Carbon
dots (CDs), one of the youngest members of the carbon nanostructure
family, are now widely experimentally studied for their tunable fluorescence
properties, bleaching resistance, and biocompatibility. Their interaction
with biomolecular systems has also been explored experimentally. However,
many atomistic details still remain unresolved. Molecular dynamics
(MD) simulations enabling atomistic and femtosecond resolutions simultaneously
are a well-established tool of computational chemistry which can provide
useful insights into investigated systems. Here we present a full
procedure for performing MD simulations of CDs. We developed a builder
for generating CDs of a desired size and with various oxygen-containing
surface functional groups. Further, we analyzed the behavior of various
CDs differing in size, surface functional groups, and degrees of functionalization
by MD simulations. These simulations showed that surface functionalized
CDs are stable in a water environment through the formation of an
extensive hydrogen bonding network. We also analyzed the internal
dynamics of individual layers of CDs and evaluated the role of surface
functional groups on CD stability. We observed that carboxyl groups
interconnected the neighboring layers and decreased the rate of internal
rotations. Further, we monitored changes in the CD shape caused by
an excess of charged carboxyl groups or carbonyl groups. In addition
to simulations in water, we analyzed the behavior of CDs in the organic
solvent DMF, which decreased the stability of pure CDs but increased
the level of interlayer hydrogen bonding. We believe that the developed
protocol, builder, and parameters will facilitate future studies addressing
various aspects of structural features of CDs and nanocomposites containing
CDs.