Python API · stjames models · API example
Optimize a molecular geometry, check whether it is a local minimum, and calculate vibrational frequencies and molecular thermochemical corrections. Frequencies describe small motions around the final geometry; they do not establish that it is the lowest-energy conformer.
A molecular minimum should have no imaginary vibrational frequencies, displayed as negative values. Click a frequency to animate its motion. Small negative values can reflect numerical noise; inspect the mode and consider tighter optimization before accepting the structure. Constraints can prevent a structure from reaching an unconstrained minimum.
Molecular frequencies come from the mass-weighted Hessian after removing translation and rotation, following Gaussian's vibrational analysis reference. IR intensities are available only when supported by the selected method. Periodic calculations return Γ-point phonons without the molecular thermochemical corrections below; these do not test stability throughout the Brillouin zone.
The molecular calculation uses a rigid-rotor/harmonic-oscillator model at 298.15 K with a 1 atm ideal-gas standard state, following Gaussian's thermochemistry reference. Selecting an implicit solvent does not automatically convert the translational entropy to a 1 M solution standard state.
| Reported quantity | Meaning |
|---|---|
| "Electronic energy" | Energy at fixed nuclear positions, excluding nuclear motion. |
| "Zero-point energy" | Vibrational energy present even at absolute zero. |
| "Thermal energy corr." | Zero-point energy plus finite-temperature translational, rotational, and vibrational energy. |
| "Enthalpy correction" | Thermal energy correction plus the ideal-gas pressure–volume term, RT per mole. |
| "Gibbs free energy corr." | Enthalpy correction minus temperature times entropy, including translational, rotational, vibrational, and electronic contributions. |
| "Total thermal energy," "Total enthalpy," and "Total Gibbs free energy" | Electronic energy plus the corresponding correction. |
Do not add zero-point energy again to a thermal correction: it is already included. Rowan excludes imaginary modes from thermochemistry and raises real frequencies below 100 cm−1 to 100 cm−1 only when calculating vibrational entropy (the Cramer–Truhlar correction). This does not change the displayed frequencies or zero-point energy.
Compare conformers or balanced reactions using consistent methods, solvent settings, temperatures, and standard states. These values describe one geometry; conformer populations and anharmonic motion can affect experimental free energies.