4352 | Phys. Chem. Chem. Phys., 2016, 18, 4352--4361 This journal is © the Owner Societies 2016 Cite this: Phys. Chem. Chem. Phys., 2016, 18, 4352 A study on the interactions of amino acids with nitrogen doped graphene; docking, MD simulation, and QM/MM studies Rahim Ghadari The binding properties of twenty amino acids with nitrogen-doped graphene structures were studied using docking, MD simulation, and QM/MM methods. TDDFT studies were carried out to investigate the change in the electronic properties of the amino acids because of the presence of the solvent and nitrogen-doped graphene. The results revealed that p–p interactions between the amino acids with a benzene moiety and the surface of the graphene are the most important interactions. The observed red shifts in the TDDFT results which were related to the lower LUMO energies and higher HOMO energies are consistent with this statement. Introduction Graphene (G) is the two dimensional allotrope of carbon which contains honeycomb networks in which the carbon atoms have sp 2 hybridization. 1,2 The mentioned compound shows special behaviors which make it suitable to be used in different areas including fuel cells, biosensors, energy storage devices, and biological systems. As an example, a graphene oxide-assisted nucleic acids assay was carried out using a conjugated polyelectrolyte-based fluorescent signal transduction approach. 3 In another study, the sensing of glucose using graphene based sensors was reported which is a highly valuable procedure in the management of diabetes. 4 To improve graphene’s desired properties and expand its usability, different structural variations have been done to it. Including nitrogen atoms in the structure of graphene, to produce nitrogen-doped graphene (NG), has attracted the con- sideration of different research groups and different synthetic procedures have been introduced. 5–8 Based on X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS) results, the nitrogen atoms can occupy three sites which are chemically different from each other. 9–12 The mentioned chemically diverse sites for the nitrogen atom are: pyridine (or pyridinium-like), pyrrole-like, and graphite- like. These three types of nitrogen moieties are abbreviated as Np, Npy, and Ng throughout this text, respectively. Including nitrogen atoms is a method to tailor the electronic and chemical properties of the compounds. 13 Doping with nitrogen will lead to an n-type property which is important in the production of semiconductors. It is suggested that the N-doping improves the biocompatibility of the graphene moiety, as well. 14,15 In the following, representative examples of the usage of NG systems are presented. NG in the presence of a disulfide/thiolate redox system was used in dye-sensitized solar cells which showed improved efficiency in comparison with the usual platinum electrodes. 16 In another work an NG/silicon nanowire system was used in photoelectrochemical hydrogen production. 17 Using NG as a catalyst support is of interest, as well. In this approach, Pt/NG and Fe/NG systems were used as the electro- catalyst for the oxygen reduction reaction (ORR). 5,18 The development of an efficient and selective catalyst is important from a synthetic viewpoint. In this way, hydrogena- tion of structurally diverse nitroarenes in the presence of an Fe 2 O 3 /NG catalyst was studied, successfully. 19 Also, the sensor usability of NG systems was investigated; as an example, an NG-based system was successfully used for the molecular sensing of organic molecules using a graphene enhanced Raman scattering method. 7 Nowadays, computational studies are playing a great role in helping to understand chemical and physical phenomena, including G and NG systems. For example, the mechanism of the ORR in the presence of NG systems was studied. It was found that the Ng moiety is the most efficient site in the ORR. Also the authors suggested an inter-conversion between Ng and Npy. 12,20,21 The change in the electronic properties of G in the presence of peptides was studied by Trohalaki et al. They proposed that the p–p stacking of the peptide backbone on the G surface plays an important role in the adsorption of peptides. 22 An ab initio study on the mechanistic features of the Computational Chemistry Laboratory, Department of Organic and Biochemistry, Faculty of Chemistry, University of Tabriz, 51664 Tabriz, Iran. E-mail: r-ghadari@tabrizu.ac.ir; Fax: +98 41 33340191; Tel: +98 41 33393159 Received 4th November 2015, Accepted 10th December 2015 DOI: 10.1039/c5cp06734k www.rsc.org/pccp PCCP PAPER