Structural Dynamics of Carbon Dots in Water and N,N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations

Abstract

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.

On the Emission Properties of Carbon Dots: Reviewing Data and Discussing Models

“…The disorder is ascribed to turbostratic stacking among multiple graphitic layers, and it is correlated well with broad diffraction peaks observed in X-ray diffraction (XRD) patterns [29]. Recently, Paloncýová et al [63] succeeded in generating rounded CDs, by means of molecular dynamics calculations, with an interlayer distance of 3.4 Å. The CD surface was functionalized by various oxygen terminations that participate in stabilizing the structure and bestowing hydrophilic character to the particle.…”

“…Recently, Righetto et al [76] claimed the observation of free molecules by combining fluorescence correlation spectroscopy and time-resolved electron paramagnetic resonance. However, the reported fluctuations and rotations of carbon layers [63] may account for the estimated molecular hydrodynamic radius, in the case of molecules attached to or inserted within the layers. In addition, aggregates of fluorophores were also reported to play a role in the absorption and emission features [48,77,78].…”

“…TEM and AFM images of CDs and structure of CDs by molecular dynamics calculations. Panels (a), (b), and (c) from[61] with permission of American Chemical Society, copyright 2015; panel (d) adapted from[47] with permission of American Chemical Society, copyright 2017; panel (e) from[63] with permission of American Chemical Society, copyright 2018.…”

Stretch‐Healable Molecular Nanofibers

“…Within 10 ns, the stacks arranged into a hexagonal lattice, as shown in Figure a and Figure S3, Supporting Information. The flakes rotated [ 20 ] and became slightly tilted, due to interactions between neighboring stacks.…”

Environmental effects on the charge transfer properties of Graphene quantum dot based interfaces

“…In order to discuss a more realistic description of the interface, to take into account the dynamic disorder (thermal and geometrical fluctuations) present in a real case, as well as to account for the effect of an environment, the GQD/N‐penta interface was selected and a 5 ns long classical MD simulation was performed. The procedure used has been validated in a recent study of similar CDs in different solvents . Two MDs were conceived, the first with the interface embedded in vacuum, to account only for the dynamic disorder, and the second one in water to assess the effect of an environment in both fluctuations and transfer abilities.…”