MolForma

Recipe 14 From a result to the next calculation (TDDFT of optimized p-nitroaniline)

Call up the p-nitroaniline optimized in recipe 3 from “History” and bring its structure into “1 Molecule” with “Apply as candidate” in the “Result viewer”. Change the kind of calculation at that structure and compute the excited states (UV spectrum) with CAM-B3LYP/6-31+G* TDDFT. Along the way, see how built and calculated structures are passed around.

What you build Details
Molecule Optimized p-nitroaniline (16 atoms)
Features History, Open in result viewer, Apply as candidate (RMSD, largest displacement), Compare, exporting results, Reuse molecule and settings, excited states (TDDFT), the absorption spectrum
Calculation CAM-B3LYP/6-31+G*, single point + TDDFT (10 singlet states)
Run time About 42 minutes (6 MPI processes)
Computer AMD Ryzen 7 2700X (8 cores, 16 threads), 32 GB of memory, NWChem 7.3.1 on Linux
Practice data p_nitroaniline_tddft.molforma.json (the imported structure and TDDFT settings)

The absorption spectrum in the Excited states tab

1. Bring the calculated structure in

  1. Open the project of recipe 3 (p_nitroaniline.molforma.json). Its molecule is the starting structure from before the calculation.
  2. Open “History” in the header. Jobs in the job folder of “3 Run settings” are listed with their calculation name (or title, for the default calculation name), composition, method, task and energy.

  3. Choose the p-nitroaniline job and press “Open in result viewer” on the right (or double-click the row).

    The p-nitroaniline job chosen in “History”: the details on the right show B3LYP/6-31G* · optimization → frequencies, the energy −492.108697994 Eh, the folder ~/MolForma/jobs/… and the button “Open in result viewer”

    Figure 1 Choosing a job in “History” shows its details and “Open in result viewer” on the right.

    “Summary” of p-nitroaniline opened in the result viewer, showing structure 17/17 (last), with “Compare”, “Apply as candidate” and “Export” in the bar at the top

    Figure 2 Opened in the “Result viewer”, showing the last structure of the optimization.

  4. Press “Apply as candidate” in the bar at the top of the “Result viewer”. The structure shown (the last one of the optimization) becomes a candidate in “1 Molecule”, and the status bar says how far it moved: “The result structure is now a candidate (RMSD 0.0615 Å, largest displacement 0.1180 Å).”

    “1 Molecule” after “Apply as candidate”: the amber bar shows the candidate with 16 atoms moved, and the status bar says the result structure is now a candidate (RMSD 0.0615 Å, largest displacement 0.1180 Å)

    Figure 3 The result structure is shown as a candidate, and the status bar says how far it moved.

  5. Press “Confirm changes”. Atom IDs, bonds and settings stay; only the coordinates are exchanged.

“Apply as candidate” accepts only results with the same number, order and elements of atoms; results in which fixed atoms moved are refused. “Compare” shows only the RMSD and the largest deviation without taking the structure.

Other ways to pass structures

Way What comes over Note
“Result viewer” → “Apply as candidate” Coordinates of the shown structure Same number and order of atoms only
“Result viewer” → “Export” → “Export shown structure as XYZ…” Structure (XYZ) Bonds are guessed from distances on opening; no residues, charges or settings
“History” → “Reuse molecule and settings” The project used for the calculation Opens the molecule and settings from before the run as a new unsaved project
.nw (NWChem input) with “File → Open…” The first geometry and the settings Input coordinates are the starting structure

2. Switch to TDDFT

  1. In “Basics” of “2 Calculation”, set the task to “Single-point energy”.
  2. Set the DFT functional to “CAM-B3LYP (range-separated)” and the basis set to “6-31+G*”. Range-separated functionals suit charge-transfer excitations.

  3. In “Excited states (TDDFT)” in the list on the left, turn on “Compute excitation energies and oscillator strengths with TDDFT” and set “Excited states (nroots)” to 10. It is closed shell, so leave “Also triplets (closed shell)” off (notriplet in the input).

    “Excited states (TDDFT)” of “2 Calculation”: TDDFT excitation energies and oscillator strengths on, 10 excited states, triplets off; the summary on the right is a CAM-B3LYP / 6-31+G* single point

    Figure 4 The settings in “Excited states (TDDFT)”.

  4. In “4 Input preview”, check the tddft block (nroots 10) and task tddft energy.

    The tddft block chosen in “4 Input preview”: nroots 10 and notriplet, with task tddft energy on the last line

    Figure 5 The tddft block of the input and task tddft energy.

TDDFT is available only with the task single-point energy (excited-state optimizations are not covered). Meta-GGAs (TPSS, SCAN, the M06 family, …) stop NWChem’s TDDFT and cannot be chosen.

3. Run and look at the results

Run with “Run calculation” (F5) and open the “Excited states” tab of the “Result viewer”: a table of excitation energies (eV, nm) and oscillator strengths, and a display spectrum with the oscillator strengths broadened by Gaussians (full width at half maximum in eV, wavelength or energy axis).

The “Excited states” tab of the TDDFT result: a table of excitation energies, wavelengths and oscillator strengths for 10 states (state 2 at 4.3189 eV, 287.1 nm, 0.38928) and the absorption spectrum against wavelength

Figure 6 The “Excited states” tab: the table of states and the absorption spectrum broadened from the oscillator strengths.

Results

The ground-state energy is −491.901382279 Eh (CAM-B3LYP/6-31+G*). The main states:

State Excitation energy Wavelength Oscillator strength
1 3.92 eV 317 nm 0.00001
2 4.32 eV 287 nm 0.389
6 5.53 eV 224 nm 0.068
8 6.29 eV 197 nm 0.168

The strongest absorption is state 2 (287 nm), a charge-transfer excitation moving an electron from the amino to the nitro group; it agrees well with the gas-phase experiment (about 290 nm). State 1 is an n→π* excitation that absorbs almost no light (oscillator strength nearly 0). In polar solvents such as water, the charge-transfer band shifts strongly to longer wavelengths (about 380 nm), so set a solvent in “Environment” to compare with solutions.

Troubleshooting

See also: “Result viewer”, “History”, recipe 3 Substituted aromatics, recipe 15 Isotopes.