In order to control and tailor the properties of nanodots, it is essential to separate the effects of quantum confinement from those due to the surface, and to gain insight into the influence of preparation conditions on the dot physical properties. We address these issues for the case of small Ge clusters (1-3 nm), using a combination of empirical and first-principles molecular dynamics techniques. Our results show that over a wide temperature range the diamond structure is more stable than tetragonal, ST12-like structures for clusters containing more than 50 atoms; however, the magnitude of the energy difference between the two geometries is strongly dependent on the surface properties. Based on our structural data, we propose a mechanism which may be responsible for the formation of metastable ST12 clusters in vapor deposition experiments, by cold quenching of amorphous nanoparticles with unsaturated, reconstructed surfaces.In semiconductor nanoparticles quantum confinement leads to an increase of the optical gap compared to the bulk value and thus opens new possibilities for controlling photoluminescence effects, with narrow emission spectra tunable over a wide range of wavelengths [1,2]. These properties make semiconductor dots attractive for many applications including photovoltaics, lasers and infrared dyes. Furthermore, their brightness, low toxicity and the ability to use a single excitation wavelength make them good alternatives to organic dyes for biological labelling, but their low water solubility has limited biological applications. However, recent experiments have shown that using specific coatings, the surface of selected semiconductor nanodots can be tailored to enhance the chemical interaction with a biological sample and the water solubility [3,4].Understanding the influence of surface reconstruction and passivation on the ground state properties of semiconductor nanodots is a key prerequisite not only in designing biological applications, but also for controlling deposition of nanoparticles on surfaces and aggregation of multiple dots into new structures. In order to tailor the properties of nanodots, it is important to separate the effects of quantum confinement from those due to the surface, and to gain insight into the mechanism by which preparation conditions can influence the dot atomic structure and thus its optical properties.Here we address these issues for the case of small Ge dots (1-3 nm), whose atomic structure is the most controversial amongst those of group IV and II-VI semiconductors. While some preparation techniques, including chemical methods [5][6][7][8][9], yield diamond-like Ge dots irrespective of size, several experiments [10-12] suggest a structural transition, as the dot diameter becomes smaller than 4-5 nm. In particular, some experiments [13,14] using vapor deposition techniques indicate a change from a cubic diamond (DIA) to a tetragonal structure, possibly ST12, in contrast to the behavior found for Si [15][16][17] and other II-VI dots [18,19]. In the bulk, the ST...