First-Principles Analysis of Protonation-Induced Electronic Effects in Tetrakis(p-aminophenyl)porphyrin (TAPP)

Repository Description This repository contains all data, computational outputs, and analysis tools required to reproduce the results of the TAPP protonation study. It provides optimized molecular structures, quantum-chemical outputs, spectral data, and post-processing scripts used for the evaluation of electronic structure and optical properties across all protonation states. The archive is organized in a transparent, folder-based structure to ensure full reproducibility and ease of navigation: Computational Data and Structures xyz_filesOptimized geometries of all protonation states and conformers in Cartesian coordinates. terachem_output_UV-visOutput files from TD-DFT calculations performed using TeraChem, including excitation energies and oscillator strengths.A bash script for parsing UV–vis data from raw outputs is also included. molden_filesMolden-format files for all optimized structures, enabling visualization of molecular orbitals and electronic structure. dipole_momentGround-state, excited-state (relaxed and unrelaxed), and transition dipole moments for all systems. Triplet_EscfTeraChem output file and corresponding summery file for ground state energy, dipole moment and centre of mass for triplet state. Spectral Data and Processing Raw_UV-vis_dataParsed UV–vis excitation data (energies and oscillator strengths) in CSV format, directly extracted from TD-DFT outputs. broadended_and_shifted_dataProcessed UV–vis spectra obtained by applying Gaussian broadening (FWHM = 0.1 eV) and an energy shift (−0.66 eV) to align with experimental observations.This folder also includes Python scripts used to generate: Broadened and Shifted absorption profiles Shifted Stick spectra Visualization and Analysis HTML_filesInteractive HTML visualizations of excitation-resolved charge density differences (CDDs). These files allow simultaneous inspection of: Electron density redistribution upon excitation Associated transition dipole moments Excitation energies and spectra The interactive format enables intuitive exploration of structure–property relationships across protonation states. Scientific Scope This repository enables detailed analysis of: Protonation-dependent changes in molecular geometry and symmetry Evolution of UV–vis absorption spectra across protonation states Charge redistribution upon electronic excitation (CDD analysis) Emergence of charge-transfer states at higher protonation levels Correlation between electronic structure, dipole moments, and spectral features Reproducibility All results presented in the study can be reproduced from the provided data and scripts: Optimized structures and full quantum-chemical outputs are included Raw and processed spectral datasets are provided separately Scripts for parsing, broadening, and shifting spectra are available Interactive visualization tools enable direct inspection of excited-state properties The repository ensures full transparency and reproducibility of the computational workflow and analysis.