This README_Parker_Cubane-DCA_dataset.txt file was generated on 24th November 2025 by Prof. Stewart F. Parker. ------------------- GENERAL INFORMATION ------------------- Title of Dataset: Parker_Cubane-DCA_dataset Author Information (Name, Institution, Address, Email) Principal Investigator: Prof Stewart F. Parker, ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxon, OX11 0QX, UK, stewart.parker@stfc.ac.uk Co-investigators: Dr James P. Tellam and Dr Sarah E. Youngs, ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, UK, james.tellam@stfc.ac.uk; sarah.youngs@stfc.ac.uk Date of data collection: 22nd - 26th July 2024 Geographic location of data collection: ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxon, OX11 0QX, UK Information about funding sources or sponsorship that supported the collection of the data: The STFC Rutherford Appleton Laboratory is thanked for funding and access to neutron beam facilities via ISIS beam time proposal RB2410038. Computing resources (time on the SCARF compute cluster for the CASTEP calculations) was provided by STFC's e-Science facility. This research has been performed with the aid of facilities at the Research Complex at Harwell, including the FT-Raman spectrometer. The authors would like to thank the Research Complex for access and support to these facilities and equipment. -------------------------- SHARING/ACCESS INFORMATION -------------------------- This dataset is licensed by the rights-holder(s) under a Creative Commons Attribution 4.0 International Licence (CC-BY): https://creativecommons.org/licenses/by/4.0/. Recommended citation for the data: S.F. Parker, J.P. Tellam and S. Youngs (2025). Parker_Cubane-DCA_dataset eData: the STFC Research Data Repository (https://edata.stfc.ac.uk/ ). DOI (this can be obtained from the ‘view item’ page, under ‘URI.’). Citation for and links to publications that cite or use the data: S.F. Parker, J.P. Tellam and S. Youngs, Vibrational spectroscopy and computational studies of cubane-1,4-dicarboxylic acid, Molecules (2025) Related data sets: INS database of analysed spectra: http://wwwisis2.isis.rl.ac.uk/INSdatabase/. -------------------- DATA & FILE OVERVIEW -------------------- The dataset consists of this file (README_Parker_Cubane-DCA_dataset.txt), five zip files: "A-Cubane-DCA_Experimental_spectra.zip", "B-Cubane-DCA_CASTEP.zip", "C-Cubane-DCA_AbINS.zip", "D-Cubane-DCA_CASTEP_convergence.zip", "E-Cubane-DCA_NMR_data.zip" and an image file (Cubane-DCA_TOC.jpg). "A-Cubane-DCA_Experimental_spectra.zip" contains the solid state experimental vibrational spectra. The infrared, Raman and INS spectra are all in ASCII and have a .dat extension,. These can be viewed with any text reader or can be loaded into programs such as Excel or Origin to display the spectra. Spectra of cubane-1,4-dicarboxylic acid have the stem Cubane-DCA and those of cubane-1,4-dicarboxylic acid-D2 have the stem Cubane-DCA-D2. For the infrared and Raman data, the filename is the name of the compound and includes the resolution, the number of scans and the laser power (Raman only) and ends in _Infrared for infrared, _Raman for FT-Raman. The infrared and Raman data consists of two columns of ASCII data. Column 1 is the energy transfer in wavenumber (cm-1), column 2 is the intensity (Absorbance for the infrared data, arbitrary units for the Raman data). The INS data recorded on TOSCA is in the files that end _INS.dat. The INS data consists of three columns: column 1 is the energy transfer in wavenumber (cm-1), column 2 is the intensity, S(Q,w) (arbitrary units), and column three is the error bar of the intensity given in column 2. There are two header lines, these start with the "#" character. "B-Cubane-DCA_CASTEP.zip" contains: The input (Cubane-DCA.cell and Cubane-DCA.param) and output (Cubane-DCA.castep) of the geometry optimisation of the complete unit cell using the CASTEP (version 23.1) program. The .castep file includes the geometry optimised structure and this is provided as a crystallographic information file (Cubane-DCA.cif). The CASTEP (version 23.1) input files used for the vibrational calculation (Cubane-DCA_Efield.cell and Cubane-DCA_Efield.param) with the output files (Cubane-DCA_Efield.castep and Cubane-DCA_Efield.phonon). The .phonon file includes both the transition energies and atomic displacements for all the atoms in each mode. The input (Cubane-cubic.cell and Cubane-cubic.param) and output (Cubane-cubic.castep) of the geometry optimisation of idealised cubane with octahedral symmetry in a cubic lattice (Cubane-cubic) unit cell using the CASTEP (version 23.1) program. The .castep file includes the geometry optimised structure and this is provided as a crystallographic information file (Cubane_cubic.cif). The CASTEP (version 23.1) input files used for the vibrational calculation (Cubane-cubic_Efield.cell and Cubane-cubic_Efield.param) with the output files (Cubane-cubic_Efield.castep and Cubane-cubic_Efield.phonon). Isotopic calculations were generated from the parent molecule using the Phonons utility which is part of the CASTEP package. Phonons uses a .cell and .param input file and generates a .phonon file from these using the force constant matrix stored in the .check file. The files generated have the stems: Cubane_cubic_Efield-D2 - cubane with Oh symmetry substituted with deuterium (mass = 2) at the 1,4 positions. Cubane_cubic_DCA-mass - cubane with Oh symmetry substituted with "hydrogen" with mass = 45 (i.e. that of a carboxylic acid group) at the 1,4 positions. Cubane-DCA_Efield_D2 - cubane-1,4-dicarboxylic acid with deuterium (mass = 2) at the 1,4 positions. The .phonon file includes both the transition energies and atomic displacements for all the atoms in each mode. These can be used to view the modes with either commercial software (Materials Studio) or freeware (Jmol). "C-Cubane-DCA_AbINS.zip" contains the ASCII files generated by the AbINS utility from the .phonon files of the CASTEP output. The data for Figure 6 are: (a) Cubane_cubic_H-fundamentals.dat (b) Cubane_cubic_D2_H-fundamentals.dat (c) Cubane_cubic_DCA-mass_H-fundamentals.dat (d) Cubane_DCA_H-fundamentals.dat Figure 6. The effect of increasing mass at the 1,4 positions of cubane on the calculated spectra: (a) cubane, (b) cubane-1,4-D2, (c) cubane-1,4-DCA-mass and (d) cubane-1,4-dicarboxylic acid. The data for Figure 7 are: (a) Cubane_DCA_H-fundamentals.dat (b) Cubane-DCA_syn-OH-only.dat (c) Cubane-DCA_anti-OH-only.dat (d) Cubane-DCA_syn-cubane-only.dat (e) Cubane-DCA_anti-cubane-only.dat Figure 7. Calculated INS spectra of cubane-1,4-dicarboxylic acid: (a) total spectrum comprising contributions from all of the hydrogen atoms, (b) contribution of only the carboxylic acid hy-drogens of the syn conformer, (c) contribution of only the carboxylic acid hydrogens of the anti conformer positions, (d) contribution of only the cubane hydrogens of the syn conformer and (e) contribution of only the cubane hydrogens of the anti conformer. "D-Cubane-DCA_CASTEP_convergence.zip" contains the CASTEP files used for the convergence checks and an Excel file that summarises the results. The file stems are called: Cubane-DCA_convX and Cubane-DCA_convX_Efield, for the geometry optimisation (.param, .cell and .castep files) and the vibrational calculation (.param, .cell, .castep and .phonon files) respectively. The "X" in the filename denotes the conditions: X = 1: Cut-off energy = 900 eV, MP grid = 6 x 4 x 6 (36 kpoints) X = 2: Cut-off energy = 1200 eV, MP grid = 6 x 4 x 6 (36 kpoints) X = 3: Cut-off energy = 1020 eV, MP grid = 4 x 3 x 4 (16 kpoints) X = 4: Cut-off energy = 1020 eV, MP grid = 8 x 6 x 8 (96 kpoints) X = 5: Cut-off energy = 1400 eV, MP grid = 6 x 4 x 6 (36 kpoints) The phonon file using the standard conditions (Cut-off energy = 1020 eV, MP grid = 6 x 4 x 6 (36 kpoints)) present in "A-Cubane-DCA_Experimental_spectra.zip" is used as the reference state. "Convergence_data.xlsx" is an Excel file summarising the results. "E-Cubane-DCA_NMR_data.zip" contains the ASCII files of the NMR spectra and plots of the spectra in a pdf file. The .dat files contain ASCII data as generated by the spectrometer. These are in an inconvenient format, so there are matching .csv files that are more convenient for plotting. These were used to generate the spectra in the pdf file. -------------------------- METHODOLOGICAL INFORMATION -------------------------- The INS spectra were measured on TOSCA at ISIS at ~20K. They were converted from time-of-flight to energy transfer using Mantid (version 6.12.0), with the rebin string "3,-0.005,500", available from: https://www.mantidproject.org/Main_Page. This is a free download). Infrared spectra were recorded in air at room temperature using a Bruker Vertex70 FTIR spectrometer, over the range 50 to 4000 cm-1 at 4 cm-1 resolution with a DLaTGS detector using 256 scans and the Bruker Diamond ATR. The spectra have been corrected for the wavelength-dependent variation in pathlength using the Bruker software. FT-Raman spectra were recorded in air at room temperature with a Bruker MultiRam spectrometer using 1064 nm excitation, 4 cm-1 resolution, 500 mW laser power and 256 scans. All Fourier transform spectra used 8x zerofilling to improve the peak shape. 1H and 13C NMR spectra of both the as-received and the deuterated compound were measured at room temperature in DMSO-D6 solution using a Bruker Avance NEO 400 MHz NMR spectrometer. The ab initio data were calculated using CASTEP (version 23.1, using the PBE functional, the Tkatchenko-Scheffler dispersion correction scheme, on-the-fly-generated norm conserving pseudopotentials, full details are included in the .castep output files. INS spectra were generated from the ab initio results (the CASTEP .phonon file) using the program AbINS, part of the Mantid package. This is freeware available at: https://www.mantidproject.org/