Interaction potential of parallel and antiparallel aligned, infinite polyanaline alpha-helices as obtained from SCC-DFTB + UFF calculations

# Polyalanine α-Helix Pair-Interaction Dataset ## Overview This dataset contains calculated interaction energies for pairs of rigid, infinite polyalanine α-helices. The calculations were used to construct helix-pair interaction potentials and to study structural ordering in self-assembled polyalanine monolayers. The helices were modeled using periodic boundary conditions along the helical axis. Pair energies were calculated using the self-consistent charge density-functional based tight-binding method (SCC-DFTB), with DFTB+ 20.1, the `mio-1-1` parameter set, and a dispersion correction based on universal force-field parameters. ## Helix geometryThe file- `alphaPA_18units.xyz` contains the atomic coordinates of a single polyalanine α-helix consisting of 18 alanine repeat units. The structure corresponds to the geometry used as the building block for the helix-pair interaction calculations described in this dataset. The file is provided in standard XYZ format. Atomic coordinates are given in Å, with the first line specifying the number of atoms and the translational repeat unit length in z-direction. This structure can be used as a reference for visualization, reproduction of the calculations, and construction of derived helix configurations. ## Interaction types The dataset contains four relative helix arrangements: | Code | Relative handedness | Axial alignment ||------|---------------------|-----------------|| `EP` | Equal | Parallel || `EA` | Equal | Antiparallel || `OP` | Opposite | Parallel || `OA` | Opposite | Antiparallel | The corresponding files are: - `E_all_EP.dat`- `E_all_EA.dat`- `E_all_OP.dat`- `E_all_OA.dat` ## File format Each file is a tab-separated table without a header. The columns are ordered as: ```textphi1 phi2 zeta R pair_energy``` where: - `phi1`: azimuthal rotation angle of the first helix, in degrees.- `phi2`: azimuthal rotation angle of the second helix, in degrees.- `zeta`: relative axial offset between the helices, in Å.- `R`: distance between the two helix axes, in Å.- `pair_energy`: calculated total energy of the two-helix system, in eV. ## Binding energy The helix-pair binding energy is calculated as ```textbinding_energy = pair_energy - 2 × isolated_helix_energy``` The isolated-helix reference energy and other machine-readable dataset properties are provided in `metadata.json`. A negative binding energy indicates an energetically favorable interaction relative to two isolated helices. ## Coordinate convention The first helix is used to define the relative coordinate system and is conventionally taken to be right-handed and oriented along the positive axial direction. The four interaction classes describe the handedness and axial orientation of the second helix relative to the first. Derived angular coordinates such as `chi` could be constructed from `phi1` and `phi2`, with the appropriate sign depending on the relative handedness. ## Reference When using this dataset, please cite: H. Ghodrati, K. Preis, T. N. H. Nguyen, C. Tegenkamp, S. Gemming, J. Kelling, and F. Günther, “Simulation of Self-Assembled Monolayers of Polyalanine α-Helices: Development and Application of an Effective Potential for Film Structure Predictions,” *ACS Applied Materials & Interfaces* **18** (2026), 30467–30479. DOI: 10.1021/acsami.6c01087 ## License See the Zenodo record for the license applying to the deposited dataset.