Benzene-Derivatives

Example: Benzene Derivatives

As a simple test of the infrared (IR) calculation routines, we compared simulated IR spectra of benzene and several derivatives to high-quality gas-phase spectra from the NIST Chemistry WebBook.[1]

Calculations

For these calculations, we used Phonopy and VASP to prepare phonon frequencies/eigenvectors and Born effective-charge tensors, and post-processed using the phonopy-ir script.

Molecular models were prepared in Avogadro[2] and optimised in large periodic simulation cells with ~15 Å between periodic images (built using the xyz2poscar script).

DFT calculations were performed with the dispersion-corrected PBE-D3 functional, an 800 eV plane-wave cutoff, and the "standard" H, C, N and O pseudopotentials (i.e. POTCAR_H, POTCAR_C, POTCAR_N and POTCAR_O) from the VASP 5.4 PAW dataset.

For the finite-displacement calculations with Phonopy, we used the default 1 × 10^-2 Å displacement step. For a subset of the molecules we also tested a smaller 5 × 10^-3 Å step. The Born effective-charge tensors were calculated using the DFPT routines in VASP (i.e. with the LEPSILON tag).

To prepare the phonon frequencies and eigenvectors:

1. Create displacements: phonopy -d --dim="1 1 1" (for a 5 × 10^-3 Å dispacement step, add --amplitude=0.005)

2. Run single-point force calculations (sample VASP input files in the VASP-Files folder)

3. Collect forces: phonopy -f vasprun-{1..X}.xml

4. Generate a mesh.yaml file containing the structure and Γ-point phonon frequencies and eigenvectors: phonopy --dim="1 1 1" --fc-symmetry --mesh="1 1 1" --eigenvectors (structures can also be read from a phonopy.yaml or VASP 5.x-format POSCAR file); for older versions of Phonopy, you may need to use --fc_symmetry=1 instead of --fc-symmetry

To prepare the Born effective-charge tensors:

1. Run a VASP DFPT calculation on the optimised structure to calculate the Born charges and dielectric tensor (sample VASP input files in VASP-Files)

2. Create a BORN file using the Phonopy outcar-born script: outcar-born > BORN

Finally, to generate the spectrum:

1. Run phonopy-ir with a nominal spectral linewidth and spectrum range: phonopy-ir --linewidth=16.5 --spectrum_range="500 4000"

Results

a. Benzene

• Raw data: Benzene; CAS/NIST database ID: 71-43-2

b. Phenol

• Raw data: Phenol; CAS/NIST database ID: 108-95-2

c. Toluene

• Raw data: Toluene; CAS/NIST database ID: 108-88-3

d. Anisole

• Raw data: Anisole; CAS/NIST database ID: 100-66-3

e. Aniline

• Raw data: Aniline; CAS/NIST database ID: 62-53-3

f. Benzoic acid

• Raw data: Benzoic acid; CAS/NIST database ID: 65-85-0

g. Benzaldehyde

• Raw data: Benzaldehyde; CAS/NIST database ID: 100-52-7

h. Benzonitrile

• Raw data: Benzonitrile; CAS/NIST database ID: 100-47-0

References

1. http://webbook.nist.gov/
2. https://avogadro.cc/