This protocol addresses how well empirical potential approaches can be tailored to address the and reasonable prediction of structural and vibrational properties of prototypical dye-sensitized solar cell systems. This is important because of the staggeringly reduced computational cost approaches with the possibility of to various sampling approaches. To perform a molecular dynamic simulation, open the DL_POLY simulation software file and use the well-validated force field of Lopez, et al.
to relax the room temperature ionic liquid configuration via empirical potentials. Then use the Matsui-Akaogi force field including the mobility of the Titania in the relaxation process to model anatase. To perform a geometry optimization with a conjugate gradient minimization relative termination gradient of 0.0001, specify optimization in the field file for 15 picoseconds with a one femtosecond time stop at 300 Kelvin in an NVT ensemble.
To run DL_POLY on the terminal, enter DL_POLY. X.In the control file, specify Nose-Hoover for NVT and opt for position velocity trajectory printing every one femtosecond. For the anatase surface, ensure it is periodic along the x and y laboratory axes projecting to the room temperature ionic liquids a pair of parallel surfaces with an x-axis of 21 angstroms and a y-axis of 21 angstroms.
Ensure that the dye-sensitized solar cell system with an explicit solvent is composed of 827 atoms. For the in vacuole case, there should be 347 atoms in the system. In the field file for Lennard-Jones parameters, apply Lorentz-Berthelot combining rules and enter the arithmetic mean of the Lennard-Jones radii and the geometric mean of the Lennard-Jones well depths for the empirical force fields in the bottom section of the field file under the non-bonded interactions tab.
To handle long range electrostatics, apply the Ewald method using a non-bonded cutoff length of 10 angstroms and set the real space decay parameter for the Ewald method in the control file to be approximately 3.14 per non-bonded cutoff length. Then select the number of Ewald wave vectors to ensure a relative tolerance in the Ewald evaluation of one times 10 to the negative fifth within the control file. Carry out a series of potential energy evaluations with a REVCON file renamed as config until the system pressure in the output converges to within a few percent to select the non-bonded cutoff length.
From the history file, use Python diatom velocity separate. py in the terminal to extract the individual x, y and z velocities at each step. To compute the velocity auto correlation function, use vacf151005.
py and enter classical_dye_autocore. sh in to the terminal. The velocity auto correlation function will be computed for all of the diatoms.
To compute the spectra from the molecular dynamics, use a mass weighted Fourier Transform of the dye's atomic velocity auto correlation function, use Python MWPS. py and enter run_all_4. sh in the terminal.
The mass weighted power spectra will be computed. To assess partial change sets in the room temperature ionic liquids for imperial potential base molecular dynamic simulation for ready comparison against each other, prepare a table of the literature charges and enter this table into the field file format for DL-POLY. To calculate the Mulliken room temperature ionic liquid charges, average over four points of the ab-initio molecular dynamics trajectory, re-normalize and prepare a table of the literature charges and enter the table into field file format for DL-POLY.
To perform the EHT analysis, average over four points of the ab-initio molecular dynamics trajectory as implemented in the molecular operating environment software package. Re-normalize and prepare a table of the literature charges and enter the field into field file format for DL-POLY. Here, representative binding motifs of the four different partial charge sets after 15 picoseconds of molecular dynamics is shown.
For the literature derived charges as demonstrated, a prominent hydrogen bonding interaction with a surface proton can be observed. However, the three ab-initio molecular dynamics derived charge sets do not feature such a strong Coulombic interaction with a surface proton. Indeed, the smaller magnitude of the partial charges in the literature derived case compared to those sampled in various ways from ab-initio molecular dynamics leads to lesser extent of charge shielding in relation to the larger magnitude partial room temperature ionic liquid charges.
Interestingly, the Mulliken derived charge set shows a certain sustained kinking of the dye to have a prominent hydrogen bond with a bridging oxygen atom at the anatase surface. The better quality charge fits from ab-initio molecular dynamics lead to more realistic N719 binding motifs that are in accord with PEV-based Born-Oppenheimer molecular dynamics featuring Grimme-D3 dispersion. The mass weighted ab-initio molecular dynamics velocity auto correlation function spectral results demonstrate a cluster of spectroscopic peaks at 300 to 400 centimeter region.
The main peaks present in the classical spectra are at 600 and 800 centimeters for the literature derived charges, 525 and 800 centimeters for the Mulliken charges, 675, 810 and 900 centimeters for the EHT charges, and 650, 800 and 900 centimeters for the Hirshfeld charge set. Be sure to check the initial structure of the geometry of the Titania in all of the directions. To optimizing, force field can be used to assess the empirical potential at vibrational spectra as predicted for the molecular dynamics.
ab-initio molecular dynamics is an effective and promising strategy. The use of molecular dynamics is also likely to be important in simulation enable dye-sensitized solar cells prototype
