The role of electrostatic potential polarization in the translocation of graphene quantum dots across membranes

The impact of chemical properties of the solid-liquid-adsorbate interfaces on the entropy-enthalpy compensation involved in adsorption

Despite extensive studies on the thermodynamic mechanism governing molecular adsorption at the solid-water interface, a comprehensive understanding of the crucial role of interface properties in mediating the entropy-enthalpy compensation during adsorption is lacking, particularly at a quantitative level. Herein, we employed two types of surface models (hydroxyapatite and graphene) along with a series of amino acids to successfully elucidate how distinct interfacial features dictate the delicate balance between entropy and enthalpy variations. The adsorption of all amino acids on the hydroxyapatite surface is an enthalpy-dominated process, where the water-induced enthalpic component of the free energy and the surface-adsorbate electrostatic interaction term alternatively act as the driving force for adsorption in different regions of the surface. Although favorable interactions are observed between amino acids and the graphene surface, the entropy-enthalpy compensation exhibits dependence on the molecular size of the adsorbates. For small amino acids, favorable enthalpy changes predominantly determine their adsorption behavior; however, larger amino acids tend to bind more tightly with the graphene surface, which is thermodynamically dominated by the entropy variations despite the structural characteristics of amino acids. This study reveals specific entropy-enthalpy mechanisms underlying amino acid adsorption at the solid-liquid interface, providing guidance for surface design and synthesis of new biomolecules.

Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation

Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.

The role of electrostatic potential in the translocation of triangulene across membranes

Triangulene and its derivatives show broad application prospects in the fields of biological imaging and biosensing. However, its interaction with cell membranes is still poorly studied. In this study, classical molecular dynamics simulations were used to adjust the electrostatic potential of triangulene to observe its interactions with cell membranes. We found that electrostatic potential not only affects the behavior as it enters the cell membrane, but also spatial distribution within the cell membrane. The angle distribution of inside-0 and all-0 triangulene when penetrating the membrane is more extensive than that of ESP triangulene. However, inside-0 triangulene could cross the midline of the cell membrane and prefers to stay in the upper leaflet, while all-0 triangulene and ESP triangulene can reach the lower leaflet. These findings can help us regulate the distribution of nanoparticles in cells, so as to design functional nanoparticles that conform to the requirements.

Carbon Nanodots from an In Silico Perspective

Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.

Nonmonotonic Relationship between the Oxidation State of Graphene-Based Materials and Its Cell Membrane Damage Effects

With the rapid development of carbon-based two-dimensional nanomaterials in biomedical applications, growing concern has emerged regarding their biocompatibility and especially their interactions with cell membranes. Our experimental studies found that the oxidation state, as one of the most important chemical parameters of graphene derivatives, regulates the hemolysis effect on human red blood cells in a nonmonotonic manner. Scanning electron microscopy and optical microscopy observations suggested that graphene oxides with medium oxygen content have the most serious destructive effects on the cell membranes. Molecular dynamics simulations and potential of mean force calculations revealed that, on the one hand, with the decrease in the surface oxygenated groups, more sp² carbon area of graphene-based materials will be exposed, playing a facilitating role in the damage of cell membranes; on the other hand, fewer oxygenated groups also lead to the accumulation of graphene-based nanosheets in solutions. The formation of the multilayer structure of graphene-based nanosheets reduces the exposed sp² carbon area, prevents the collective extraction of lipid molecules, and eventually results in a weakened extraction effect on cell membranes. Together, these factors generate a nonmonotonic relationship between the oxidation state of graphene oxides and their destructive effects on cell membranes.

Molecular insights into the resistance of phospholipid heads to the membrane penetration of graphene nanosheets

The interaction between nanomaterials and phospholipid membranes underlies many emerging biological applications. To what extent hydrophilic phospholipid heads shield the bilayer from the integration of hydrophobic nanomaterials remains unclear, and this open question contains important insights for understanding biological membrane physics. Here, we present molecular dynamics (MD) simulations to clarify the resistance of phospholipid heads to the membrane penetration of graphene nanosheets. With 130 simulation trials, we observed that ∼22% graphene nanosheets penetrate the POPC bilayer. Sharp corners of the nanosheets should have a lower energy barrier than nanosheet edges, but interestingly, the membrane penetration mainly starts from the edge-approaching orientation. We thoroughly analyzed the pentration pathway and propulsion, indicating that the membrane penetration of graphene nanosheets is dominated by the joint effects of nanosheet edges and corners. Furthermore, the molecular origin of the resistance is clarified by evaluating the bilayers of different phospholipids, which successfully correlates the penetration resistance of phospholipid heads with the correlated motions of neighboring phospholipids for the first time. These results are expected to inspire future studies on the dynamic behavior of phospholipids, bio-nano interfaces, and design of biological nanomaterials.

Destructive Extraction and Enhanced Diffusion of Phospholipids on Lipid Membranes by Phosphorene Oxide Nanosheets

Phosphorene is a novel two-dimensional nanomaterial with a puckered surface morphology, which has broad potential application prospects in the fields of biology and medicine. Phosphorene nanosheets are easily oxidized and form phosphorene oxide (PO) in an aerobic environment, whose biological effect remains unknown. In this paper, using large-scale molecular dynamics simulations, we show that the PO nanosheets can penetrate into and destructively extract large amounts of phospholipids from the lipid membrane. The PO nanosheets with a higher oxidation concentration have less extraction of phospholipids, while its oxidation mode has no effect on the extraction of phospholipids. Moreover, inserting PO nanosheets into the lipid membrane can enhance the diffusion of phospholipids on the membrane. These findings can shed light on understanding/designing the membrane-nanomaterial interactions.

A review on the cytotoxicity of graphene quantum dots: from experiment to simulation

Graphene quantum dots (GQDs) generate intrinsic fluorescence and improve the aqueous stability of graphene oxide (GO) while maintaining wide chemical adaptability and high adsorption capacity. Despite GO's remarkable advantages in bio-imaging, bio-sensing, and other biomedical applications, many experiments and simulations have focused on the biosafety of GQDs. Here, we review the findings on the biosafety of GQDs from experiments; then, we review the results from simulated interactions with biological membranes, DNA molecules, and proteins; finally, we examine the intersection between experiments and simulations. The biosafety results from simulations are explained in detail. Based on the literature and our experiments, we also discuss the trends toward GQDs with better biosafety.

Theoretical Evaluation of DNA Genotoxicity of Graphene Quantum Dots: A Combination of Density Functional Theory and Molecular Dynamics Simulations

Owing to their unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the fields of electrochemical biosensors, bioimaging, drug delivery, gene delivery, etc. Their biosafety and potential genotoxicity to human and animal cells have been a growing concern in recent years. Especially, the potential DNA damage caused by GQDs is very crucial but still unclear. In this study, the effect of GQDs on DNA damage has been evaluated by a combination of molecular dynamics (MD) simulations and density functional theory. Our results demonstrate that the DNA damaging mechanism of GQDs depends on the size of GQDs. The small GQDs (seven benzene rings) tend to enter into the interior of DNA molecules and cause a DNA base mismatch. The relatively large GQDs (61 benzene rings) tend to adsorb onto the two ends of a DNA molecule and cause DNA unwinding. Due to the strong interaction between guanine (G) and GQDs, the effect of GQDs is much larger on G than on the other three bases (A, C, and T). In addition, the concentration of GQDs could also affect the results of DNA damaging.