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4 results for “furylfulgide”
Simulated trajectories of furylfulgide ring opening
<p><strong>Description</strong></p> <p>This dataset contains the results of nonadiabatic molecular dynamics (NAMD) simulations of the photoinduced ring-opening reaction of a prototypical furylfulgide. The nuclear wavepacket is represented by an ensemble of 60 trajectories, which are numbered 0000, 0001, ..., 0059. Each trajectory is formatted as a standard XYZ file, and it can be viewed with molecular editing software such as Jmol, GDIS, or VMD. The atomic coordinates are given in units of angstrom. The frames are written every time step (at intervals of 0.5 fs). Each trajectory lasts 1 ps. </p> <p>Each trajectory is accompanied by a CSV file which contains information on the state energies during given trajectory. The first line is a header: "t(fs),E0(Eh),E1(Eh),Ecur(Eh),Etot(Eh)". The subsequent lines give the time <em>t</em> (in units of fs), the energy of the S<sub>0</sub> state at time <em>t</em> (in units of hartree), the energy of the S<sub>1</sub> state at time <em>t</em>, the energy of the current state at time <em>t</em>, and the total energy at time <em>t</em>. (Total energy is not perfectly conserved.)</p> <p><strong>Acknowledgement</strong></p> <p>This research was supported by the NCN grant Miniatura no. 2022/06/X/ST4/00523, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847413.</p>
Photocyclisation of furylfulgide tBu-1
<p><strong>Description</strong></p> <p>This dataset contains the results of nonadiabatic molecular dynamics (NAMD) simulations of the photocyclisation reaction of a furylfulgide with a <em>tert</em>-butyl group at position C3. The nuclear wavepacket is represented by a set of 50 trajectories, which are numbered from 0 to 49. Each trajectory is formatted as a standard XYZ file, and it can be viewed with molecular editing software such as Jmol, GDIS, or VMD. The atomic coordinates are given in units of angstrom. The frames are written every time step (at intervals of 0.5 fs). Each trajectory lasts 500 fs.</p> <p>Each frame in each trajectory has a comment line, which gives the time t (in units of fs), the energy of the S<sub>0</sub> state, the energy of the S<sub>1</sub> state, the energy of the current state, and the total energy (in units of hartree).</p> <p><strong>Acknowledgement</strong></p> <p>This research was supported by the NCN grant Miniatura no. 2022/06/X/ST4/00523, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847413.</p>
Simulated Trajectories of a Furylfulgide
<p>This dataset contains the results of nonadiabatic molecular dynamics simulations of the photorelaxation processes of two isomers, Eα and Eβ, of a prototypical furylfulgide. There are 75 simulated trajectories for the Eα isomer, and 50 for the Eβ isomer. The trajectories can be viewed with standard molecular editing software such as Jmol, GDIS, or VMD. Each trajectory is formatted as a standard .xyz file. The atomic coordinates are given in units of angstrom. The frames are written at intervals of 0.5 fs. Each trajectory lasts 500 fs.</p>
Electronic structure calculations for model furylfulgides
<p>This dataset is intended as an attachment to the Response to the Reviewers for manuscript NJ-ART-10-2023-004752, submitted to the <em>New Journal of Chemistry.</em></p> <p><strong>Contents:</strong></p> <p><strong>1. Vertical_excitation_spectra</strong> - This section of the dataset is related to the response to question 5 from Reviewer 1. It contains input and output files from the calculations of the excitation spectra of the Eα and the C isomers of the truncated furylfulgide (compound 2). </p> <p><strong>2. DFTB_SSR_based_NAMD_simulations</strong> - This section of the dataset is related to the response to question 9 from Reviewer 1. It contains the results of nonadiabatic molecular dynamics (NAMD) simulations of the photorelaxation process of furylfulgide tBu-1, carried out at the DFTB/SSR level of theory. The individual trajectories are located in the subdirectories run_0001, run_0002, etc. </p> <p>• wrapper.cpp is the source code for the interface to DFTB+. At each time step of the simulation, the interface calls DFTB+ for the calculation of state energies, gradients, and the S1-S0 nonadiabatic coupling vector. It then parses the output files from DFTB+, and propagates the time evolution of the system.</p> <p>• The files initial_coordinates.xyz and initial_velocities specify the initial positions (in units of Angstrom) and velocities (in atomic units) of the nuclei.</p> <p>• The file control specifies the number of NAMD steps, the classical time step (in atomic units), the time step for the integration of the electronic time-dependent Schrödinger equation, the number of states, the initially occupied state, and the initial wavefunction coefficients</p> <p>• trajectory.xyz is the nuclear trajectory</p> <p>• energy.csv contains the energy of state S0, the energy of state S1, the energy of the occupied state, and the total energy during the simulation</p> <p>• coefficients.csv contains the wavefunction coefficients and the state populations during the trajectory</p>
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