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Heteroassociation of caffeine (CAF) with the antibiotic mitoxanthrone (novatrone, NOV) in aqueous solution was studied by one-dimensional (1D) and two-dimensional (2D) 1H NMR spectroscopy (500 MHz). The concentration and temperature dependences of the proton chemical shifts of the molecules in aqueous solution have been measured. The equilibrium constants of heteroassociation between CAF and NOV and the limiting proton chemical shifts of the aromatic ligands of the associates have been determined. The most plausible structure of the 1:1 CAF–NOV heterocomplex in aqueous solution was inferred from the calculated values of the induced proton chemical shifts and quantum-mechanical screening curves for CAF and NOV. The thermodynamic parameters of the formation of the CAF–NOV heterocomplex have been calculated. The relatively high heteroassociation constant (K = 256 ± 31 M–1, T = 318 K), the positive value of entropy for heteroassociation [Δ S = 15.3 ± 4.0 J/(mole⋅K)], and the structural features of the chromophore of the novatrone molecule indicate that hydrophobic interactions play a significant role in stabilization of the CAF–NOV heterocomplex.