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In this paper, thermal properties, atomic-scale structure, and molecular dynamics (at ambient and high pressure) of native melatonin (MLT) and its partially-deuterated derivative (MLT-d2) have been investigated. Based on infrared spectroscopy, it was shown that treating MLT with D2O causes the replacement of hydrogen atoms attached to the nitrogen by deuterium. The degree of such substitution was very high (> 99%) and the deuterated sample remained stable after exposure to the air as well as during the melting and vitrification processes. Further calorimetric studies revealed the appearance of a peculiar thermal event before the melting of crystalline MLT-d2, which was assigned by the X-ray diffraction to a local negative thermal expansion of the unit cell. Finally, the high-pressure dielectric experiments indicated a few interesting findings, including the variation in the shape of the structural relaxation peak during compression, the difference in the pressure evolution of the glass transition temperature, and the temperature dependence of activation volume for both MLT species. The variations in these parameters manifest a different impact of the compression/densification on the dynamics of hydrogen and deuterium bonds in the native and partially-deuterated MLT, respectively. [ABSTRACT FROM AUTHOR]