Intermolecular Interaction Energy

Compute the interaction energy between two molecular fragments using the counterpoise-uncorrected formula:

E_int = E(AB) − E(A) − E(B)

The job takes a single atoms geometry containing both fragments. It automatically detects connected components via bond guessing, separates them into two fragments, and runs three single-point energy calculations. The result is the interaction energy together with each term in the equation.

Negative interaction energies indicate attractive interactions (e.g. hydrogen bonds, dispersion); positive values indicate repulsion.

from atomiverse import Atoms, IntermolecularInteractionEnergy
from atomiverse.levels import GFN2_XTB

# Two water molecules in a single geometry
dimer = Atoms(
    numbers=[8, 1, 1, 8, 1, 1],
    positions=[
        [0.0, 0.0, 0.0],
        [0.0, 0.757, 0.587],
        [0.0, -0.757, 0.587],
        [2.9, 0.0, 0.0],
        [2.9, 0.757, 0.587],
        [2.9, -0.757, 0.587],
    ],
)

job = IntermolecularInteractionEnergy(
    atoms=dimer,
    charge=0,
    multiplicity=1,
    level_of_theory=GFN2_XTB,
)
job.submit()

result = job.require_result()
print(f"Interaction energy: {result.interaction_energy:.6f} Hartree")
print(f"  Complex:          {result.complex_energy:.6f} Hartree")
print(f"  Fragment A:       {result.fragment_a_energy:.6f} Hartree")
print(f"  Fragment B:       {result.fragment_b_energy:.6f} Hartree")

Inputs

Field	Type	Default	Description
atoms	Atoms	required	Geometry containing both fragments together
charge	int	0	Total charge of the complex
multiplicity	int	1	Spin multiplicity (2S + 1); must be ≥ 1
level_of_theory	LevelOfTheory	required	Computational method for all three energy evaluations

Results

job.require_result() returns an IntermolecularInteractionEnergyResult:

Field	Type	Units	Description
interaction_energy	float	Hartree	E(AB) − E(A) − E(B)
complex_energy	float	Hartree	Total energy of the full complex
fragment_a_energy	float	Hartree	Energy of the first fragment
fragment_b_energy	float	Hartree	Energy of the second fragment

How It Works

1. Bond guessing — The job uses a cheminformatics-based bond guesser to detect covalent connectivity in the complex.
2. Fragment separation — Connected components in the bond graph are identified. The largest two components become fragment A and fragment B.
3. Energy evaluation — Single-point energies are computed for the complex and each fragment at the specified level of theory.
4. Interaction energy — The difference yields the counterpoise-uncorrected interaction energy.

The total charge and multiplicity are assigned to fragment A. Fragment B defaults to neutral singlet. This is a reasonable default for neutral dimers and ion–molecule complexes where one partner is neutral.

Fragment Detection

The job expects exactly two connected components. If the bond guesser finds only one component (all atoms covalently bonded), the job raises an error. If it finds three or more, the job also raises an error — submit such systems pairwise.

The detection algorithm sorts fragments by atom count so that fragment A is always the larger (or equally sized) component, making results deterministic for a given geometry.

Limitations

• No counterpoise correction — The interaction energy is not basis set superposition error (BSSE) corrected. For methods and basis sets where BSSE is significant, use the individual fragment energies with your own counterpoise workflow.
• Two fragments only — Systems with three or more separate molecules must be split into pairwise calculations.
• Charge partitioning — The total charge is assigned entirely to fragment A. Complexes with distributed charge require manual SPE jobs for correct fragment charge states.

Compute Resources

The walltime multiplier is 3.0× the base single-point energy estimate because three evaluations (complex, fragment A, fragment B) run sequentially. CPU cores and memory follow the same automatic tiering as regular single-point energy jobs, based on the largest molecule in the calculation.