![]() 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. Further, we monitored changes in the CD shape caused by an excess of charged carboxyl groups or carbonyl groups. We observed that carboxyl groups interconnected the neighboring layers and decreased the rate of internal rotations. We also analyzed the internal dynamics of individual layers of CDs and evaluated the role of surface functional groups on CD stability. These simulations showed that surface functionalized CDs are stable in a water environment through the formation of an extensive hydrogen bonding network. Further, we analyzed the behavior of various CDs differing in size, surface functional groups, and degrees of functionalization by MD simulations. We developed a builder for generating CDs of a desired size and with various oxygen-containing surface functional groups. ![]() Here we present a full procedure for performing MD simulations of CDs. ![]() 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. However, many atomistic details still remain unresolved. Their interaction with biomolecular systems has also been explored experimentally. 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.
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