Recipe 3 Substituted aromatics (p-nitroaniline)

Put substituent templates on the benzene skeleton to make p-nitroaniline. A substituent replaces the hydrogen you click, so the hydrogen you choose decides ortho, meta or para. Optimize and compute frequencies with B3LYP/6-31G*, and compare the energy with the o- and m-isomers built the same way.

What you build	Details
Molecule	p-Nitroaniline C₆H₆N₂O₂ (16 atoms, charge 0, singlet); o- and m-isomers for comparison
Features	Skeleton and substituent templates, the tool after placing a part, atom numbers, cleanup
Calculation	B3LYP/6-31G*, optimization → frequencies (optimization for the o- and m-isomers)
Run time	About 35 minutes (6 MPI processes, mostly the analytic Hessian of the frequencies)
Computer	AMD Ryzen 7 2700X (8 cores, 16 threads), 32 GB of memory, NWChem 7.3.1 on Linux
Practice data	`p_nitroaniline.molforma.json`, `o_nitroaniline.molforma.json`, `m_nitroaniline.molforma.json`

p-Nitroaniline: amino and nitro groups on benzene

1. Place benzene

Start an empty molecule with “File → New”.
Choose the category “Skeleton” at the top of the parts palette and click “Benzene”. The tool becomes “Place”.

Figure 1 Choosing “Benzene” in “Skeleton” switches to the “Place” tool.
Click in empty space in the 3D view. Benzene (C6H6 · 12 atoms) is placed and the tool returns to “Select”. Placing one part (skeleton, substituent, …) returns to selection; to keep placing, turn on “Keep tool after placing a part” above the 3D view.

Figure 2 The placed benzene: ring carbons C1 to C6, hydrogens H7 to H12. A part just placed is shown selected.

In the labels, the ring carbons are C1–C6 and their hydrogens H7–H12. If no numbers are shown, turn on “View → Show numbers”.

2. Add the amino and nitro groups

Choose the category “Substituent” and click “Amino”. Under the 3D view: “Place (Amino): click the hydrogen to replace (or drop on it)”.
Click hydrogen H7 of benzene. H7 becomes NH2: aniline (C6H7N · 14 atoms). Substituents go on hydrogens only; clicking empty space does not place them.

Figure 3 Clicking H7 with “Amino” replaces that hydrogen with NH2: aniline.
Choose “Nitro” and click H10, the hydrogen of the carbon three steps around the ring from C1 (C4, para). You get C6H6N2O2 · 16 atoms; the labels show the formal charge “(+1)” on N and “(−1)” on one O (one resonance structure of the nitro group). The total charge stays 0.

Figure 4 p-Nitroaniline (C6H6N2O2 · 16 atoms), with the para hydrogen H10 replaced by “Nitro”.
Press “Clean up all”, look at the candidate and press “Confirm changes”.

A hydrogen next to the amino carbon (C2, C6) gives the ortho isomer, two steps away (C3, C5) the meta isomer. Undo a misplaced group with Ctrl+Z. To exchange a placed substituent for another, choose the new substituent in the palette, choose “Replace” (R) in the left column and click the atom where the old substituent is attached (N for the amino group); the exchange is a candidate.

3. Set up the calculation

In “Basics” of “2 Calculation”, set the task to “Optimization → frequencies”, the method to “DFT” (B3LYP) and the basis set to “6-31G*”.

Figure 5 “2 Calculation” with the task, method and basis set chosen.
Check total charge 0 and multiplicity 1 (→ RKS (closed shell)).

4. Run and look at the results

Run with “Run calculation” (F5) in the header. The frequency task (analytic Hessian) takes longer than the optimization; the run panel marks each task as done, running or waiting.

“Summary” of the result viewer: energy −492.108697994 Eh, optimization converged, no imaginary frequencies, HOMO–LUMO gap 4.30 eV, dipole moment 7.12 D

Figure 6 “Summary” of the “Result viewer” after the run.

The “Vibrations” tab with the strongest IR band, the NO2 symmetric stretch (1391 cm⁻¹), selected

Figure 7 The strongest IR band (NO2 symmetric stretch, 1391 cm⁻¹) chosen in the “Vibrations” tab.

Results

Item	Value
Energy of the calculation	−492.108697994 Eh
Optimization	Converged in 14 steps; no imaginary frequencies (42 vibrations)
Dipole moment	7.12 D (large through charge transfer from amino to nitro)
Main IR bands	NO₂ symmetric stretch 1391 cm⁻¹ (strongest), NH₂ stretches 3579 and 3682 cm⁻¹
Zero-point correction	75.39 kcal/mol

Compared with the o and m isomers optimized under the same conditions (for the p isomer, the energy of the optimization part of optimization → frequencies):

Isomer	Energy of the calculation	Relative to o	Dipole moment	Optimization
o-Nitroaniline	−492.109508350 Eh	0	4.74 D	15 steps
p-Nitroaniline	−492.108697994 Eh	+0.51 kcal/mol	7.12 D	14 steps
m-Nitroaniline	−492.104968503 Eh	+2.85 kcal/mol	5.65 D	11 steps

In the o isomer a hydrogen of the amino group comes within 1.91 Å of an oxygen of the nitro group, an intramolecular hydrogen bond. The p isomer is stabilized by resonance (charge transfer) from the amino to the nitro group, which also gives it the largest dipole moment. The m isomer lacks this resonance and is highest in energy. The optimizations of o and m took about 14 and 8 minutes with 8 processes.

The optimized structure is used for the excited states (TDDFT) of recipe 14.

Troubleshooting

“Click or drop on the hydrogen to replace.”The substituent was clicked on empty space or a carbon. Click on the hydrogen to replace.
After pressing an element button (C, N, O, …), substituents are goneThe element buttons switch the palette to “Atom”. Choose the category “Substituent” again.
A part is not in the paletteText left in the search field above the palette shows only the parts containing it. Clear the search field.
The formal charges of the nitro groupN(+1) and O(−1) write the nitro group as one resonance structure and add up to 0. The calculation uses the total charge of “2 Calculation” (0).

See also: tools and parts palette in “1 Molecule”: layout, tools and selection, recipe 14 From a result to the next calculation.