Basic Information: Title: Data for "Computational vibrational spectra for formic acid adsorbed on magnetite surfaces from DFT calculations" DOI: 10.15480/882.15191 Data creators and contributors: Gregor Vonbun-Feldbauer, Hamburg University of Technology (Germany), gregor.feldbauer@tuhh.de, orcid: 0000-0002-9327-0450 Kai Sellschopp, University of Canterbury (New Zealand), kai.sellschopp@canterbury.ac.nz, orcid: 0000-0002-0003-2075 Date of creation of this repository: June 27, 2025 Version: 1.0.0 Software: DFT calculations: Vienna Ab-initio Simulation Package (VASP), Version 5.4.4 Content information: Research context: The data presented here was created within the collaborative research center (CRC) 986 "Tailor-made Multi-scale Materials systems (M3)" funded by the German Research Foundation (DFG). In this collaborative project inorganic nanoparticles functionalized by organic ligands were investigated for their to self-assemble into well-ordered supercrystalline nanocomposites with extraordinary mechanical properties among others. For a detailed understanding of the involved processes these systems were studied on all relevant length scales. The hybrid organic-inorganic interface, particularly formic acid adsorbed on magnetite surfaces as a model system, were investigated on the atomistic scale using experimental and computational approaches. Among others infrared (IR) spectroscopy and calculated vibrational properties were used to learn more about adsorption properties, including adsorption type, geometry, and site. This data set contains input structures for the calculations of such vibrational properties and calculated IR spectra for the adsorption of formic acid and formate on different magnetite surfaces, namely Fe3O4 (001) and Fe3O4 (111). Methods for data creation and data processing: This dataset contains input files for and output data of density functional theory calculations (DFT) for obtaining the vibrational frequencies of formic acid and formate molecules adsorbed on the magnetite (001) and (111) surfaces. Details on the DFT calculations taken from supporting information of Creutzburg et al. (doi: 10.1021/acs.jpclett.1c00209): "Spin-polarized calculations based on Density Functional Theory (DFT) were performed with the Vienna Ab-initio Simulation Package (VASP, version 5.4.4) using a plane-wave basis set.[1,2] Pseudopotentials created with the Projector Augmented Wave (PAW) method allow treating only the valence electrons, namely 2s2 2p4 for oxygen, 3d7 4s1 for iron, 1s1 for hydrogen, and 2s2 2p2 for carbon, explicitly. Energies and forces are calculated within the Generalized Gradient Approximation (GGA) by employing the PBE exchange-correlation functional.[3] The Hubbard model with a parameter U = 4.0 eV accounts for the localization of the d-electrons of iron.[4–6] Convergence with respect to energy cut-off and k-point sampling was achieved within 1 meV/atom. [...] Vibrational frequencies and relative intensities are calculated in the harmonic approximation with Density Functional Perturbation Theory (DFPT) and using the Born Effective Charges (BEC).[7–12]" Further information on the specific model systems can be obtained from the corresponding publications. Using the output of the DFT/DFPT calculations (mainly the OUTCAR for VASP calculations which are not provided here, but can be calculated with VASP using the INCAR and POSCAR files), IR spectra and animations of the vibrational motions of the atoms can be calculated and visualised. Form the output, first the vibrational intensities have to be calculated. This can be done, e.g., using the tool "VASP-infrared-intensities" by David Karhanek (https://github.com/dakarhanek/VASP-infrared-intensities). The results can be plotted for obtaining IR spectra. Here, we are supplying an own python script "plotIR.py" for that. Moreover, the eigenvectors of the vibrational motions can be used to produce animations of the vibrations. Here, we provide an python script "vibrations.py" for producing snapshots of the motions as xyz-files that can be visualised using additional software such as VMD (Visual Molecular Dynamics, https://www.ks.uiuc.edu/Research/vmd/). The vibrations.py script is using two additionally provided scripts "poscarRW.py" and "xyzRW.py" for reading and writing POSCAR and XYZ files. Those scripts can also be easily replaced by using other tools as e.g. ASE (Atomic Simulation Environment, https://wiki.fysik.dtu.dk/ase/). The provided scripts are currently not well documented and should only be used with care and at your own risk. We accept no liability. References: [1] Kresse, G.; Furthmüller, J.; Phys. Rev. B 1996, 54, 11169–11186. [2] Kresse, G.; Furthmüller, J.; Comput. Mater. Sci. 1996, 6, 15–50. [3] Perdew, J. P.; Burke, K.; Ernzerhof, M.; Phys. Rev. Lett. 1996, 77, 3865–3868. [4] Yu, X.; Huo, C.-F.; Li, Y.-W.; Wang, J.; Jiao, H.; Surf. Sci. 2012, 606, 872–879. [5] Noh, J.; Osman, O. I.; Aziz, S. G.; Winget, P.; Brédas, J.-L. ; Sci. Technol. Adv. Mater. 2014, 15, 044202. [6] Meier, M.; Jakub, Z.; Balajka, J.; Hulva, J.; Bliem, R.; Thakur, P. K.; Lee, T.-L.; Franchini, C.; Schmid, M.; Diebold, U.; Nanoscale 2018, 10, 2226–2230. [7] Baroni, S.; Giannozzi, P.; Testa, A.; Phys. Rev. Lett. 1987, 58, 1861–1864. [8) Giannozzi, P.; Baroni, S.; J. Chem. Phys. 1994, 100, 8537–8539. [9] Gonze, X.; Phys. Rev. A 1995, 52, 1086–1095. [10] Giannozzi, P.; Baroni, S.; Handbook of Materials Modeling; Springer, Dordrecht, 2005; pp 195–214. [11] Karhánek, D.; Bučko, T.; Hafner, J.; J. Phys. Condens. Matter 2010, 22, 265006. [12] Würger, T.; Heckel, W.; Sellschopp, K.; Müller, S.; Stierle, A.; Wang, Y.; Noei, H.; Feldbauer, G.; J.Phys. Chem. C 2018, 122, 19481–19490. Structure and content of the data: As input a prototypical VASP INCAR file for calculating vibrational frequencies and various pre-relaxed atomic coordinate files of adsorption structures in VASP's POSCAR-format are given. As output data xyz-files containing snapshots of the atomic positions during vibrations are available. Those files allow to create animations of the vibrational modes using additional software such as VMD (Visual Molecular Dynamics, https://www.ks.uiuc.edu/Research/vmd/). Further details on the computational settings, related calculations such as structural pre-relaxations and vibrational spectra can be found in the corresponding publications (DOIs: 10.1038/s42004-019-0197-1, 10.1021/acs.jpclett.1c00209, 10.15480/882.3791, 10.1039/D5CP00848D). Provided files: Information and Nomenclature INCAR_vib_prototyp : Prototypical VASP INCAR file for calculation of vibrational properties using DFPT, particularly for magnetite. The number atoms and the center of mass have to be adjusted for the used simulation cell. Also other settings might have to adapted depending on the studied materials. The POSCAR files contain the atomic coordinates used for the calculations of the vibrational properties. The POSCAR files follow the structure for VASP input files and are saved here as text files. For using the POSCARs with other codes than VASP adaptions might be necessary. For visualisation with common tools as VESTA it is advisable to replace the ".txt" with ".vasp". The disp zip-files hold xyz files containing snapshots of the atomic positions during vibrations with a given wave number. The file names follow the same nomenclature. "Filetype"_"material"-"surface"_"adsorbate"-"coverage"-"adsorption mode"-"adsorption geometry" with the following possibilities: - Filetype: POSCAR / disp - Material: fe3o4 - Surface: 001 / 111 - Adsorbate: FA (Formic acid or formate) - Coverage: tm / hm / fm (third / half / full monolayer, defined as the number of adsorbates divided by the number of Fe ions in the top surface layer) - Adsorption mode: mol / dis (molecular / dissociative adsorption) - Adsorption geometry: bd / md / qdr / chel / qdc (bi-dentate / mono-dentate / quasi-dentate-restgroup_H / chelating / quasi-bi-dentate-carboxy_H) additional geometrical information: int / tet / parallel / triangle (specifying placement or orientation of adsorbates), H1/2/3/4NN (nearest neighbour shell of surface O atoms where carboxy H atoms bind to, measured from the surface Fe where adsorbate binds to) Provided files: List of files INCAR_vib_prototyp.txt POSCAR_fe3o4-001_FA-hm-dis-bd-int.txt POSCAR_fe3o4-001_FA-hm-dis-bd-tet.txt POSCAR_fe3o4-001_FA-hm-dis-md.txt POSCAR_fe3o4-001_FA-hm-mol-md.txt POSCAR_fe3o4-001_FA-hm-mol-qdr.txt POSCAR_fe3o4-111_FA-fm-dis-chel-parallel.txt POSCAR_fe3o4-111_FA-fm-dis-chel-trianlge.txt POSCAR_fe3o4-111_FA-fm-dis-md.txt POSCAR_fe3o4-111_FA-fm-dis-qdr.txt POSCAR_fe3o4-111_FA-fm-mol-md.txt POSCAR_fe3o4-111_FA-fm-mol-qdr.txt POSCAR_fe3o4-111_FA-tm-dis-chel-H4NN.txt POSCAR_fe3o4-111_FA-tm-dis-qdc-H1NN.txt POSCAR_fe3o4-111_FA-tm-dis-qdc-H2NN.txt POSCAR_fe3o4-111_FA-tm-dis-qdc-H3NN.txt disp_fe3o4-001_FA-hm-dis-bd-int.tar disp_fe3o4-001_FA-hm-dis-bd-tet.tar disp_fe3o4-001_FA-hm-dis-md.tar disp_fe3o4-001_FA-hm-mol-md.tar disp_fe3o4-001_FA-hm-mol-qdr.tar disp_fe3o4-111_FA-fm-dis-chel-parallel.tar disp_fe3o4-111_FA-fm-dis-chel-triangle.tar disp_fe3o4-111_FA-fm-dis-md.tar disp_fe3o4-111_FA-fm-dis-qdr.tar disp_fe3o4-111_FA-fm-mol-md.tar disp_fe3o4-111_FA-fm-mol-qdr.tar disp_fe3o4-111_FA-tm-dis-chel-H4NN.tar disp_fe3o4-111_FA-tm-dis-qdc-H1NN.tar disp_fe3o4-111_FA-tm-dis-qdc-H2NN.tar disp_fe3o4-111_FA-tm-dis-qdc-H3NN.tar Several python scripts are provided for processing and visualising DFT/DFPT output data. The provided scripts are currently not well documented and should only be used with care and at your own risk. We accept no liability. Provided scripts: - plotIR.py (for plotting calculated IR spectra) - vibrations.py (for creating snapshots for vibrational motions for animations) - poscarRW.py (for reading and writing POSCAR files) - xyzRW.py (for reading and writing XYZ files) Abbreviations: Born Effective Charges (BEC) Density Functional Perturbation Theory (DFPT) Density Functional Theory (DFT) Generalized Gradient Approximation (GGA) Infrared (IR) Perdew-Burke-Ernzerhof (PBE) Vienna Ab-initio Simulation Package (VASP) License, access rules and usage: Creative Commons Zero (CC0) Recommended citation: G. Vonbun-Feldbauer and K. Sellschopp, Data for ”Computational vibrational spectra for formic acid adsorbed on magnetite surfaces from DFT calculations”. TUHH Open Research (TORE) Repository, DOI: 10.15480/882.15191, 2025. Bib entry @misc{Tore_DFT-IR-data, doi = {10.15480/882.15191}, url = {https://tore.tuhh.de/handle/11420/55635}, author = {Vonbun-Feldbauer, Gregor and Sellschopp, Kai}, language = {en}, title = {{Data for "Computational vibrational spectra for formic acid adsorbed on magnetite surfaces from DFT calculations".}}, publisher = {TUHH Universit\"{a}tsbibliothek}, year = {2025}, copyright = {Creative Commons Zero (CC0)}, howpublished = {TUHH Open Research (TORE) Repository, DOI: 10.15480/882.15191} }