Atomistic models of graphene oxide sheets with different degrees of oxidation, built for molecular dynamics simulations of the adsorption of biological molecules.

Each model is a periodic sheet of about 15 × 15 nm with the same carbon backbone (8540 carbon atoms), decorated with hydroxyl and epoxy groups to reach a C/O ratio between 1.8 and 3.0. The atomic charges and non-bonded parameters (GAFF2-AIM) were derived from linear-scaling DFT calculations in CP2K, with DDEC6 charges and atomic volumes from Chargemol. The topologies are ready to use in GROMACS.

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I - Models

The number in each folder name is the C/O ratio of the sheet (GO_18 has C/O = 1.8). The counts come from the files in each folder.

Model	C/O ratio	Atoms	Hydroxyl groups	Epoxy groups	Files	DFT and parameter files
GO_18	1.8	15 597	2312	2433	GO_18	Zenodo
GO_20	2.0	14 964	2154	2116	GO_20	Zenodo
GO_22	2.2	14 352	1930	1952	GO_22	Zenodo
GO_24	2.4	13 827	1726	1833	GO_24	Zenodo
GO_26	2.6	13 439	1614	1671	GO_26	Zenodo
GO_28	2.8	13 122	1532	1518	GO_28	Zenodo
GO_30	3.0	12 819	1432	1415	GO_30	Zenodo

The Zenodo records hold the files from the linear-scaling DFT and non-bonded parameter calculations of each model.

II - Files

Each model folder contains:

• GO_sheet_#_#.gro: the initial coordinates (built with the MakeGraphitics library) in GROMACS format.

• GO_sheet_#_#.top: the GAFF2-AIM topology in GROMACS format.

• CP2K_OPT_GEO.xyz: the coordinates optimized with CP2K, in XYZ format.

• DDEC6_even_tempered_net_atomic_charges.xyz and DDEC_atomic_Rcubed_moments.xyz: the Chargemol output files with the atomic charges and volumes.

The amber99sb-ildn.ff-modified folder holds the amber99sb-ildn force field in GROMACS format, modified with the graphene oxide sheet parameters (taken from ACPYPE).

III - Using the models in GROMACS

The sheets are periodic in the XY plane, so the bonds across the box edges are part of the topology. Use them with the following option in the *.mdp file:

periodic-molecules = yes

The coordinate files define a box of 14.937 × 14.870 × 8.000 nm with the sheet in the XY plane.

IV - Citation

If you use these models, please cite:

Pinto, A. V.; Ferreira, P.; Fernandes, P. A.; Magalhães, A. L.; Ramos, M. J. Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules. J. Phys. Chem. B 2023, 127 (2), 557-566. https://doi.org/10.1021/acs.jpcb.2c06037

@article{Pinto2023GO,
  author  = {Pinto, Alexandre V. and Ferreira, Pedro and Fernandes, Pedro A. and Magalh{\~a}es, Alexandre L. and Ramos, Maria J.},
  title   = {Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules},
  journal = {The Journal of Physical Chemistry B},
  year    = {2023},
  volume  = {127},
  number  = {2},
  pages   = {557--566},
  doi     = {10.1021/acs.jpcb.2c06037}
}