Data for: Bistable carbon nanobracelets
Description
Folder "High symmetry" contains raw data for carbon nanobracelets made of 2-5 monomer fragments. Folder "Low symmetry" contains raw data for carbon nanobracelets made of 4-5 monomer fragments. ├ ARC files - result of PM3 optimization by MOPAC2016 with symmetry constraints for high-symmetry molecules and without symmetry constraints for low symmetry molecules, ├ OUT files - result of DFT optimization by PRIRODA which uses for input configuration the PM3 pre-optimized geometry; should be opened by Chemcraft software to see list of optimization steps and frequencies for optimized geometry, ├ PNG files - visualization of DFT optimized geometry by Chemcraft software, └ XLS files - calculation of the molecule outer radius, the variation of bond lengths in chains by Eq. (1), and interchain distances shown in Figure 2. Folder "MEP Jmol" contains Jmol visualizations of the Molecular electrostatic potential (MEP) of the studied molecules. ├ XYZ files - input files containing PRIRODA optimized geometry (three columns XYZ; in angstroms) and partial atomic charges (last column; in elementary charge e), ├ SPT file - Jmol script used for MEP visualization; scale factor e²/4πε₀Å = 1.439964548·10⁴ meV converts e/Å (Jmol MEP units) to meV, ├ PNG files - MEP visualizations, ├ JAR file - Jmol v. 14.31.41; 2021-05-29, └ BAT file - command/batch file for execution Jmol under Windows environment. Folder "Molden" contains Chemcraft visualizations of HOMO and LUMO of the studied molecules. ├ OUT files - PRIRODA single point Molden calculations of the optimized molecules containing only HOMO and LUMO orbitals prepared by the GAWK script from the large (~100-500 Mb) output, ├ PNG files - HOMO and LUMO visualizations; render settings, ├ TXT files - Camera settings for HOMO and LUMO visualizations, ├ AWK file - GAWK script used for preparing short OUT files containing only HOMO and LUMO orbitals, ├ ZIP file - GAWK v. 3.1.0-2; 2001-06-03, └ BAT file - command/batch file for GAWK script execution under Windows environment.
Files
Steps to reproduce
- ARC and TXT files can be viewed in the text mode with the Notepad, - OUT and XYZ files can be viewed in Chemcraft; in the left panel, you can select to view: "Starting geometry", "Optimization steps", "Optimized geometry", and "Frequency ..." - molecule animations from the calculated vibrational spectrum, - PNG files can be viewed in Internet browser, - XLS files can be viewed in Internet browser. To reproduce MEP visualizations: - run "jmol2021.bat" in the "MEP Jmol" folder, - in the Jmol window go to menu File/Script Editor..., - copy the content of the MEP.spt to the Script Editor, - run the script by pressing the "Run" button, - at the end of the script, uncomment the lines //normal_output=true; and //rotate45=true; - press "Run"; in the "MEP Jmol" folder PNG visualization files will be created, - at the beginning of the script, comment out the line: molecule = "ooooo7_C2_chr"; - uncomment the line: //molecule = "oooo7_D4h_chr"; press "Run", - repeat for molecules: "oooo7_D2d_chr" and "ooooo7_D5h_chr"; To reproduce HOMO-LUMO visualizations: - run Chemcraft; open the OUT file from the "Molden" folder, - go to the menu Tools/Orbitals/Render molecular orbitals, - select "Molecular orbital 1 (Occ., ...)" and "Molecular orbital 2 (Unocc., ...)", - set Map points per angstrom: 10; press "Ok", - wait for the 3D map to build, - in the left panel select "Molecular orbital 1 (Occ., ...)", - below the panel, press the buttons "Show isosurface" and "Both signs", - select menu Display/CPK coloring 2, then Display/Customize, - press "Edit scheme", check the bottom-left option "Depth cueing", move slider to maximum; "Ok", "Close", - press the Camera button, - set the slider close to Height: 1300, - press "Ok", - open Paint, paste (Ctrl-V), crop to the selection (Ctrl-Shift-X), - save as PNG, - to change the camera position open file "Camera HL-...txt", copy the lines below the desired position to the clipboard, - go to menu "View/Restore the "Camera" position from Clipboard". To create a compact OUT file from a large Molden PRIRODA output (~500 Mb) with GAWK script: - in the "Molden" folder, extract "GAWK3102.zip" to the current folder, - copy the large OUT file to the "Molden" folder, - rename the large OUT file to "1.OUT", - execute the script by running "HLstrip.bat", - numbers of HOMO and LUMO will be detected automatically by the script, - a compact OUT file "HL.out" will be created in the "Molden" folder, - "HL.out" contains only geometry and HOMO and LUMO of the molecule, - the autodetected HOMO and LUMO are indicated in "HL.out" by the lines: Autodetected HOMO: 510 Autodetected LUMO: 511 - to manually set HOMO and LUMO numbers, in "HLstrip.bat", comment out the second line and uncomment the first line, where you can manually set the desired orbital numbers (e.g.): -v homo=408 -v lumo=409 - the manually set HOMO and LUMO numbers are indicated in "HL.out" by the lines: HOMO defined in command line: 408 LUMO defined in command line: 409