 studies that reported fractionation and bulk measurements of organic carbon across depths. This dataset includes measurements of mineral-associated, particulate, and bulk soil organic carbon, as well as ancillary data on edaphic, climate, and vegetation characteristics. We also performed a separate observational synthesis of soil carbon accrual from manipulation and chronosequence studies, which included changes in carbon stocks or concentrations, bulk density, experimental duration, and edaphic properties. This latter synthesis included 103 observations from 34 studies that spanned crop, pasture, grassland, and forest ecosystems across climates and soil types. Further details for both syntheses can be found in the methods and supplementary materials of the associated manuscript.</p>
Synthesis of Phenol-Tagged Ruthenium Alkylidene Olefin Metathesis Catalysts for Robust Immobilisation Inside Met-al-Organic Framework Support
<p>Data confirming the structure of the new compounds obtained within the project, published in <em>Catalysts</em> <strong>2023</strong>, <em>13</em>(2), 297; <a href="https://doi.org/10.3390/catal13020297">https://doi.org/10.3390/catal13020297</a></p> <p>The research was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 860322 for the ITN-EJD “Coordination Chemistry Inspires Molecular Catalysis” (CCIMC) and by the National Science Centre, Poland (OPUS grant 2017/27/B/ST5/00941).</p>
Raw data for the article "Organic Dye Photocatalyzed Synthesis of Functionalized Lactones and Lactams via a Cyclization-Alkynylation Cascade"
<p>Raw NMR and MS data for the article "Organic Dye Photocatalyzed Synthesis of Functionalized Lactones and Lactams via a Cyclization-Alkynylation Cascade" published in Organic Letters, DOI: </p> <p><a title="DOI URL" href="https://doi.org/10.1021/acs.orglett.3c03603">https://doi.org/10.1021/acs.orglett.4c01078</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>
Upcycling a Plastic Cup: One-Pot Synthesis of Lactate Containing Metal Organic Frameworks from Polylactic Acid
<p>Data supporting publication: <strong>Upcycling a plastic cup: one-pot synthesis of lactate containing metal organic frameworks from polylactic acid</strong>, Benjamin Slater, So-On Wong, Andrew Duckworth, Andrew J. P. White, Matthew R. Hill and Bradley P. Ladewig, Chen. Commun. (2019), DOI: <a href="https://doi.org/10.1039/c9cc02861g">10.1039/c9cc02861g</a>. </p> <p>Includes raw data for XRD spectra for all materials, CIF file and checkCIF file.</p> <p>v2 includes additional high-resolution photos and diagrams supporting the publication</p>
On-Surface Synthesis of Disilabenzene-Bridged Covalent Organic Frameworks
<p>Here you will find the list of folders and their contents used to generate the data and the figures published on "On-Surface Synthesis of Disilabenzene-Bridged Covalent Organic Frameworks" paper</p> <p><strong>On SiCOF_data.zip you will find the following folders:</strong><br> <strong>2D_network_on_au:</strong><br> outcar_k3.fin: VASP output file. Contains the DFT parameters used to relax the Si-COF network geometry on gold<br> poscar_k3.fin: VASP geometry file. This is the relaxed geometry of the Si-COF network on gold obtained in the previous calculation<br> output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si-COF network on gold<br> <strong>C4Si2_ribb_on_au:</strong><br> outcar.fin: VASP output file. Contains the DFT parameters used to relax the Si ribbon 1 geometry on gold<br> poscar.fin: VASP geometry file. This is the relaxed geometry of the Si ribbon 1 on gold obtained in the previous calculation<br> output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si ribbon 1 network on gold<br> <strong>C4Si_ribb_on_au:</strong><br> outcar.fin: VASP output file. Contains the DFT parameters used to relax the Si ribbon 2 network geometry on gold<br> poscar.fin: VASP geometry file. This is the relaxed geometry of the Si ribbon 2 network on gold obtained in the previous calculation<br> output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si ribbon 2 network on gold<br> <strong>critic2</strong>:<br> - Example of input files to simulate constant current (cc) and constant height (ch) stm using the Tersoff-Hamann approximation through the critic2 code:<br> stm_cc.inp stm_ch.inp<br> <strong>NICs</strong>:<br> - ORCA output files. Contains the DFT parameters and geometries used to calculate the nucleus independent nuclear shift (NICs) of several molecules:<br> 2D-buckled.out<br> benzene.out<br> disilahexa.out<br> mol2Br.out<br> 2D-flat.out<br> Brsila.out<br> mol2Br+2Au.out<br> silaben.out<br> <strong>PPSTM</strong>:<br> params.ini: control file for the PPM (PP-AFM) code, that is used to calculate the position of oxygen for the relaxed STM scan calculated by PP-STM<br> <strong>PPSTM_simple.py</strong>: Script running PP-STM simulations with 13% of s and 87% of pxy orbitals (one possibility for simulating CO tip)</p> <p><strong>On Source_data.zip you will find all the unprocessed images used in the paper. Additionally, it is included in CHGCAR_files.zip the charge densities used to generate the supplementary figure 5. </strong></p> <p><strong>Version of the softwares and workflow on the PP-STM:</strong><br> FHI-aims version ( https://aimsclub.fhi-berlin.mpg.de ) was aims.191119.mpi.scalapack.x .<br> cirtic2: https://aoterodelaroza.github.io/critic2/examples/example_14_01_stmqe/<br> PPM (PP-AFM) version was a master version from Nov 4, 2021: https://github.com/ProkopHapala/ProbeParticleModel/commit/327c61cdbd348307c5255c4618f12d28f4ababd5<br> PP-STM version was a master version from Nov 16, 2021: https://github.com/Probe-Particle/PPSTM/commit/4434739bd737e58a2fc556dff24e8e7d6eab084e</p> <p>The workflow for the PP-STM (CO-tip STM) images was as follows:<br> Using the poscar*.fin for creating the geometry.<br> Run a single point (no optimization) calculation with FHI-aims for creating the hartree potential ("cube_001_hartree_potential.cube") and <br> then with control.in and PPSTM_simple.py file in the folder and with properly set way to<br> PP-AFM folder and PP-STM path (in the top of the PPSTM_simple.py file) running following commands in command line:</p> <p>python3 PPAFM_PATH/generate_LJFF.py -i cube_001_hartree_potential.cube<br> python3 PPAFM_PATH/generate_ElFF.py -i cube_001_hartree_potential.cube # these will create force-field for PP-AFM calculations #<br> python3 PPAFM_PATH/relaxed_scan.py --pos # this will create position of Probe Particle (simulating oxygen postions ) for the STM scan #<br> python3 PPSTM_simple.py # will create the PPSTM images #</p>
Data for "Competitive aminal formation during the synthesis of a highly soluble, isopropyl-decorated imine porous organic cage"
<div>In the following subdirectories are the input and output of DFT and conformer calculations for this publication:</div> <div> </div> <div>DOI: 10.1039/D3CC00072A</div> <div> </div> <div>Previously uploaded in <span>10.5281/zenodo.8432296 and </span><a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer"><span>https://github.com/andrewtarzia/citable_data</span></a></div> <div> </div> <div>sub-directories:</div> <div> <ul> <li>intermediate_calculations/<br> <ul> <li>Input intermediate structures, incl. amine, aldehyde and water precursors, as `.mol` files.</li> <li>Output structures from GFN2-xTB optimisation as `_opt.mol` and `_opt.xyz` files.</li> <li>GFN2-xTB energies for different solvents as `_SOLV.ey` files.</li> <li>`.csv` files containing:<br> <ul> <li>all_total_energies.csv : Total energy of all intermediates from all methods. [column `xtbgas` is the one used in the manuscript]</li> <li>all_formation_energies.csv : Formation energy of all intermediates from all methods. [column `xtbgas` is the one used in the manuscript]</li> <li>all_formation_energies_per_imine.csv : Formation energy per imine bond formed of all intermediates from all methods. [column `xtbgas` is the one used in the manuscript]</li> </ul> </li> </ul> </li> <li>intermediate_calculations/gaussian_calculations/ [note that these are not used in the manuscript] <ul> <li>Gaussian16 input and output for DFT calculations on the intermediates.</li> <li>Structures are the GFN2-xTB optimised structures.</li> <li>File names match the directory above as such `NAME_opt_SOLV_METHOD.gau/log`<br> <ul> <li>SOLV include `gas`, `dcm` (dichloromethane) and `cfm` (chloroform).</li> <li>METHOD inclde `pbe` (PBE1PBE/Def2TZVP) and `mp2` (MP2/aug-cc-pVDZ).</li> </ul> </li> </ul> </li> <li>intermediate_calculations/orca_calculations/ [note that these are not used in the manuscript]<br> <ul> <li>Orca input and output for DFT calculations on the intermediates.</li> <li>Structures for B97-3c optimisation are the GFN2-xTB optimised structures.<br> <ul> <li>Result for each intermediate are saved as `_o_NAME_opt_B97-3c.xyz`.</li> </ul> </li> <li>Structures for the MP2 single-point are the B97-3c output. [note that these are not used in the manuscript]</li> <li>File names match the directory above as such `o_NAME_opt_METHOD.in/out`<br> <ul> <li>All calculations performed in gas phase.</li> <li>METHOD inclde `B97-3c` (composite method) and `MP2` (RI-MP2 cc-pVTZ). [note that these are not used in the manuscript]</li> </ul> </li> </ul> </li> <li>conformer_calculations/<br> <ul> <li>Eight zipped directories for four diamines and four imines used in conformer analysis including all optimised conformer structures and their energies.</li> <li>Four zipped directories (`opls_structures`) containing Macromodel/OPLS3e conformers.</li> </ul> </li> </ul> </div> <p> </p>
Raw data files for the "The Mechanism of Rapid and Green Metal–Organic Framework Synthesis by In Situ Spectroscopy and Diffraction" manuscript
<p>All files are organized by figures in the main text of the original publication: https://doi.org/10.1021/acs.chemmater.4c00879, in the form of .csv files.</p>
Research Data supporting "Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures"
<p>Raw research data supporting the article A. Sarkar, T. Behera, R. Sasmal, R. Capelli, C. Empereur-mot, J. Mahato, S. S. Agasti, G. M. Pavan, A. Chowdhury, S. J. George "Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures".</p>
Facile synthesis of magnesium-based metal-organic framework with tailored nanostructure for effective VOCs adsorption
<p class="16">A novel Mg(II) metal–organic framework (Mg-MOF) was synthesised based on the ligand of 2,2'-bipyridine-4,4'dicarboxylic acid (Bpdc). Single-crystal X-ray structural analysis confirmed that 3D-nanostructure Mg-MOFs formed a monoclinic system with a channel size of 15.733 Å × 23.736 Å. The N<sub><span>2</span></sub> adsorption isotherm, Fourier-transform infrared spectroscopy, thermogravimetric analysis and high-resolution transmission electron microscopy were performed to characterise the thermal stability and purity of the Mg-MOFs. The adsorption studies on four typical volatile organic compounds (VOCs) emitted during wood drying showed that Mg-MOFs have noteworthy adsorption capacities, especially for benzene and β-pinene with adsorptions of 182.26 mg/g and 144.42 mg/g, respectively. In addition, the adsorption of Mg-MOFs mainly occurred via natural adsorption, specifically, multi-layer physical adsorption, accompanied by chemical forces, which occurred in the pores where the VOCs molecules combined with active sites. As an adsorbent, Mg-MOFs exhibit versatile behaviour for toxic-gas accumulation.</p>
Expanding the Diversity of Linkages in Covalent Organic Frameworks through Staudinger Cycloaddition: Synthesis of cis-β-Lactam and cis-β-Thiolactam COFs
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Facile synthesis of magnesium-based metal-organic framework with tailored nanostructure for effective VOCs adsorption
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Synthesis, characterization and CO2 adsorption studies of DABCO based pillared Zn-BDC and Co-BDC metal organic frameworks
<p><span>This study focuses on pre-synthetic functionalized MOF material normally known as pillared layer MOFs. An additional component DABCO (1,4-diazabicyclo[2.2.2] octane) is added to the MOFs which works as a pillar to produce 3d structured MOFs. Zn-BDC-DABCO and Co-BDC-DABCO were studied for their performance in CO<sub>2</sub> capture application. The addition of DABCO turns the 2d-layered metal-BDC lattice to a 3d structure with enhance performance for CO<sub>2</sub> capture. The MOFs were characterized using XRD, SEM, TGA, FTIR and BET and the CO<sub>2</sub> capture capacity was tested at 25</span><span>°C and 0-25 bar. Zn-BDC-DABCO and Co-BDC-DABCO showed a maximum adsorption capacity of 6.3 and 4.4 mol/kg CO<sub>2</sub>.</span></p>
The Molecular Diversity Scope of Oxindole Derivatives in Organic Synthesis
<p>The role of oxindole derivatives is discussed as starting materials in diverse organic reactions including two and more components between the years 2014 until 2020. Oxindoles are famous because of their biological properties for instance chromanone-fused polycyclic pyrrolidinyl-dispirooxindoles, functionalized polycyclic spiro-fused carbocyclicoxindole, and 3,3-disubstituted oxindoles have anti-cancer, anti-tumor, and anti-microbial properties, respectively. Therefore, various methods for synthesizing the oxindole structures have received more attention in organic chemistry.</p>
Scheme 5 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Scheme 5 Synthesis of substituted pyrroles from 1,4-diaryl-2-butene-1,4-diones and ammonium formate.
Scheme 2 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Scheme 2 Pathways for the Paal-Knorr synthesis of pyrroles: A. the enamine pathway and B. the hemiaminal pathway.
Scheme 3 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Scheme 3 Formation of N-unsubstituted pyrrole by the reaction of urea and acetonylacetone absorbed over K10 in a microwave oven.
Scheme 15 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Scheme 15 A plausible mechanism of calcium(II) chloride catalyzed Paal-Knorr condensation under MW irradiation.
Scheme 23 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Scheme 23 Synthesis of new pyrrole-based compound by reaction of 3-nitro-2H-chromenes with an ethyl isocyanoacetate.
Scheme 8 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Scheme 8 MW assisted Paal-Knorr condensation of cyclopentenone to a set of tricyclic pyrrole- 2-carboxamides.
Figure 3 from: Mateev E, Irfan A, Mateeva A, Georgieva M, Zlatkov A (2024) Microwave-assisted organic synthesis of pyrroles (Review). Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e119866
Figure 3 Number of published articles containing "microwave synthesis" indexed in Scopus (accessed 09.2023).
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Annotated Behaviour and Observability Dataset (ABODe)
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