{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T16:34:46Z","timestamp":1768322086403,"version":"3.49.0"},"reference-count":16,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T00:00:00Z","timestamp":1768262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF22SA0078767"],"award-info":[{"award-number":["NNF22SA0078767"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Graphene (GRA) and graphene oxide (GO) have drawn significant attention in materials science, chemistry, and nanotechnology because of their tunable physicochemical properties and wide range of potential uses in biomedical and environmental applications. Building reliable, large-scale molecular models of GRA and GO is essential for molecular simulations of wetting, adsorption, and catalytic behavior. However, current methods often struggle to generate large, chemically consistent sheets at high oxidation levels. In addition, the resulting structures are frequently incompatible across different simulation packages. This work introduces a step-by-step protocol with custom Tool Command Language (Tcl) and modified Python version 3.12 scripts for building large-scale, AMBER-compatible GO structures with oxidation levels from 0% to 68%. The workflow applies a systematic surface modification strategy combined with post-processing and atom-type assignment routines to ensure chemical accuracy and force field consistency. The dataset includes fifteen MOL2 format files of 20 \u00d7 20 nm2 GO sheets, ranging from pristine to highly oxidized surfaces, each validated through oxidation-ratio analysis and structural integrity checks. Together, the dataset and protocol provide a design of scalable and chemically reliable GO molecular models for molecular dynamics simulations.<\/jats:p>","DOI":"10.3390\/data11010018","type":"journal-article","created":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T10:13:51Z","timestamp":1768299231000},"page":"18","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Comprehensive Dataset and Workflow for Building Large-Scale, Highly Oxidized Graphene Oxide Models"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6471-2408","authenticated-orcid":false,"given":"Merve","family":"Fedai","sequence":"first","affiliation":[{"name":"Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2221-3843","authenticated-orcid":false,"given":"Albert L.","family":"Kwansa","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8557-9992","authenticated-orcid":false,"given":"Yaroslava G.","family":"Yingling","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Zhan, M., Xu, M., Lin, W., He, H., and He, C. (2025). Graphene Oxide Research: Current Developments and Future Directions. Nanomaterials, 15.","DOI":"10.3390\/nano15070507"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1515\/ntrev-2012-0078","article-title":"Interactions of Graphene and Graphene Oxide with Proteins and Peptides","volume":"2","author":"Zhang","year":"2013","journal-title":"Nanotechnol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"10190","DOI":"10.1002\/anie.201404144","article-title":"High Correlation between Oxidation Loci on Graphene Oxide","volume":"53","author":"Yang","year":"2014","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1016\/j.carbon.2011.11.010","article-title":"The Reduction of Graphene Oxide","volume":"50","author":"Pei","year":"2012","journal-title":"Carbon"},{"key":"ref_5","unstructured":"Sinclair, R.C. (Velocirobbie\/Make-Graphitics, 2019). Velocirobbie\/Make-Graphitics, v0.1.0 (Software)."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1021\/acs.jcim.9b00114","article-title":"Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold","volume":"59","author":"Sinclair","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"108171","DOI":"10.1016\/j.cpc.2021.108171","article-title":"LAMMPS\u2014A Flexible Simulation Tool for Particle-Based Materials Modeling at the Atomic, Meso, and Continuum Scales","volume":"271","author":"Thompson","year":"2022","journal-title":"Comput. Phys. 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Discovery Studio Visualizer (Software), Dassault Syst\u00e8mes."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD\u2014Visual Molecular Dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_13","unstructured":"Fedai, M. (Yingling-Group\/AmberGO: AmberGO (Dataset), 2025). Yingling-Group\/AmberGO: AmberGO (Dataset), Version 1.0."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"044705","DOI":"10.1063\/1.4890503","article-title":"An Atomic Charge Model for Graphene Oxide for Exploring Its Bioadhesive Properties in Explicit Water","volume":"141","author":"Stauffer","year":"2014","journal-title":"J. Chem. Phys."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1601168","DOI":"10.1002\/admi.201601168","article-title":"Effect of Graphene Oxidation Rate on Adsorption of Poly-Thymine Single Stranded DNA","volume":"4","author":"Kim","year":"2017","journal-title":"Adv. Mater. Interfaces"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"8508","DOI":"10.1002\/anie.201803076","article-title":"Wrapping Nanocellulose Nets around Graphene Oxide Sheets","volume":"57","author":"Xiong","year":"2018","journal-title":"Angew. Chem. Int. 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