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.本数据集为与Bo Durbeej、Simone Pintér、Andreas Hirsch及Michał Andrzej Kochman合著的论文《基于降冰片二烯的分子开关储能异构体的光化学：开环、再杂化分子内电荷转移及异构化生成卡宾光产物》（Photochemistry of the Energy-Storing Isomer of a Norbornadiene-Based Molecular Switch: Ring Opening, Rehybridized Intramolecular Charge Transfer, and Isomerization into a Carbene Photoproduct）相关的计算机程序与模拟数据集合。 ## 内容列表 1. 基于含单双电子近似含时密度泛函理论（Time-Dependent Density Functional Theory With One Double，TDDFT-1D）的非绝热分子动力学（Nonadiabatic Molecular Dynamics，NAMD）模拟程序 2. 基于降冰片二烯的分子开关的四环烷异构体光弛豫过程非绝热分子动力学轨迹 3. 模拟轨迹动画 4. 本研究中电子结构计算的输入与输出文件 ### 1. 基于TDDFT-1D方法的非绝热分子动力学模拟程序 子目录：`1_NAMD_Program` 本子目录包含用于开展TDDFT-1D级别非绝热分子动力学模拟的“封装器”程序的C++源代码。该程序与电子结构软件包Q-Chem 6.3.1版本对接。在模拟的非绝热分子动力学轨迹的每个时间步中，该封装器会生成Q-Chem输入文件，调用Q-Chem计算态能量、当前态的梯度以及非绝热耦合矢量，随后解析输出文件并提取相关物理量。此外，该封装器还会传播核与电子运动方程。 #### 输入文件 部分模拟参数（如基组、交换关联泛函、积分网格、收敛阈值等）已在源代码中硬编码，其余参数由以下输入文件定义： - `control`：包含非绝热分子动力学模拟的核心参数，具体包括： - `nsteps`：待执行的非绝热分子动力学时间步数 - `h mts`：经典时间步长（原子单位，1飞秒=41.34原子单位）及经典时间步长划分为含时薛定谔方程时间步的份数。`h`应不大于20.67原子单位（即0.5飞秒），`mts`应不小于500 - `nstates`：模拟中包含的态数目（含基态S0）。本程序版本中仅支持`nstates=3`，即包含S0、S1、S2三个态 - `curstate`：模拟初始时刻占据的态，0对应S0，1对应S1，2对应S2 - `Re(a0) Im(a0)`：模拟初始时刻S0态的波函数展开系数（实部与虚部） - `Re(a1) Im(a1)`：模拟初始时刻S1态的波函数展开系数（实部与虚部） - `Re(a2) Im(a2)`：模拟初始时刻S2态的波函数展开系数（实部与虚部） - `initial_coordinates.xyz`：原子核的初始位置，单位为埃（Å） - `initial_velocities`：原子核的初始速度，单位为原子单位 - `initial_nacvs`：初始非绝热耦合矢量（用于从先前的模拟结果重启计算） 本目录附带一组示例输入文件。`run_simulation.bash`为编译并运行该封装器程序的脚本。 #### 输出文件 - `energy.csv`：模拟中包含的绝热态的能量数据 - `coefficients.csv`：模拟中包含的绝热态的系数与布居数据 - `trajectory.xyz`：原子核运动轨迹，单位为埃（Å） #### 许可声明 版权所有 © 2026 Michał Andrzej Kochman。 本程序为自由软件：您可按照自由软件基金会发布的GNU通用公共许可证第3版，或（按您的选择）任何更新版本的条款对其进行再分发和/或修改。 本程序的发布旨在希望其具有实用性，但不提供任何担保；甚至不隐含适销性或特定用途适用性的担保。有关详细信息，请参阅GNU通用公共许可证。 您应随本程序一同收到GNU通用公共许可证的副本。若未收到，请访问<https://www.gnu.org/licenses/>获取。 ### 2. 基于降冰片二烯的分子开关的四环烷异构体光弛豫过程非绝热分子动力学轨迹 子目录：`2_NAMD_Trajectories` 本数据集部分包含共同表征光激发分子核波包的非绝热分子动力学轨迹。本研究共传播100条轨迹，模拟时长为750飞秒，时间步长为0.5飞秒。轨迹文件采用标准XYZ文件格式（https://en.wikipedia.org/wiki/XYZ_file_format），文件编号从`trajectory_0001.xyz`至`trajectory_0100.xyz`，原子坐标单位为埃（Å）。 每条轨迹均附带一个CSV文件（如`trajectory_0001_state_energies.csv`等），包含对应轨迹过程中的态能量信息。文件首行为表头：`t(fs) E0(Eh) E1(Eh) E2(Eh) Ecur(Eh) Etot(Eh)`，后续各行依次给出时间`t`（单位：飞秒）、S0、S1、S2态的能量（单位：哈特里，Eh）、时刻`t`占据态的能量以及时刻`t`的总能量。总能量无法严格守恒，部分原因源于TDDFT-1D计算中的收敛问题。 上述轨迹可通过标准分子编辑软件（如Jmol、GDIS或VMD）进行可视化。 ### 3. 模拟轨迹动画 子目录：`3_Animations_of_NAMD_Trajectories` 本数据集部分包含模拟轨迹的动画文件。每个动画均展示分子几何结构的时间演化，以及S0、S1、S2态的能量与布居情况。模拟过程中的时间流逝通过沿时间轴移动的黑色竖线标识，当前占据的态以黑色圆圈标记。初始光激发发生在`t=0`飞秒时刻。 动画采用MP4格式，可通过VLC等媒体播放器播放。 ### 4. 本研究中电子结构计算的输入与输出文件 子目录：`4_Electronic_Structure_Calculations` 本数据集的最后一部分收集了本研究中报道的电子结构计算（几何优化与势能面扫描）的输入与输出文件。计算细节已在论文中进行讨论。 ## 致谢 本研究得到波兰国家科学中心OPUS项目（编号2025/57/B/ST4/01066）的资助。Bo Durbeej感谢瑞典研究理事会（编号2019-03664）、Olle Engkvist基金会（编号204-0183）以及Carl Trygger基金会（编号CTS 24:3446）的支持。Michał Andrzej Kochman感谢亚历山大·冯·洪堡基金会授予的研究奖学金。