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4 results for “on-surface synthesis”
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>
Electrochemical on-surface synthesis of a strong electron-donating graphene nanoribbon catalyst
<p><span>On-surface synthesis of edge-functionalized graphene nanoribbons (GNRs) has attracted much attention. However, producing such GNRs on a large scale through on-surface synthesis</span><span> </span><span>under ultra-high vacuum on thermally activated metal surfaces has been challenging. This is mainly due to decomposition of functional groups at temperatures </span><span>of</span><span> 300 to 500°C and limited monolayer GNR growth based on the metal catalysis. To overcome these obstacles, we developed an on-surface electrochemical technique that utilizes redox reactions of asymmetric precursors at an electric double layer where a strong electric field is confined to the liquid-solid interface. <a name="_Hlk164526696"></a>We successfully demonstrate layer-by-layer growth of strong electron-</span><span><span>donating</span><span> GNRs on electrodes at temperatures </span><span><</span><span>80°C without decomposing functional groups.</span></span><span> </span><span>We show</span><span> that high-voltage facilitates previously unknown heterochiral di-cationic polymerization. <a name="_Hlk164368440"></a>Electro</span><span><span>chemically produced</span><span> GNRs exhibiting one of the strongest electron-</span><span>donating</span><span> properties known, enable extraordinary silicon-etching catalytic activit</span><span>y,</span><span> </span><span>exceeding those of </span><span>noble metals, with superior photoconductive properties.</span></span><span> </span><span>Our technique advances the possibility of producing various edge-functional GNRs.</span></p>
Supporting Information for On-Surface Synthesis of a Doubly Anti-Aromatic Carbon Allotrope
<p>This dataset contains computational outputs associated with the publication On-Surface Synthesis of a Doubly Anti-Aromatic Carbon Allotrope. </p>
On-Surface Synthesis of a π-Extended Diaza[8]circulene
<p><strong>All the data necessary for reproducing Probe-Particle Simulations published in :</strong></p> <p>On-Surface Synthesis of a π-Extended Diaza[8]circulene</p> <p>Kimihiro Nakamura, Qiang-Qiang Li, Ondřej Krejčí, Adam S. Foster<strong>*</strong>, Kewei Sun, Shigeki Kawai<strong>*</strong>, and Shingo Ito<strong>*</strong></p> <p><em>J. Am. Chem. Soc.</em> 2020, 142, 26, 11363–11369</p> <p>Publication Date:May 15, 2020</p> <p><a href="https://doi.org/10.1021/jacs.0c02534">https://doi.org/10.1021/jacs.0c02534</a></p> <p>The protocol (and description of the files) is as follows:</p> <p>1. <strong>POSCAR</strong>, which contains: DFT optimised geometry of DBCOT/Au(111) (w. 5 layers of Au) as calculated via <a href="https://www.vasp.at">VASP</a> by Adam. S. Foster</p> <p><strong>2. INCAR,</strong> Input file for DFT-<a href="https://www.vasp.at">VASP</a> optimisation performed by Adam S. Foster containing physical and output settings of the DFT calculations</p> <p><strong>3. geometry.in.</strong> <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> input geometry w. 3 Au layers used for eigenvectors output (1st <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> run) and PDOS (2nd <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> run)</p> <p><strong>4. control-eigenvectors.in,</strong> Input file containing physical and output settings of the DFT calculations performed with <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a>. To run the actual calculation renaming to "control.in" is necessary. This file was used for printing out the eigenvectors </p> <p><strong>5. control-pdos.in, </strong> Input file containing physical and output settings of the DFT calculations performed with <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a>. To run the actual calculation renaming to "control.in" is necessary. The file used for printing out atom Projected Density Of States (PDOS).</p> <p><strong>6. NO FILE</strong>: <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> PBE calculation performed on Triton (Aalto Uni.) cluster w. developers version of <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> from 19th November 2019 compiled with OpenMPI and Intel (2017) ifort & mkl:<br> 1) KS. eigenvectors with only mpi version aims.191119.mpi.x (personal note: not needed any more, one can use the scalapack version as well)<br> 2) PDOS w. mpi and scalapack version aims.191119.mpi.scalapack.x</p> <p> Except for the txt (ASCII) output files, all the other files not shown. (too much data, can be reproduced with given geometry.in & control.in files)</p> <p><strong>7. output_mpi.txt</strong>, <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> 1st run text output in ASCII format(used for eigenvectors production)</p> <p><strong>8. output_scalapack.txt</strong>, <a href="https://aimsclub.fhi-berlin.mpg.de">FHI-AIMS</a> 2nd run output in ASCII format (used for PDOS production)</p> <p><strong>9. LOCPOT.xsf.tar.gz </strong>gunzip compressed LOCPOT.xsf file containing electrostatic potential from the original <a href="https://www.vasp.at">VASP</a> calculation. LOCPOT -> LOCPOT.xsf conversion were proceeded via <a href="http://theory.chm.tu-dresden.de/~jk/software.html">v2xsf</a></p> <p><strong>10. NO FILE</strong>, <a href="https://github.com/ProkopHapala/ProbeParticleModel">PP-AFM</a> master github <a href="https://github.com/ProkopHapala/ProbeParticleModel/commit/aab812d8f38f2192a1ccb71359f60ea06a4b8454">this version</a> used for creation of relaxed Probe Particle (PP) positions above the sample. </p> <p><strong>11. params-stright.ini</strong>, input file for the <a href="https://github.com/ProkopHapala/ProbeParticleModel">PP-AFM</a> simulations with physical settings. Before the run necessary to rename to "params.ini". This file was used for the simulation with a straight tip. !!! Small mistake here - monopole instead of 4pole used for the calculations !!!</p> <p><strong>12. params-tilt.ini</strong>, input file for the <a href="https://github.com/ProkopHapala/ProbeParticleModel">PP-AFM</a> simulations with physical settings. Before the run necessary to rename to "params.ini". This file was used for the simulation with a straight tip. !!! Small mistake here - monopole instead of 4pole used for the calculations !!!</p> <p><strong>13. NO FILE</strong>, the <a href="https://github.com/ProkopHapala/ProbeParticleModel">PP-AFM</a> workflow goes as written on the <a href="https://github.com/ProkopHapala/ProbeParticleModel/wiki">wiki</a>:</p> <pre><code>python PP-AFM/generateElFF.py -i LOCPOT.xsf python PP-AFM/generateLJFF.py -i LOCPOT.xsf python PP-AFM/relaxed_scan.py --pos</code></pre> <p>The inter-created files are not saved here, but can be recreated with given files and workflow.</p> <p><strong>14. NO FILE</strong>, <a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a>, version used for CO-tip STM (close aka High Resolution; and far away) and for "reconstruction" of electronic densities within certain energy window: Master b66fa0d commited on 24 Oct 2019. The PP-AFM (used internally in PP-STM for xsf and npy reading, was <a href="https://github.com/ProkopHapala/ProbeParticleModel/tree/d8ece8f13920449747c2ab2920df9128729befa3">the last version of python2</a> ) </p> <p><strong>15. PPSTM_simple_e0.3.py</strong>, Script running <a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> simulations for "s" orbital of CO-tip for straight scan</p> <p><strong>16. PPSTM_simple_e0.3_pxy.py</strong>, Script running <a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> simulations for "pxy" orbitals of CO-tip for straight scan</p> <p><strong>17. SUM_no_atoms.py</strong>, Script for creating images using pre-calculated "s" and "pxy" orbitals.</p> <p><strong>18. Straight_tip_height_002.jpg</strong>, a different visualisation of the image with height 002, which is used in the article.</p> <p><strong>19. distance_measurements.png</strong>, Screenshot from measurements of distances - using <a href="http://gwyddion.net/">Gwyddion</a> and original PNG file as input - the black and white image was coloured by <a href="http://gwyddion.net/">Gwyddion</a> - written distances are 10x lower, than in reality, see measurement 9 for comparison with plotted ticks.</p> <p><strong>20. PPSTM_simple_e0.3_pz_tilt.py, </strong><a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> script for calculation of tilting "pz" orbital on CO-tip, as the tip is relaxing. The tip has originally tilted equilibrium position.</p> <p><strong>21. PPSTM_simple_e0.3_pxy_tilt.py, </strong><a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> script for calculation of tilting "<em>px</em>" and "<em>py</em>" orbitals on CO-tip, as the tip is relaxing. The tip has originally tilted equilibrium position.</p> <p><strong>22. SUM_no_atoms_tilt.py</strong>, <a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> script for summing contribution of tilting "pz" and "pxy" orbitals of CO-tip and production of images</p> <p><strong>23. PPSTM_simple_f_e0.3.py</strong>, <a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> script for creation of dI/dV images w. fixed CO-tip (25%s + 75%pxy) - 4Å above the molecule</p> <p><strong>25. fixed_tip_dIdV_simulations.png</strong>, all far away -fixed- CO-tip (25%s,75%pxy) dIdV simulations 4Å above the molecule</p> <p><strong>26. DOS_plot_and_view.nb</strong>, Density of states were plotted using slightly modified <a href="https://github.com/ondrejkrejci/MathemticaForDFTnSPM/blob/master/DOS_plot_and_view.nb">DOS_plot_and_view.nb</a> Wolfram Mathematica notebook (from<a href="https://github.com/ondrejkrejci/MathemticaForDFTnSPM">MathemticaForDFTnSPM github repository</a>); here is the original mathematica notebook.</p> <p><strong>27. DOS_plot_and_view.pdf</strong>, printed out important part of the Mathematica notebook.</p> <p><strong>28. PPSTM_xsf</strong>, <a href="https://github.com/ondrejkrejci/PPSTM">PP-STM</a> script for creation of XSF files for "reconstruction" of real space electron density within given energy windows. We used energy windows: {-0.95,-0,85} for HOMO-1, {-0.65,-0,55} for HOMO,{+1.35,+1.45} for LUMO and {+1.55,+1.65} for LUMO+1. All the energies are in eV. The XSF file, which was visually checked via <a href="http://jp-minerals.org/vesta/en/">VESTA software</a>. The XSF files are not stored here, but can be recreated using this workflow.</p> <p><strong>29. measurement_gwyddion.gwy</strong>, <a href="http://gwyddion.net/">Gwyddion</a> file w. saved distances measurements.</p> <p> </p>
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