Dataset on the Photochemistry of the Energy-Storing Isomer of a Norbornadiene-Based Molecular Switch

This dataset is a collection of computer programs and simulation data related to the manuscript Photochemistry of the Energy-Storing Isomer of a Norbornadiene-Based Molecular Switch: Ring Opening, Rehybridized Intramolecular Charge Transfer, and Isomerization into a Carbene Photoproduct by Bo Durbeej, Simone Pintér, Andreas Hirsch, and Michał Andrzej Kochman. List of contents: 1. Program for Nonadiabatic Molecular Dynamics (NAMD) Simulations with the Time-Dependent Density Functional Theory With One Double (TDDFT-1D) Method2. NAMD Trajectories of the Photorelaxation Process of the Quadricyclane Isomer of a Norbornadiene-Based Molecular Switch3. Animations of Simulated Trajectories4. Input and Output Files for the Electronic Structure Calculations Reported in our Study 1. Program for NAMD Simulations with the TDDFT-1D Method Subdirectory: 1_NAMD_Program This subdirectory contains the C++ source code of the "wrapper" program which was used to carry out NAMD simulations at the TDDFT-1D level. The program is interfaced to the electronic structure software package Q-Chem, version 6.3.1. At each time step of the simulated NAMD trajectory, the wrapper generates Q-Chem input files, calls Q-Chem for the calculation of state energies, the gradient of the current state, and nonadiabatic coupling vectors, then parses the output files, and extracts the relevant quantities. Moreover, the wrapper propagates the nuclear and electronic equations of motion. Input files Some simulation parameters such as the basis set, exchange-correlation functional, integration grid, convergence thresholds, etc. are hard-coded in the source code. The remaining parameters are defined in the following input files: control – this file contains the main parameters of the NAMD simulation:nsteps – number of NAMD time steps that are to be performedh mts – classical time step (in au; 1 fs = 41.34 au) and subdivision of the classical time step into the TDSE time step. h should be 20.67 au (=0.5 fs) or less. mts should be 500 or higher.nstates – number of states included in the simulation (including S0). In this version of the program, nstates=3 is the only acceptable setting, meaning that states S0, S1, and S2 are includedcurstate – occupied state at the outset of the simulation. 0 is S0, 1 is S1, 2 is S2.Re(a0) Im(a0) – wavefunction expansion coefficients for state S0 at the outset of the simulation (real and imaginary parts)Re(a1) Im(a1) – wavefunction expansion coefficients for state S1 at the outset of the simulation (real and imaginary parts)Re(a2) Im(a2) – wavefunction expansion coefficients for state S2 at the outset of the simulation (real and imaginary parts) initial_coordinates.xyz – the initial positions of the nuclei, in units of Ångström initial_velocities – the initial velocities of the nuclei, in atomic units initial_nacvs – the initial nonadiabatic coupling vectors (if restarting the simulation from a previous run) A set of example input files is included. run_simulation.bash is the script which compiles and runs the wrapper program. Output files energy.csv - energies of the adiabatic states included in the simulation coefficients.csv - coefficients and populations of the adiabatic states includes in the simulation trajectory.xyz - the trajectory described by the nuclei, in units of Ångström License notice Copyright (C) 2026, Michał Andrzej Kochman. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>. 2. NAMD Trajectories of the Photorelaxation Process of the Quadricyclane Isomer of a Norbornadiene-Based Molecular Switch Subdirectory: 2_NAMD_Trajectories This section of the dataset contains the NAMD trajectories which collectively represent the nuclear wavepacket of the photoexcited molecule. A set of 100 trajectories were propagated for a time of 750 fs with a time step of 0.5 fs. The files containing the trajectories are formatted in the standard XYZ file format (https://en.wikipedia.org/wiki/XYZ_file_format), and they are numbered from trajectory_0001.xyz to trajectory_0100.xyz . The atomic coordinates are given in units of Ångström. Each trajectory is accompanied by a CSV file (trajectory_0001_state_energies.csv, etc.) which contains information on the state energies during the given trajectory. The first line is a header: "t(fs) E0(Eh) E1(Eh) E2(Eh) Ecur(Eh) Etot(Eh)". The subsequent lines give the time t (in femtoseconds), the energies of states S0, S1, and S2 (in units of Hartree – Eh), the energy of the occupied state at time t, and the total energy at time t. Total energy is not perfectly conserved; this is partly due to convergence issues in the TDDFT-1D calculation. They trajectories can be visualized with standard molecular editing software such as Jmol, GDIS, or VMD. 3. Animations of Simulated Trajectories Subdirectory: 3_Animations_of_NAMD_Trajectories This section of the dataset contains animations of the simulated trajectories. Each animation shows the time-evolution of the molecular geometry, and the energies and populations of states S0, S1, and S2. The passage of time during the simulation is indicated with a vertical black line moving along the time axis. The currently occupied state is marked with a black circle. The initial photoexcitation occurs at t = 0 fs. The animations are in the MP4 format, and they can be viewed with a media player such as VLC. 4. Input and Output Files for the Electronic Structure Calculations Reported in our Study Subdirectory: 4_Electronic_Structure_Calculations The final section of the dataset collects the input and output files for the electronic structure calculations (geometry optimizations and potential energy surface scans) reported in this study. The details of the calculations are discussed in our manuscript. Acknowledgements This work was supported by the National Science Center (Poland) under the OPUS grant no. 2025/57/B/ST4/01066. Bo Durbeej acknowledges support from the Swedish Research Council (Grant No. 2019-03664), the Olle Engkvist Foundation (Grant No. 204-0183), and the Carl Trygger Foundation (Grant No. CTS 24:3446). Michał Andrzej Kochman thanks the Alexander von Humboldt Foundation for the award of a research fellowship.