Molecular dynamics calculations reveal that the main trapping site for porphyrin embedded in a xenon matrix corresponds to a hexagonal cavity formed after removal of seven host atoms. Tautomerization involving two inner hydrogen atoms leads to two trans forms that interact differently with the matrix cage. Therefore, both electronic and infrared spectra are split into doublets. Comparison of the experimentally observed splitting patterns with the results of density functional theory calculations that explicitly include the nearest xenon atoms allows assigning each spectral feature to one of two different configurations of the chromophore inside the xenon cavity. The main factor responsible for the splittings is a distortion of the molecular skeleton from a squarelike towards rectangular geometry. (C) 2004 American Institute of Physics.