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We develop a multi-scale theoretical approach aimed at calculating from firstprinciples X-ray absorption spectra of liquid solutions and disordered systems.We test the method by considering the paradigmatic case of Zn(II) in waterwhich, besides being relevant in itself, is also of interest for biology. Withthe help of classical molecular dynamics simulations we start by producingbunches of configurations differing for the Zn(II)-water coordination mode.Different coordination modes are obtained by making use of the so-called dummyatoms method. From the collected molecular dynamics trajectories, snapshots ofa more manageable subsystem encompassing the metal site and two solvationlayers are cut out. Density functional theory is used to optimize and relaxthese reduced system configurations employing a uniform dielectric to mimic thesurrounding bulk liquid water. On the resulting structures, fully quantummechanical X-ray absorption spectra calculations are performed by includingcore-hole effects and core-level shifts. The proposed approach does not rely onany guessing or fitting of the force field or of the atomic positions of thesystem. The comparison of the theoretically computed spectrum with theexperimental Zn K-edge XANES data unambiguously demonstrates that among thedifferent a priori possible geometries, Zn(II) in water lives in an octahedralcoordination mode.

Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(II) in water