Structural Dynamics of Carbon Dots in Water and NN-Dimethylformamide Probed byAll-Atom Molecular Dynamics Simulations

摘要

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 surfacefunctional groups on CD stability. We observed that carboxyl groupsinterconnected the neighboring layers and decreased the rate of internalrotations. Further, we monitored changes in the CD shape caused byan excess of charged carboxyl groups or carbonyl groups. In additionto simulations in water, we analyzed the behavior of CDs in the organicsolvent DMF, which decreased the stability of pure CDs but increasedthe level of interlayer hydrogen bonding. We believe that the developedprotocol, builder, and parameters will facilitate future studies addressingvarious aspects of structural features of CDs and nanocomposites containingCDs.