Abstract
The crystal structure of 1-[2-fluoro-6-(trifluoromethyl)benzyl]-5-iodo-6-methylpyrimidine-2,4(1
H
,3
H
)-dione (C
13
H
9
F
4
IN
2
O
2
, IFMBU), a key intermediate for Elagolix synthesis, was determined and reported for the first time, and further investigated by theoretical calculations. The molecule adopts a twisted `V'-shaped conformation, wherein the substituted benzene ring plane is nearly orthogonal to the uracil plane. In the crystal, molecules are linked by strong intermolecular N—H...O hydrogen bonds into centrosymmetric dimers, generating a highly stable
R
2
2
(8) supramolecular ring motif. Hirshfeld surface analysis reveals that O...H/H...O (22.0%) and F...H/H...F (18.1%) contacts dominate the molecular packing. Pairwise interaction energy calculations highlight the critical role of strong dispersion forces (
E
dis
= −302.1 kJ mol
−1
) and electrostatic interactions (
E
ele
= −168.9 kJ mol
−1
) in stabilizing the 3D supramolecular framework. Furthermore, frontier molecular orbital (FMO) analysis demonstrates a distinct spatial separation of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), establishing a typical donor–acceptor architecture that highly facilitates intramolecular charge transfer. The combined experimental and theoretical results provide a detailed characterization of the molecular geometry, noncovalent interactions and electronic structure of this key Elagolix intermediate, which may serve as a useful reference for understanding its solid-state behaviour.