  Functionalised metal nanoparticles (NPs) have been proposed as promising
radiosensitising agents for more efficient radiotherapy treatment using photons
and ion beams. Radiosensitising properties of NPs may depend on many different
parameters (such as size, composition and density) of the metal core, organic
coatings and the molecular environment. A systematic exploration of each of
these parameters on the atomistic level remains a formidable experimental task
but it can be addressed by means of advanced computational modelling. This
paper presents a detailed computational protocol for the construction and
atomistic-level characterisation of radiosensitising metal NPs in explicit
molecular media. The protocol is general and extensible to many different
combinations of the core, coating and environment. As an experimentally
relevant case study we consider gold nanoparticles coated with
thiol-poly(ethylene glycol)-amine molecules of different length and surface
density and solvated in water at ambient conditions. Radial distribution of
different atoms in the coatings as well as distribution and structural
properties of water around the coated NPs are analysed and linked to
radiosensitising properties of the NPs. It is revealed that structure of the
coating layer of the solvated NPs depends strongly on the surface density of
ligands. At surface densities below 3 molecules per nm$^{2}$ the coating
represents a mixture of different conformation states, whereas elongated
"brush"-like structures are formed predominantly at higher densities of
ligands. The water content in denser coatings is significantly lowered at
distances from 1 nm up to 3 nm from the gold surface depending on the length of
ligand molecules. Dense and thick coatings may suppress the production of
hydroxyl radicals by low-energy electrons emitted from the metal NPs and thus
diminish their radiosensitising properties.
