Computational protocol: Driving Forces of Conformational Changes in Single-Layer Graphene Oxide

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Protocol publication

[…] Molecular dynamic (MD) simulations of SLG and SLGO models (carbon sheets with ∼3300 to 7000 atoms of 81.4–165.3 nm2 in size and in a hydrated state with ∼6200–13000 atoms) were made using the CharMM force field (VEGA ZZ, version 2.4 with NAMD 2.7b3). The MD calculations were used to analyze the temperature effects on the dynamic changes of hydrated SLGO sheets (details are shown in the ESI). Quantum chemical calculations of the SLG (6146 atoms with no O atoms) and SLGO (6357 atoms with ∼6 at% of O atoms) models were carried out using semi-empirical method PM6 (MOPAC 2009, versions 10.341 L and 11.038 L with the MOZYME algorithm). The O-containing groups totally covered the graphene edges and a portion of the O atoms in the form of different groups (COH, COOH, C=O, C–O–C) was attached to C atoms in the inner-sheet defects randomly distributed in the sheets. Ab initio calculations (Gaussian 03 with HF/6-31G(d,p) basis set) of the geometry of relatively small models (∼220 atoms) of SLGO were performed (without consideration of the solvation effects) to show the oxidizing effects on the bending of the SLGO sheets. Simple but pictorial calculations of potential fields (positive, negative, hydrophobic, van der Waals, vdW) with the FieldView 2.0.2 program are described in detail elsewhere.30 The ab initio method was used to analyze the oxidizing effects on the geometry (bending) of relatively small fragments (∼220 atoms) of SLG and SLGO. The PM6 method was used to study certain geometric features of relatively large SLG and SLGO sheets. The MD method was used to study the bending/folding/unfolding and temperature effects of hydrated SLGO (up to 13000 atoms). The initial geometry of the SLGO and SLG sheets was both flat and strongly bent, and then it was optimized within all the used methods. […]

Pipeline specifications

Software tools VEGA ZZ, NAMD
Application Drug design
Diseases Neural Tube Defects
Chemicals Graphite, Oxygen