Adsorption mechanisms of glycine onto graphene oxide models: a computational approach from DFT and AIMD simulations

Abstract

Nanomedicine is a nanotechnology application based on the engineering of nanomaterials to develop tools for diagnosis, prevention, imaging, and treatment of diseases. Understanding the interaction mechanisms between nanomaterials and biomolecules is essential in creating novel sensing platforms such as electrochemical devices, drug delivery systems, and biosensors. Carbon has become the most widely used nanomaterial in the 21st century. Graphene (G) is the most important allotrope because of its intrinsic properties, such as a zero bandgap. However, due to the sophisticated synthesis procedures, several related G materials are proposed to be used in applications. Graphene oxide (GO) contains oxidized functional groups on the surface, which can serve to functionalize with other molecules and thus enhance the chemical and physical properties as compared to graphene. Moreover, structural defects can appear in both G and GO materials which are also influenced by the properties of these materials. G and GO can have a perfect lattice or contain Stone-Wales structural defects that are formed by rotating a C-C bond 90º, which creates a 5-7 ring pair. The investigation of interactions of important biomolecules with carbon-based nanomaterials (CNMs) has emerged in an explosion of research since CNMs are extensively proposed for biological assays to detect biomarkers facilitating their detection and optical imaging in biological systems. In this way, amino acids (AAs) are the critical chemical structures in organisms. AAs are known as the building blocks of proteins. AAs can manifest the common physical-chemical properties of more significant biomolecules. Glycine (GLY) is the simplest amino acid; therefore can serve as a simple novel to evaluate this amino acid's adsorption process in CNMs. A first approximation of the interaction mechanism between G (or GO) with GLY can be studied at a fundamental level using theoretical approaches. Density functional theory (DFT) and Ab-initio molecular dynamics (AIMD) are modern tools to gain insights into the interaction mechanisms and microscopic details of chemical processes in both gas-phase and solvent medium (e.g., water). DFT is a set of quantum mechanical approaches to investigate the electronic structure of a system at its ground state. However, DFT is not accurate for accounting for noncovalent intermolecular interactions, and they can be described using semi-empirical approaches. Atom-pairwise specific dispersion coefficients (–C6/R6) and cutoff radii that are both computed from time-dependent first principles have proved to be a valuable alternative to capture dispersion interactions in the G∙∙∙GLY complexes adequately. On the other hand, AIMD resolves the classical dynamics of the nuclei numerically, and at each time step, the forces are computed to minimize the Kohn-Sham DFT energy functional at a current nuclear configuration. AIMD can allow both equilibrium thermodynamic and dynamical properties of G∙∙∙GLY interactions at finite temperature to be computed. The objective is to analyze the adsorption mechanisms of neutral glycine onto graphene oxide models using dispersion-corrected DFT and AIMD approaches and compare their stability when including Stone-Wales structural defects. DFT studies were computed to study the adsorption sites of GLY on G and GO flakes models. A molecular system of C42 atoms (including 16 H atoms saturating dangling bonds) was used to model the graphene flakes. These graphene structures were varied with hydroxyl groups, glycine moieties, and structural defects on the surface. In particular, Stone-Wales (SW) sites containing 5 and 7 member rings at the center of the graphene flake were used to mimic structural detects. Interactions of GLY neutral molecules with the perfect lattice and SW sites were investigated in both the gas-phase (vacuum) and dissolvent medium (water). AIMD simulations at room-temperature and total relaxation of atomic positions are performed to study adsorption sites on the perfect lattice and SW defects for G and GO models. Interactions of GLY neutral molecules with both models are investigated. DFT and AIMD simulations were carried out using the ORCA quantum chemistry package. It was found that the GLY molecule interacts with the perfect graphene lattice through noncovalent bonds, and the interaction energy was computed in about −16 kcal/mol. Hydrogen bridges between the hydroxyl groups of GOs models and the –NH2 from GLY lead to total interaction energy of about −24 kcal/mol. However, the –COOH moiety of GLY binds to the hydroxyl groups of GOs with interaction energy of about −33 kcal/mol. The respective interaction energy amounts to about −44.53 kcal/mol for a configuration with Stone-Wales defects. AIMD simulations showed that GLY could stay bonded to the graphene surface to reach a thermodynamic equilibrium (>25 fs) and form simultaneous hydrogen bonds. The molecular dynamics simulations indicate that the complexes and the reservoir tend to thermal equilibrium when the temperature is lowered by about 100 K. The AIMD simulations suggested that after 25 fs, the configuration for the complexes is not different from 0 K. It was suggested that GLY form mainly noncovalent complexes depending on the G (or GO) model. G and GLY can interact from –16 kcal/mol to -34 kcal/mol. This energy value is about 3 to 9 times the average noncovalent interaction energy. Furthermore, it was shown that Stone-Wales defects cause minor changes in the complex configurations, interaction energies, and thermodynamic stability. AIMD results indicate that after 25 fs, the initial structure at 0 K will not differ after the relaxation of atomic positions at room temperature. In summary, we studied and discussed the interaction mechanisms between neutral glycine and graphene, graphene oxide models to gain insights into the adsorption interaction, potential energies, and their thermodynamic stability based on DFT and AIMD approaches. As future work, it is proposed to study the noncovalent interaction for these proposed graphene oxide models with other AAs to gain a complete understanding of the adsorptive properties for these critical biomolecules. It is proposed to increase the time frame for AIMD simulations because biochemical events of interest, such as structural changes in proteins, take place on timescales in the nano or microseconds order. Finally, the basis set level might have an impact on the accuracy of the obtained energies, and thus it is recommendable to extend to a triple-zeta basis set.